The bacterial world inside the plant

Sustainable agriculture requires the recruitment of bacterial agents to reduce the demand for mineral fertilizers and pesticides such as bacterial endophytes. Bacterial endophytes represent a potential alternative to the widespread use of synthetic fertilizers and pesticides in conventional agriculture practices. Endophytes are formed by complex microbial communities and microorganisms that colonize the plant interior for at least part of their life. Their functions range from mutualism to pathogenicity. Bacterial endophytes colonize plant tissues, and their composition and diversity depend on many factors, including the plant organ, physiological conditions, plant growth stage, and environmental conditions. The presence of endophytes influences several vital activities of the host plant. They can promote plant growth, elicit a defense response against pathogen attack, and lessen abiotic stress. Despite their potential, especially with regard to crop production and environmental sustainability, research remains sparse. This review provides an overview of the current research, including the concept of endophytes, endophytes in plant organs, endophyte colonization, nutrient efficiency use, endophytes and crop nutrition, inoculation with synergistic bacteria, the effect of inoculum concentration on plant root microbiota and synthetic communities. It also examines the practical opportunities and challenges when utilizing endophytes in the field of sustainable agriculture. Finally, it explores the importance of these associations with regard to the future of agriculture and the environment

Polymyxa betae - Beta vulgaris : understanding the molecular interactions through transcriptome and plant defense analysis

Polymyxa betae is a biotrophic obligate endoparasite of sugar beet roots, belonging to the Plasmodiophorids (Cercozoa, Protozoa). The infection by this parasite is asymptomatic, excepted when P. betae transmits to a susceptible plant the Beet necrotic yellow vein virus (BNYVV), the causal agent of the rhizomania. This disease is controlled by the use of BNYVV tolerant varieties. But the emergence of viral resistance breaking isolates requires the development of alternate control strategies. The prevention of vector infection represents an interesting alternative. In this view, we investigated P. betae genome and molecular interactions between P. betae and its host. Two model studies, using Arabidopsis thaliana and sugar beet hairy roots, were developed and evaluated to investigate molecular biology of P. betae. A differential transcript analysis between healthy and P. betae infected sugar beets allowed the identification of 76 new ESTs from P. betae and 120 ESTs from sugar beet. The dynamic of expression of selected genes revealed the potential role of two P. betae proteins, the profilin and a Von Willebrand factor domain containing protein, in the first phase of infection. This study also highlighted an overexpression of some sugar beet genes involved in the defense, such as PR proteins, stress resistance proteins or lectins, especially during the plasmodial stage. The induction of systemic acquired resistance (SAR) by P. betae was confirmed in a further bioassay showing the protection offered by the protist against Cercospora beticola. P. betae seems thus to by-pass the SAR. In contrast, the protist is affected by the induced systemic resistance. Indeed, the elicitation of sugar beet by Bacillus lipopeptides allowed a significant reduction of infection by the protist. This thesis highlighted the biological processes involved in the P. betae-sugar beet interactions, potential new targets for sugar beet selection and rhizomania control. The results concerning defense ways enabled to consider P. betae not only as the target of the plant defenses but also as an actor of these defenses.(AGRO 3) -- UCL, 201

In Vitro Dual Culture of Polymyxa betae in Agrobacterium rhizogenes Transformed Sugar Beet Hairy Roots in Liquid Media

Polymyxa betae is a soil-borne protist and an obligate parasite of sugar beet that transmits the beet necrotic yellow vein virus. Sugar beet hairy roots, transformed by Agrobacterium rhizogenes, were inoculated with surface-sterilized root fragments infected by P. betae. After 10 wk in a liquid medium, typical structures of P. betae were observed in this in vitro system. This first in vitro culture of P. betae in liquid medium will contribute to a better understanding of this protist's biology through providing a way to conserve and produce purified isolates of the protist

Plant Microbiota Beyond Farming Practices: A Review

Plants have always grown and evolved surrounded by numerous microorganisms that inhabit their environment, later termed microbiota. To enhance food production, humankind has relied on various farming practices such as irrigation, tilling, fertilization, and pest and disease management. Over the past few years, studies have highlighted the impacts of such practices, not only in terms of plant health or yields but also on the microbial communities associated with plants, which have been investigated through microbiome studies. Because some microorganisms exert beneficial traits that improve plant growth and health, understanding how to modulate microbial communities will help in developing smart farming and favor plant growth-promoting (PGP) microorganisms. With tremendous cost cuts in NGS technologies, metagenomic approaches are now affordable and have been widely used to investigate crop-associated microbiomes. Being able to engineer microbial communities in ways that benefit crop health and growth will help decrease the number of chemical inputs required. Against this background, this review explores the impacts of agricultural practices on soil- and plant-associated microbiomes, focusing on plant growth-promoting microorganisms from a metagenomic perspectiv

A new phenotype of Polymyxa betae in Arabidopsis thaliana

The understanding of the molecular biology of Polymyxa betae, the protist vector of Beet necrotic yellow vein virus, remains limited because of the obligate nature of this root endoparasite and the limited data on the genome of Beta vulgaris, its most common host plant. The aim of this work was to assess the infection of P. betae in Arabidopsis thaliana in order to learn more about the P. betae genome and its interaction with the host. The susceptibility of a set of ecotypes of various origins to a monosporosorus and aviruliferous isolate of P. betae was analyzed in a series of bioassays conducted under controlled conditions. P. betae was detected in roots of A. thaliana using light microscopy and PCR. The infection severity was relatively low in this species compared with B. vulgaris, but the different stages of the life cycle were present. The phenotype of P. betae in A. thaliana root cells differed from the phenotype in B. vulgaris: the spore-forming phase was more prevalent in comparison with the sporangial phase, and the sporosori contained a lower number of spores. The compatible interaction between P. betae and A. thaliana obtained after the inoculation of zoospores and optimal conditions for the development of P. betae provide a new model system that can be used to improve the knowledge on the P. betae genome and on the mechanisms of the spore-forming phase of P. betae

In vitro and in vivo screening of bacteria that have antagonistic and elicitation effects on potato pathogens

The increase in organic farming adhering to European regulations on the sustainable use of pesticides has stimulated research into new strategies for controlling plant pathogens. A high-throughput screening method was used to select bacterial strains for potential use as growth promoting bacteria or as biopesticides. More than 2,600 strains of Pseudomonas spp. and Bacillus spp. were isolated from soils, compost and potato plants sampled in the Walloon region. Their antagonistic effects on Phytophthora infestans, Fusarium solani, Streptomyces scabies and Pectobacterium carotovorum were assessed in vitro. Fifty-four strains of Bacillus spp. and 16 strains of Pseudomonas spp. with antagonistic effects on at least one of the tested pathogens were selected. The elicitation effect of these strains was tested using mutant Arabidopsis plants expressing the GUS reporter system fused with the plant defensin gene PDF1.2. The induced systemic resistance (ISR) of nine bacteria inducing high defensin expression in Arabidopsis was tested on potato under greenhouse conditions. Potato tubers were coated with powder composed of lyophilized bacteria and the gene expression involved in ISR was quantified by RT-qPCR. The antagonistic effects of the 70 strains were also assessed in vivo. Bacterial suspensions were sprayed on the leaves of potato plants grown in the greenhouse and in the field. Their antagonistic effects on P. infestans were assessed by quantifying the progression of late blight disease after inoculation with P. infestans. In vivo tests were also conducted on the antagonistic effects of some strains on three tuber diseases caused by F. solani, S. scabies and P. carotovorum. The potential of using such bacteria for protecting potato against plant pathogens is discussed

Molecular interactions between sugar beet and Polymyxa betae during its life cycle

Polymyxa betae is a biotrophic obligate sugar beet parasite that belongs to plasmodiophorids. The infection of sugar beet roots by this parasite is asymptomatic, except when it transmits Beet necrotic yellow vein virus (BNYVV), the causal agent of rhizomania. To date, there has been little work on P. betae–sugar beet molecular interactions, mainly because of the obligate nature of the parasite and also because research on rhizomania has tended to focus on the virus. In this study, we investigated these interactions through differential transcript analysis, using suppressive subtractive hybridization. The analysis included 76 P. betae and 120 sugar beet expressed sequence tags (ESTs). The expression of selected ESTs from both organisms was monitored during the protist life cycle, revealing a potential role of two P. betae proteins, profilin and a Von Willebrand factor domain-containing protein, in the early phase of infection. This study also revealed an over-expression of some sugar beet genes involved in defence, such as those encoding PR proteins, stress resistance proteins or lectins, especially during the plasmodial stage of the P. betae life cycle. In addition to providing new information on the molecular aspects of P. betae–sugar beet interactions, this study also enabled previously unknown ESTs of P. betae to be sequenced, thus enhancing our knowledge of the genome of this protist

First report of Plasmodiophora brassicae on rapeseed in Grand Duchy of Luxembourg

Rapeseed (Brassica napus L.) is the third most important crop after wheat and barley in the Grand Duchy of Luxembourg. Since 2005, clubroot symptoms in this crop have been reported by farmers in the Gutland Region. In February 2009, plants of the hybrid rapeseed cv. Exocet, with stunted growth, yellow leaves, and club-shaped roots, were sampled from a field in Oberkorn village near Differdange. Microscopic observations of the rapeseed root fragments revealed the presence of the three life stages characteristic of Plasmodiophora brassicae Woronin. Plasmodia and zoosporangia were observed in the root hairs and resting spores were present in root galls. Individual spores were 2 to 3 μm in diameter. Total DNA was extracted from the root galls with a FAST DNA Kit (MP Biomedicals, Irvine, CA). The internal transcribed spacer region (ITS) and 5.8S gene of the rDNA region were amplified with ITS5 and ITS4 primers as described by White et al. (2) and part of this region was sequenced. A BLASTn search in GenBank revealed that the sequence closely resembled (98% identity) sequences of P. brassicae (Genbank Accession No. EF195335) from an isolate of the pathogen from Switzerland. To confirm the presence of the pathogen, seeds of the susceptible ecotype cvi-0 of Arabidopsis thaliana were grown in a soil sample (1 liter) collected near the infected rapeseed plants. After 55 days of growth in a glasshouse at 15 to 20°C, the roots of 11 plants were analyzed. Two showed clear clubroot symptoms and four others exhibited small swellings. The remaining five plants were symptomless, but plasmodia and zoosporangia were found in root hair cells. Clubroot caused by P. brassicae has previously been described on B. napus and other crucifers (1). To our knowledge, this is the first report of clubroot disease caused by P. brassicae in Luxembourg. Because its presence has since been observed in new fields in the Gutland Region and because of the ability of the pathogen to survive for a long period in the soil, this disease could represent a severe threat for cropping of Brassicaceae in Luxembourg and neighboring countries

Interactions between Polymyxa betae and plant systemic defense ways

Polymyxa betae is the vector of Beet necrotic yellow vein virus (BNYVV), the causal agent of sugar beet rhizomania disease. Because of the widespread use of cultivars partially resistant to BNYVV, resistance breaking BNYVV isolates have been reported. In order to develop alternative control strategies, we investigated interactions between P. betae and plant defenses. A first set of bioassays was conducted in order to assess P. betae infection after the elicitation of inducible defenses in sugar beet. The systemic acquired resistance (SAR) or the induced systemic resistance (ISR) was induced by a treatment of the plants with an analogue of the salicylic acid (SA) or with lipopeptides (LPs) from Bacillus amyloliquefaciens, respectively. While P. betae infection, quantified by real time PCR, was not reduced in plants treated with SA, the intensity of infection was significantly lower (up to 95 % of reduction) in plants after a treatment with LPs. LPs were shown to effectively induce systemic resistance in both roots and leaves of sugar beet, resulting in a reduction in P. betae infection. The absence of any effect of SAR against P. betae could be explained by the coevolution of P. betae and sugar beet, allowing the biotrophic endoparasite to bypass self-induced SAR. This hypothesis was validated in another bioassay. SAR was efficiently induced in sugar beet after the infection by P. betae, allowing the plants to resist (75% reduction) to a further infection by Cercospora beticola. These results suggest that P. betae has to be considered not only as a target but also as an actor of plant defenses