Sugar Beet Rhizosphere Research Articles

Root Exudates Promoted Microbial Diversity in the Sugar Beet Rhizosphere for Organic Nitrogen Mineralization

Rhizosphere environments play a vital role in the nutrient cycling of crops and soil organic nitrogen mineralization. Sugar beet is a highly nitrogen (N)-demanding crop, and it is necessary to explore the relationship between the sugar beet root exudates, the microbial community, and nitrogen utilization. In this study, a special separation method was employed to create rhizosphere (H3) and non-rhizosphere (H2 and H1) environments for sugar beet. After 50 d of cultivation in nearly inorganic-free soil, the microbial diversity and its correlation with root metabolites and N were examined. The results showed that in H3, the inorganic N content was over 23 times higher than in H1 and H2, with a 13.1% higher relative abundance of ammonia-oxidizing bacteria compared to H2 and a 32% higher abundance than H1. The relative abundance of nitrite-oxidizing bacteria was also 18.8% higher than in H1. Additionally, a significant positive correlation was observed between inorganic nitrogen content and serine (Ser) and isoleucine (Ile). The organic nitrogen content exhibited positive correlations with glycine (Gly), alanine (Ala), and tyrosine (Tyr) but displayed negative correlations with certain amino acids, organic acids, and glucose. The co-linearity network indicated that the microbial composition in H3 also exhibited higher node connectivity. It can be inferred that under the influence of sugar beet root exudates, the changes in the rhizosphere’s microbial diversity were more intricate, thereby benefiting soil nitrogen cycling and inorganic N accumulation. These findings provide profound insight into sugar beet soil organic nitrogen mineralization and contribute to the sustainable and environmentally friendly development of modern agriculture.

Response of the rhizospheric soil microbial community of sugar beet to nitrogen application: A case of black soil in Northeast China

Nitrogen (N) is the most crucial mineral element for the growth of sugar beet (Beta vulgaris L.) plant. Rational application of N fertilizer is known to increase sugar beet yields and influence the rhizospheric microbial communities, but there is an uncertainty about the response of sugar beet rhizosphere soil microbes to the seasonal nitrogen fertilizer application in black soil region of northeast China. Under field conditions, we set up nitrogen (N 90 kg / ha) and no nitrogen (N 0 kg / ha) treatments. Soil chemistry and high-throughput sequencing analysis were carried out on the soil samples of sugar beet rhizosphere at harvest. Application of N fertilizer significantly increased rhizospheric soil bacterial diversity and reduced bacterial and fungal abundance and fungal diversity. Post-N fertilization, the dominant bacterial groups were Actinobacteria, Proteobacteria, Firmicutes, and the dominant fungal groups were Ascomycota and Mortierellomycota. The community structure of sugar beet rhizospheric bacteria and fungi was significantly altered. Redundancy analysis showed that organic matter (OM), available nitrogen (AN) and available potassium (AK) were the main soil properties affecting soil bacterial community structure, whereas fungal community structure was affected by AK, pH and available phosphorus (AP). FAPROTAX analysis demonstrated that fermentation is the main metabolic mode of sugar beet rhizosphere soil microorganisms, followed by nitrification, automatic compound degradation, manganese oxidation and hydrocarbon degradation. Analysis of the KEGG metabolic pathways revealed that N fertilization enhances the abundance of xenobiotics biodegradation and metabolism; moreover, the transport and catabolism pathways increased after nitrogen fertilization. The application of N fertilizer affected the diversity of microbes, changing the composition and structure of bacterial and fungal communities, which consequently changed the ecological environment of sugar beet rhizosphere in northeastern black soils.

Waterlogging stress alters the structure of sugar beet rhizosphere microbial community structure and recruiting potentially beneficial bacterial

Waterlogging has been shown to have a significant inhibitory effect on plant growth. However, the response mechanisms of the soil environment of sugar beet seedlings under waterlogging conditions still need to be fully understood. This study aimed to investigate the effects of waterlogging treatments on the content of effective nutrients and the microbial communities in the rhizosphere and non-rhizosphere using high-throughput sequencing. We set up waterlogging and non-waterlogging treatments, sampled sugar beet seedlings after 10 days of waterlogging, determined the effective soil nutrients in the rhizosphere and non-rhizosphere of the plants, and analyzed the differences in microbial diversity at ten days of waterlogging. The results showed that waterlogging significantly affected available potassium (AK) content. The Ak content of waterlogged soil was significantly higher than that of non-waterlogged soil. Waterlogging caused no significant difference in available nitrogen (AN) content and pH. Moreover, the plant growth-promoting bacteria Pseudomonas was significantly enriched in sugar beet waterlogged rhizospheres compared with the non-waterlogged ones. Similarly, the harmful fungi Gibellulopsis and Alternaria were enriched in sugar beet non-waterlogged rhizosphere. The network analysis revealed that waterlogging built a less complex root-microbial network than non-waterlogging. These findings implied that sugar beets subjected to waterlogging stress were enriched with beneficial microorganisms in the rhizosphere, potentially alleviating the stress.

The response of sugar beet rhizosphere micro-ecological environment to continuous cropping.

Continuous cropping can lead to increased soil-borne diseases of sugar beet (Beta vulgaris L.), resulting in a reduction in its yield quality. However, our understanding of the influence of continuous cropping on sugar beet-associated microbial community is limited and their interactions remain unclear. Here, we described and analyzed microbial diversity (N = 30) from three sugar beet belowground compartments (bulk soil, rhizosphere soil, and beetroot) using 16S rRNA and ITS sequencing. The continuous cropping showed lower bacterial alpha diversity in three belowground compartments and higher fungal alpha diversity in roots compared to the non-continuous cropping. There were significant differences in fungal community composition between the two groups. Compared with non-continuous cropping, continuous cropping increased the relative abundance of potentially pathogenic fungi such as Tausonia, Gilbellulopsis, and Fusarium, but decreased the relative abundance of Olpidium. The fungal flora in the three compartments displayed different keystone taxa. Fungi were more closely related to environmental factors than bacteria. Overall, changes in microbial diversity and composition under continuous cropping were more pronounced in the fungal communities, and the results of the study could guide development strategies to mitigate continuous crop adversity.

Effect of long-term sugar beet cultivation on rhizosphere bacterial diversity, community structure and sugar yield of sugar beet

Long-term sugar beet cultivation in the black soil region of China not only affected sugar beet yield but also influenced rhizosphere soil bacteria. However, the relationship between sugar beet growth and rhizosphere soil bacteria is still indeterminate. Therefore, this study analyzed the sugar beet growth status, rhizosphere soil bacterial diversity, species, and functional composition of long-term cultivation fields (LCF) and initial planting fields (IPF) of sugar beet. The results showed that sugar beet leaf disease in the long-term cultivation fields was significantly aggravated and the sugar beet yield was significantly reduced compared with the initial planting fields. The content of available phosphorus in sugar beet rhizosphere soil and the diversity of the rhizosphere bacterial community were significantly decreased. The Proteobacteria and Actinobacteria were increased, while Acidobacteria were decreased, and the difference in species composition was significant. The abundance of metabolic functions related to nutrient cycling and the abundance of chemoheterotrophy ecological functions was decreased. The bacterial diversity of sugar beet rhizosphere soil was negatively correlated with the leaf disease index and positively correlated with sugar yield. The sugar beet yield was negatively correlated with the abundance of proteobacteria and actinobacteria, while positively correlated with the abundance of acidobacteria, chemoheterotrophy function, and nitrogen fixation function. This study identified the soil reasons for the decline of sugar beet yield in long-term sugar beet cultivation areas and provided a reference basis for improving soil properties and sugar beet productivity.

Biocontrol potential of plant growth-promoting rhizobacteria (PGPR) against Sclerotiorum rolfsii diseases on sugar beet (Beta vulgaris L.)

A total of 49 bacterial isolates were collected from the sugar beet rhizosphere in two regions of Morocco (Kenitra and Meknes). These bacteria were tested for their inhibitory activity against Sclerotium rolfsii Sacc., the causative pathogen of damping-off and root rot of sugar beet. Ten isolates showed a high ability to inhibit the mycelial growth of the pathogenic fungus in dual culture bioassays. The molecular identification based on 16S ribosomal DNA gene revealed that these isolates belong to the Bacillus genus. In addition, these bacterial isolates have also been characterized in terms of the production of certain antifungal products as well as for their capacities as plant growth-promoting traits. Under greenhouse conditions, sugar beet seeds treated with the each bacterium showed significant reduction in damping-off disease. Plants from treated seeds showed significant increases in both the length of shoots and roots, and the plant fresh and dry weight. Iinterestingly, these selected bacterial isolates displayed high antagonistic activity against S. rolfsii, and significantly reduced the severity and incidence of root rot disease. Therefore, these results highlighted that the soil harbors antagonistic bacteria offering several plant growth-promoting (PGP) traits, which can be exploited as a powerful growth promoter and/or biological control agent in sugar beet plants.

Influence of fertilization and pre-seeding inoculation systems on phosphate-mobilizing bacteria of sugar beets rhizosphere

This article presents the results of research the influence of fertilizer systems and seeds inoculation on phosphate-mobilizing bacteria in sugar beet rhizosphere. For seeds bacterization was applied the Polymyxobacterin (contains spores and cells of Paenibacillus polymyxa, which can transform insoluble inorganic phosphates and organophosphates and to produce the phytohormonal substances) and mixture of the Polymyxobacterin with Trichoderma (Trichoderma). Microbiological analysis of rhizosphere soil of non-inoculated sugar beet plants was shown that the distribution of phosphate solubilizing microorganisms depends on the agricultural conditions. The using of both mineral and organo-mineral fertilizers stimulates the development of studied microorganisms. For increasing in rhizosphere of non-inoculated sugar beet plants a quantity of microorganisms that soluble mineral phosphates the use of mineral fertilizers (N160P120K160) with the addition of 32 t/ha manure is optimal. The application only mineral fertilizers to increase the number of microorganisms which capable to transform organic phosphorus compounds. In all trials including control without fertilizers, seed treatment by Polymyxobacterin increases the number of bacteria that soluble mineral phosphates. The most optimal conditions for the development of microorganisms that solubilize mineral and organic phosphorus compounds are the treatment of sugar beet seeds by mixture of Polymyxobacterin and Trichoderma and application of mineral fertilizers. Therefore, the obtained results indicate about significant impact of fertilizer types and seed treatment by microorganisms on the amount and composition of phosphate-mobilizing bacteria in the rhizosphere of sugar beet plants.

FORMATION OF THE EUBACTERIAL COMPLEX IN THE RHYOSPHERE OF SUGAR BEET (Beta vulgaris) UNDER DIFFERENT FERTILIZATION SYSTEMS

The aim of the work was to determine the quantitative, qualitative composition and taxonomic structure of the eubacterial complex in the rhizosphere of sugar beet under different fertilizer systems. Microbiological methods were used to determine the content of microorganisms in the rhizosphere of sugar beet. Molecular methods were used to determine taxonomic structure as well as metagenome of the eubacterial complex of microorganisms. In the agrocenosis of sugar beet under different fertilizer systems the representatives of such families were prevailed as Alcaligenaceae, Pseudomonadaceae, Nitrososphaeraceae, Gaiellaceae, Micrococcaceae, Solirubrobacteraceae, Streptomycetaceae, Intrasporangiaceae, Solimonadaceae, Syntrophobacteraceae, Xanthomonadaceae, Enterobacteriaceae, Nocardioidaceae, Hyphomicrobiaceae, Comamonadaceae. It was found that under the biological system of fertilizers the species diversity of soil microbiota increased due to phyla: Alcaligenaceae, Gaiellaceae, Solirubrobacteraceae, Streptomycetaceae, Solimonadaceae, Syntrophobacteraceae, Xanthomonadaceae, Enterobacteriaceae, Nocardioidaceae, Hyphomicrobiaceae, Hyphomicrobiaceae. It was detected that the basis of the eubacterial complex of sugar beet included representatives of phyla Proteobacteria, Actinobacteria, Gemmatimonadetes, Chloroflexi, Acidobacteria, Firmicutes, Planctomycetes, Verrucomicrobia, Bacteroidetes, and the absolute dominants were Proteobacteria – 76.9%, Actinobacteria – 13,4 %.

Understanding the Impact of Cultivar, Seed Origin, and Substrate on Bacterial Diversity of the Sugar Beet Rhizosphere and Suppression of Soil-Borne Pathogens.

The rhizosphere microbiome is crucial for plant health, especially for preventing roots from being infected by soil-borne pathogens. Microbiota-mediated pathogen response in the soil-root interface may hold the key for microbiome-based control strategies of phytopathogens. We studied the pathosystem sugar beet—late sugar beet root rot caused by Rhizoctonia solani in an integrative design of combining in vitro and in vivo (greenhouse and field) trials. We used five different cultivars originating from two propagation sites (France, Italy) with different degrees of susceptibility towards R. solani (two susceptible, one moderately tolerant and two cultivars with partial resistance). Analyzing bacterial communities in seeds and roots grown under different conditions by 16S rRNA amplicon sequencing, we found site-, cultivar-, and microhabitat-specific amplicon sequences variants (ASV) as well as a seed core microbiome shared between all sugar beet cultivars (121 ASVs representing 80%–91% relative abundance). In general, cultivar-specific differences in the bacterial communities were more pronounced in seeds than in roots. Seeds of Rhizoctonia-tolerant cultivars contain a higher relative abundance of the genera Paenibacillus, Kosakonia, and Enterobacter, while Gaiellales, Rhizobiales, and Kosakonia were enhanced in responsive rhizospheres. These results indicate a correlation between bacterial seed endophytes and Rhizoctonia-tolerant cultivars. Root communities are mainly substrate-derived but also comprise taxa exclusively derived from seeds. Interestingly, the signature of Pseudomonas poae Re*1-1-14, a well-studied sugar-beet specific biocontrol agent, was frequently found and in higher relative abundances in Rhizoctonia-tolerant than in susceptible cultivars. For microbiome management, we introduced microbial inoculants (consortia) and microbiome transplants (vermicompost) in greenhouse and field trials; both can modulate the rhizosphere and mediate tolerance towards late sugar beet root rot. Both, seeds and soil, provide specific beneficial bacteria for rhizosphere assembly and microbiota-mediated pathogen tolerance. This can be translated into microbiome management strategies for plant and ecosystem health.

The Response of the Soil Microbiota to Long-Term Mineral and Organic Nitrogen Fertilization is Stronger in the Bulk Soil than in the Rhizosphere.

The effects of different agronomic practices, such as fertilization regimes, can be experimentally tested in long-term experiments (LTE). Here, we aimed to evaluate the effect of different nitrogen fertilizations on the bacterial microbiota in both rhizosphere and bulk soil of sugar beet, in the Giessen-LTE (Germany). Fertilization treatments included mineral-N, manure, mineral-N + manure and no N-amendment. Metabarcoding and co-occurrence analysis of 16S rRNA genes, qPCR of amoA, nirK, nirS, nosZ-I and nosZ-II genes and soil physico-chemical analyses were performed. The effect of the fertilization treatments was more evident in the bulk soil, involving 33.1% of the microbiota. Co-occurrence analysis showed a rhizosphere cluster, dominated by Proteobacteria, Actinobacteria and Verrucomicrobia (hub taxa: Betaproteobacteriales), and a bulk soil cluster, dominated by Acidobacteria, Gemmatominadetes and “Latescibacteria” (hub taxa: Acidobacteria). In the bulk soil, mineral N-fertilization reduced nirK, amoA, nosZ-I and nosZ-II genes. Thirteen Operational taxonomic units (OTUs) showed 23 negative correlations with gene relative abundances. These OTUs likely represent opportunistic species that profited from the amended mineral-N and outgrew the species carrying N-cycle genes. Our results indicate trajectories for future research on soil microbiome in LTE and add new experimental evidence that will be helpful for sustainable management of nitrogen fertilizations on arable soils.

ВЛИЯНИЕ БИОПРЕПАРАТА МЕТАБОЛИТ НА КОМПЛЕКСЫ МИКРОМИЦЕТОВ В РИЗОСФЕРЕ И ФИЛЛОСФЕРЕ САХАРНОЙ СВЕКЛЫ В УСЛОВИЯХ ЗАГРЯЗНЕНИЯ ПОЧВЫ НЕФТЯНЫМИ УГЛЕВОДОРОДАМИ

ВЛИЯНИЕ БИОПРЕПАРАТА МЕТАБОЛИТ НА КОМПЛЕКСЫ МИКРОМИЦЕТОВ В РИЗОСФЕРЕ И ФИЛЛОСФЕРЕ САХАРНОЙ СВЕКЛЫ В УСЛОВИЯХ ЗАГРЯЗНЕНИЯ ПОЧВЫ НЕФТЯНЫМИ УГЛЕВОДОРОДАМИ

Особливості формування різноманіття еубактеріального комплексу ризосфери буряка цукрового (Beta vulgaris) при застосуванні різних агрозаходів

Особливості формування різноманіття еубактеріального комплексу ризосфери буряка цукрового (Beta vulgaris) при застосуванні різних агрозаходів

Changes in the species composition of the rhizosphere and phyllosphere of sugar beet under the impact of biological preparations based on endophytic bacteria and their metabolites

The species structure of the mycobiota in the rhizosphere and phyllosphere of sugar beet in ontogenesis was studied. The treatment of the plants with biopreparations based on endophytic bacteria and their metabolites (Phytosporin-M, Vitaplan, and Albit) were shown to create conditions for the colonization of the plant rhizosphere and phyllosphere by bacteria–antagonists displacing phytopathogenic microorganisms and stimulating plant growth, which induces the transformation of the microbial cenosis.

Bacillus amyloliquefaciens SB14 from rhizosphere alleviates Rhizoctonia damping-off disease on sugar beet

The use of biocontrol strains recently has become a popular alternative to conventional chemical treatments. A set of bacteria isolated from sugar beet rhizosphere and from roots and shoots of apple and walnut were evaluated for their potential to control sugar beet seedling damping-off caused by R. solani AG-4 and AG2-2.The results of in vitro assays concluded that three isolates, SB6, SB14, SB15, obtained from rhizosphere of sugar beet and five isolates, AP2, AP4, AP6, AP7, AP8, obtained from shoots and roots of apple were the most effective antagonists that inhibited the mycelial growth of both R. solani isolates. Combination of several biochemical tests and partial sequencing of 16S rRNA and gyrBgenes revealed that eight efficient bacterial isolates could be assigned to the genus Bacillus and all could tolerate high temperatures and salt concentrations in their vegetative growth. The potential biocontrol activity of the eight bacterial antagonists were tested in greenhouse condition. The results indicated that four strains,B. amyloliquefaciens SB14, B. pumilus SB6,B. siamensis AP2 and B. siamensisAP8 exerted a significant influence on controlling of seedling damping-off and performed significantly better than others.However, the treatment of the seeds with bacteria was most effective when the isolate SB14 was used, which significantly controlled damping-off disease by 58% caused by R. solani AG-4 and by 52.5% caused by R. solani AG-2-2. This indicates that the use of beneficial bacterial native to the host plant may increase the success rate in screening biocontrols, because these microbes are likely to be better adapted to their host and its associated environmental conditions than are strains isolated from other plant species grown in different environmental conditions. We can infer from the results reported here that sugar beet plantsmay recruitbeneficial microbes to the rhizosphere to help them solve context-specific challenges.

Microbial cenosis of typical chernozem at the biological and intensive agrarian systems

The results of investigations on studying of the impact of agromeasures at the functioning of microbial communities in chernozem typical has been shown. The aim of article was a comparative analysis of the functioning of bacterial and fungal microbiota in sugar beet rhizosphere at the application of biological and intensive (industrial) agrarian systems during culture ontogenesis. We applied a microbial (identification of microorganism’s number and their qualitative composition), ecological (ecological index calculation), biochemical (estimation of the microbial biomass and metabolic coefficient) and statistical (establishing the results probability) research methods is to achieve of this purpose.
 The application of agromeasures are significant impact on microbial communities in chernozem typical in sugar beet rhizosphere during ontogeny and are caused the change of trophic relationships and different direction of microbial processes in soil has been established. The phase of plant development is also had a significant impact on the activity of soil microorganisms functioning. The number of root exudates is increased and plant debrises are accumulated in the soil during sugar beet ontogeny. It is promotes to the growth of numbers, biomass and diversity of microbial communities’ in chernozem typical and consequently intensification of soil organic matter transformation. Thus the application of biological agrarian system compared to intensive is helped to optimization of soil microbial complex. It is accompanied the increasing of the number, diversity and content of microbial biomass and growth of microbial groups resistance. This helps to enhance of microbial transformation of organic matter and improve of soil trophic metabolic profile. The use of intensive agrarian system are involved the reducing of the number, diversity and biomass of microorganisms, that accompanied by a simplification of trophic relationships and deregulation of plant-microbe systems.

THE SOIL MICROBIAL COENOSIS STATE UNDER VARIOUS CROPS IN CASE OF INTRODUCING THE MIXTURE OF SILICON-CONTAINING MINERALS

In the conditions of stationary experiment the features of the formation of microbial coenosis in the rhizosphere of sugar beet, soybean and corn plants were studied in case of introducing silicon-containing mixtures into the soil. It was shown that the number of representatives of separate eco-trophic groups of microorganisms varies depending on the culture and introduced mixture. Soil microbial communities from under soybean and corn were characterized by the biggest changes, especially in case of mineralized sapropel introduction. Positive effect on sugar beet rhizospheric soil microbiota was made by mixtures: high-bog peat + siliconcontaining minerals and potassium silicate + silicon-containing minerals + sapropel. The processes of soil organic matter mineralization were quite balanced.

Evaluation of rhizobacterial colonisation and the ability to induce Globodera pallida hatch

Three bacterial isolates, SB13 (Acinetobacter sp.), SB14 (Arthrobacter sp.) and SB15 (Bacillus sp.), were previously isolated from the rhizosphere of sugar beet (Beta vulgaris ssp. vulgaris) plants and shown to increase hatch of potato cyst nematodes in vitro. In this study, the three isolates were assayed for rhizosphere competence. Each isolate was applied to seeds at each of four concentrations (105-108 CFU ml−1) and the inoculated seeds were planted in plastic microcosms containing coarse sand. All three isolates were shown to colonise the rhizosphere, although to differing degrees, with the higher inoculation densities providing significantly better colonisation. The isolates increased sugar beet root and shoot dry weight. Isolates SB14 and SB15 were analysed for their ability to induce in vivo hatch of Globodera pallida in non-sterile soil planted with sugar beet. After 4 and 6 weeks, both isolates had induced significantly greater percentage hatch compared to controls.

QUALITY INTENSIFICATION OF COMPOST PREPARED FROM AGRO-INDUSTRIAL WASTES BY PHOSPHATE SOLUBILIZING FUNGI

Compost, a soil amendment or a growth medium to plants is prepared by combining organic wastes in proper quotients. Efficient decomposing culture accelerates composting process. Present investigation was carried out to assess the composting power of consortium of five phosphate solubilizing fungi isolated from sugarcane and sugar beet rhizosphere including Aspergillus niger (NFCCI 1991), Aspergillus awamori (NFCCI 1992), Penicillium oxalicum (NFCCI 1997), Penicillium rubrum (NFCCI 1998) and Trichoderma viridae (NFCCI 1999), on availability of nutrients along with different kinds of agro- industrial wastes viz., sugar cane trash, farm yard manure, spent wash, press mud cake, molasses and dairy waste. The highest values of available phosphorous and nitrogen were recorded in the fungal consortium inoculated treatments, showing rise by 72.49 to 89.71 per cent and 61.92 to 92.51 per cent, respectively as compared to uninoculated control. In fungal inoculated treatments available potassium, enzyme activities and CO 2 evolution rate were also found to be increased. Inoculation of fungal consortium developed mature compost within 60-65 days.

Characterization of the SPI‐1 and Rsp type three secretion systems in Pseudomonas fluorescens F113

SummaryPseudomonas fluorescens F113 is a plant growth‐promoting rhizobacterium (PGPR) isolated from the sugar beet rhizosphere. The recent annotation of the F113 genome sequence has revealed that this strain encodes a wide array of secretion systems, including two complete type three secretion systems (T3SSs) belonging to the Hrp1 and SPI‐1 families. While Hrp1 T3SSs are frequently encoded in other P. fluorescens strains, the presence of a SPI‐1 T3SS in a plant‐beneficial bacterial strain was unexpected. In this work, the genetic organization and expression of these two T3SS loci have been analysed by a combination of transcriptional reporter fusions and transcriptome analyses. Overexpression of two transcriptional activators has shown a number of genes encoding putative T3 effectors. In addition, the influence of these two T3SSs during the interaction of P. fluorescens F113 with some bacterial predators was also assessed. Our data revealed that the transcriptional activator hilA is induced by amoeba and that the SPI‐1 T3SS could potentially be involved in resistance to amoeboid grazing.

Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction

BackgroundPseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar-beet rhizosphere. This bacterium has been extensively studied as a model strain for genetic regulation of secondary metabolite production in P. fluorescens, as a candidate biocontrol agent against phytopathogens, and as a heterologous host for expression of genes with biotechnological application. The F113 genome sequence and annotation has been recently reported.ResultsComparative analysis of 50 genome sequences of strains belonging to the P. fluorescens group has revealed the existence of five distinct subgroups. F113 belongs to subgroup I, which is mostly composed of strains classified as P. brassicacearum. The core genome of these five strains is highly conserved and represents approximately 76% of the protein-coding genes in any given genome. Despite this strong conservation, F113 also contains a large number of unique protein-coding genes that encode traits potentially involved in the rhizocompetence of this strain. These features include protein coding genes required for denitrification, diterpenoids catabolism, motility and chemotaxis, protein secretion and production of antimicrobial compounds and insect toxins.ConclusionsThe genome of P. fluorescens F113 is composed of numerous protein-coding genes, not usually found together in previously sequenced genomes, which are potentially decisive during the colonisation of the rhizosphere and/or interaction with other soil organisms. This includes genes encoding proteins involved in the production of a second flagellar apparatus, the use of abietic acid as a growth substrate, the complete denitrification pathway, the possible production of a macrolide antibiotic and the assembly of multiple protein secretion systems.