We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45–52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire.

The micronutrient zinc has an essential role in physiological and metabolic processes in plants as a cofactor or structural element in 300 catalytic and noncatalytic proteins, but it is very toxic when available in elevated amounts. Plants tightly regulate their internal zinc concentrations in a process called zinc homeostasis. The exceptional zinc hyperaccumulator species Thlaspi caerulescens can accumulate up to 3% of zinc, but also high amounts of nickel and cadmium, without any sign of toxicity. This should have drastic effects on the zinc homeostasis mechanism. We examined in detail the transcription profiles of roots of Arabidopsis thaliana and T. caerulescens plants grown under deficient, sufficient, and excess supply of zinc. A total of 608 zincresponsive genes with at least a 3-fold difference in expression level were detected in A. thaliana and 352 in T. caerulescens in response to changes in zinc supply. Only 14% of these genes were also zinc responsive in A. thaliana. When comparing A. thaliana with T. caerulescens at each zinc exposure, more than 2,200 genes were significantly differentially expressed ($5-fold and false discovery rate , 0.05). While a large fraction of these genes are of yet unknown function, many genes with a different expression between A. thaliana and T. caerulescens appear to function in metal homeostasis, in abiotic stress response, and in lignin biosynthesis. The high expression of lignin biosynthesis genes corresponds to the deposition of lignin in the endodermis, of which there are two layers in T. caerulescens roots and only one in A. thaliana.

Systemic resistance induced in plants by nonpathogenic rhizobacteria is typically effective against multiple pathogens. Here, we show that root-colonizing Pseudomonas fluorescens strain SS101 (Pf.SS101) enhanced resistance in Arabidopsis (Arabidopsis thaliana) against several bacterial pathogens, including Pseudomonas syringae pv tomato (Pst) and the insect pest Spodoptera exigua. Transcriptomic analysis and bioassays with specific Arabidopsis mutants revealed that, unlike many other rhizobacteria, the Pf.SS101-induced resistance response to Pst is dependent on salicylic acid signaling and not on jasmonic acid and ethylene signaling. Genome-wide transcriptomic and untargeted metabolomic analyses showed that in roots and leaves of Arabidopsis plants treated with Pf.SS101, approximately 1,910 genes and 50 metabolites were differentially regulated relative to untreated plants. Integration of both sets of "omics" data pointed to a prominent role of camalexin and glucosinolates in the Pf.SS101-induced resistance response. Subsequent bioassays with seven Arabidopsis mutants (myb51, cyp79B2cyp79B3, cyp81F2, pen2, cyp71A12, cyp71A13, and myb28myb29) disrupted in the biosynthesis pathways for these plant secondary metabolites showed that camalexin and glucosinolates are indeed required for the induction of Pst resistance by Pf. SS101. Also for the insect S. exigua, the indolic glucosinolates appeared to play a role in the Pf.SS101-induced resistance response. This study provides, to our knowledge for the first time, insight into the substantial biochemical and temporal transcriptional changes in Arabidopsis associated with the salicylic acid-dependent resistance response induced by specific rhizobacteria.

The Medicago truncatula expressed sequence tag (EST) database (Gene Index) contains over 140,000 sequences from 30 cDNA libraries. This resource offers the possibility of identifying previously uncharacterized genes and assessing the frequency and tissue specificity of their expression in silico. Because M. truncatula forms symbiotic root nodules, unlike Arabidopsis, this is a particularly important approach in investigating genes specific to nodule development and function in legumes. Our analyses have revealed 340 putative gene products, or tentative consensus sequences (TCs), expressed solely in root nodules. These TCs were represented by two to 379 ESTs. Of these TCs, 3% appear to encode novel proteins, 57% encode proteins with a weak similarity to the GenBank accessions, and 40% encode proteins with strong similarity to the known proteins. Nodule-specific TCs were grouped into nine categories based on the predicted function of their protein products. Besides previously characterized nodulins, other examples of highly abundant nodule-specific transcripts include plantacyanin, agglutinin, embryo-specific protein, and purine permease. Six nodule-specific TCs encode calmodulin-like proteins that possess a unique cleavable transit sequence potentially targeting the protein into the peribacteroid space. Surprisingly, 114 nodule-specific TCs encode small Cys cluster proteins with a cleavable transit peptide. To determine the validity of the in silico analysis, expression of 91 putative nodule-specific TCs was analyzed by macroarray and RNA-blot hybridizations. Nodule-enhanced expression was confirmed experimentally for the TCs composed of five or more ESTs, whereas the results for those TCs containing fewer ESTs were variable. , and organ development (Ruan et al., 1998;Girke et al., 2000; Zhu and Wang, 2000). Although Arabidopsis serves as the model system for most plant processes, it suffers from two major weaknesses in consideration of plant-microbe interactions: the absence of symbiotic associations with mycorrhizal fungi and with rhizobia.In recent years, Medicago truncatula and Lotus japonicus have emerged as model systems for genomic approaches to plant-microbe symbiotic associations (Barker et al., 1990;Handberg and Stougaard, 1992; Cook et al., 1997; Cook, 1999;Oldroyd and Geurts, 2001;Thoquet et al., 2002). Both species possess small genomes, are diploid, have fast generation times, and can be transformed with Agrobacterium tumefaciens and regenerated (Handberg and Stougaard, 1992; Blondon et al., 1994;Handberg et al., 1994; Chabaud et al., 1996;Jiang and Gresshoff, 1997;Stiller et al., 1997;Trinh et al., 1998;Trieu et al., 2000). Currently, both functional and structural genomics approaches are being pursued within each of these species. Covitz et al. (1998) reported the sequencing of about 900 cDNA tags from the M. truncatula root hairs. In addition, hundreds more expressed sequence tags (ESTs) have been isolated and characterized from effective root nodules of L. japonicus and M. truncatula, and a ...

Cadmium (Cd) is a widespread, naturally occurring element present in soil, rock, water, plants and animals. Cd is a non-essential element for plants and is toxic at higher concentrations. Transcript profiles of roots of Arabidopsis thaliana (Arabidopsis) and Thlaspi caerulescens plants exposed to Cd and zinc (Zn) are examined, with the main aim to determine the differences in gene expression between the Cd-tolerant Zn-hyperaccumulator T. caerulescens and the Cd-sensitive non-accumulator Arabidopsis. This comparative transcriptional analysis emphasized the role of genes involved in lignin, glutathione and sulphate metabolism. Furthermore the transcription factors MYB72 and bHLH100 were studied for their involvement in metal homeostasis, as they showed an altered expression after exposure to Cd. The Arabidopsis myb72 knockout mutant was more sensitive to excess Zn or iron (Fe) deficiency than wild type, while Arabidopsis transformants overexpressing bHLH100 showed increased tolerance to high Zn and nickel (Ni) compared to wild-type plants, confirming their role in metal homeostasis in Arabidopsis.

Summary There is consensus that plant species richness enhances plant productivity within natural grasslands, but the underlying drivers remain debated. Recently, differential accumulation of soil‐borne fungal pathogens across the plant diversity gradient has been proposed as a cause of this pattern. However, the below‐ground environment has generally been treated as a ‘black box’ in biodiversity experiments, leaving these fungi unidentified.Using next generation sequencing and pathogenicity assays, we analysed the community composition of root‐associated fungi from a biodiversity experiment to examine if evidence exists for host specificity and negative density dependence in the interplay between soil‐borne fungi, plant diversity and productivity.Plant species were colonised by distinct (pathogenic) fungal communities and isolated fungal species showed negative, species‐specific effects on plant growth. Moreover, 57% of the pathogenic fungal operational taxonomic units (OTUs) recorded in plant monocultures were not detected in eight plant species plots, suggesting a loss of pathogenic OTUs with plant diversity.Our work provides strong evidence for host specificity and negative density‐dependent effects of root‐associated fungi on plant species in grasslands. Our work substantiates the hypothesis that fungal root pathogens are an important driver of biodiversity‐ecosystem functioning relationships.

Bois noir (BN) associated with ‘Candidatus Phytoplasma solani’ (Stolbur) is regularly found in Austrian vine growing regions. Investigations between 2003 and 2008 indicated sporadic presence of the confirmed disease vector Hyalesthes obsoletus and frequent infections of bindweed and grapevine. Infections of nettles were rare. In contrast present investigations revealed a mass occurrence of H. obsoletus almost exclusively on stinging nettle. The high population densities of H. obsoletus on Urtica dioica were accompanied by frequent occurrence of ‘Ca. P. solani’ in nettles and planthoppers. Sequence analysis of the molecular markers secY, stamp, tuf and vmp1 of stolbur revealed a single genotype named CPsM4_At1 in stinging nettles and more than 64 and 90 % abundance in grapevine and H. obsoletus, respectively. Interestingly, this genotype showed tuf b type restriction pattern previously attributed to bindweed associated ‘Ca. P. solani’ strains, but a different sequence assigned as tuf b2 compared to reference tuf b strains. All other marker genes of CPsM4_At1 clustered with tuf a and nettle derived genotypes verifying distinct nettle phytoplasma genotypes. Transmission experiments with H. obsoletus and Anaceratagallia ribauti resulted in successful transmission of five different strains including the major genotype to Catharanthus roseus and in transmission of the major genotype to U. dioica. Altogether, five nettle and nine bindweed associated genotypes were described. Bindweed types were verified in 34 % of grapevine samples, in few positive Reptalus panzeri, rarely in bindweeds and occasionally in Catharanthus roseus infected by H. obsoletus or A. ribauti. ‘Candidatus Phytoplasma convolvuli’ (bindweed yellows) was ascertained in nettle and bindweed samples.

Phytophthora capsici causes devastating diseases on a broad range of plant species. To better understand the interaction with its host plants, knowledge obtained from a model pathosystem can be instrumental. Here, we describe the interaction between P. capsici and Arabidopsis and the exploitation of this novel pathosystem to assign metabolic pathways involved in defence against P. capsici. Inoculation assays on Arabidopsis accessions with different P. capsici isolates revealed interaction specificity among accession-isolate combinations. In a compatible interaction, appressoriummediated penetration was followed by the formation of invasive hyphae, haustoria and sporangia in leaves and roots. In contrast, in an incompatible interaction, P. capsici infection elicited callose deposition, accumulation of active oxygen species and cell death, resulting in early pathogen encasement in leaves. Moreover, Arabidopsis mutants with defects in salicylic acid signalling, camalexin or indole glucosinolates biosynthesis pathways displayed severely compromised resistance to P. capsici. It is anticipated that this model pathosystem will facilitate the genetic dissection of complex traits responsible for resistance against P. capsici.