Long-term conservation tillage with reduced nitrogen fertilization intensity can improve winter wheat health via positive plant-microorganism feedback in the rhizosphere

Microbiome-based solutions are regarded key for sustainable agroecosystems. However, it is unclear how agricultural practices affect the rhizosphere microbiome, plant-microorganism interactions and crop performance under field conditions. Therefore, we installed root observation windows in a winter wheat field cultivated either under long-term mouldboard plough (MP) or cultivator tillage (CT). Each tillage practice was also compared at two nitrogen (N) fertilization intensities, intensive (recommended N-supply with pesticides/growth regulators) or extensive (reduced N-supply, no fungicides/growth regulators). Shoot biomass, root exudates and rhizosphere metabolites, physiological stress indicators, and gene expression were analyzed together with the rhizosphere microbiome (bacterial/archaeal 16S rRNA gene, fungal ITS amplicon, and shotgun metagenome sequencing) shortly before flowering. Compared to MP, the rhizosphere of CT winter wheat contained more primary and secondary metabolites, especially benzoxazinoid derivatives. Potential copiotrophic and plant-beneficial taxa (e.g. Bacillus, Devosia, and Trichoderma) as well as functional genes (e.g. siderophore production, trehalose synthase, and ACC deaminase) were enriched in the CT rhizosphere, suggesting that tillage affected belowground plant-microorganism interactions. In addition, physiological stress markers were suppressed in CT winter wheat compared to MP. In summary, tillage practice was a major driver of crop performance, root deposits, and rhizosphere microbiome interactions, while the N-fertilization intensity was also relevant, but less important.

Does Constitutive Expression of Defense-Related Genes and Salicylic Acid Concentrations Correlate with Field Resistance of Potato to Black Scurf Disease?

Black scurf disease on potato caused by Rhizoctonia solani AG3 occurs worldwide and is difficult to control. The use of potato cultivars resistant to black scurf disease could be part of an integrated control strategy. Currently, the degree of resistance is based on symptom assessment in the field, but molecular measures could provide a more efficient screening method. We hypothesized that the degree of field resistance to black scurf disease in potato cultivars is associated with defense-related gene expression levels and salicylic acid (SA) concentration. Cultivars with a moderate and severe appearance of disease symptoms on tubers were selected and cultivated in the same field. In addition, experiments were conducted under controlled conditions in an axenic in vitro culture and in a sand culture to analyze the constitutive expression of defense-related genes and SA concentration. The more resistant cultivars did not show significantly higher constitutive expression levels of defense-related genes. Moreover, the level of free SA was increased in the more resistant cultivars only in the roots of the plantlets grown in the sand culture. These results indicate that neither expression levels of defense-related genes nor the amount of SA in potato plants can be used as reliable predictors of the field resistance of potato genotypes to black scurf disease.

Beneficial microbial consortium improves winter rye performance by modulating bacterial communities in the rhizosphere and enhancing plant nutrient acquisition

The beneficial effect of microbial consortium application on plants is strongly affected by soil conditions, which are influenced by farming practices. The establishment of microbial inoculants in the rhizosphere is a prerequisite for successful plant-microorganism interactions. This study investigated whether a consortium of beneficial microorganisms establishes in the rhizosphere of a winter crop during the vegetation period, including the winter growing season. In addition, we aimed for a better understanding of its effect on plant performance under different farming practices. Winter rye plants grown in a long-time field trial under conventional or organic farming practices were inoculated after plant emergence in autumn with a microbial consortium containing Pseudomonas sp. (RU47), Bacillus atrophaeus (ABi03) and Trichoderma harzianum (OMG16). The density of the microbial inoculants in the rhizosphere and root-associated soil was quantified in autumn and the following spring. Furthermore, the influence of the consortium on plant performance and on the rhizosphere bacterial community assembly was investigated using a multidisciplinary approach. Selective plating showed a high colonization density of individual microorganisms of the consortium in the rhizosphere and root-associated soil of winter rye throughout its early growth cycle. 16S rRNA gene amplicon sequencing showed that the farming practice affected mainly the rhizosphere bacterial communities in autumn and spring. However, the microbial consortium inoculated altered also the bacterial community composition at each sampling time point, especially at the beginning of the new growing season in spring. Inoculation of winter rye with the microbial consortium significantly improved the plant nutrient status and performance especially under organic farming. In summary, the microbial consortium showed sufficient efficacy throughout vegetation dormancy when inoculated in autumn and contributed to better plant performance, indicating the potential of microbe-based solutions in organic farming where nutrient availability is limited.

Monitoring of an Applied Beneficial Trichoderma Strain in Root-Associated Soil of Field-Grown Maize by MALDI-TOF MS

The persistence of beneficial microorganisms in the rhizosphere or surrounding soil following their application is a prerequisite for the effective interaction with the plant or indigenous microbial communities in the respective habitats. The goal of the study was to analyze the establishment and persistence of the applied beneficial Trichoderma harzianum (OMG16) strain in the maize root-associated soil depending on agricultural practice (soil management practice, N-fertilizer intensity) in a field experiment. A rapid identification of the inoculated strain OMG16 is essential for its monitoring. We used a culture-based approach coupled to matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis for the rapid identification of the inoculated Trichoderma strain as part of the beneficial microbe consortium (BMc). We isolated 428 fungal isolates from eight treatments of the field experiment. Forty eight percent of the isolated fungi equivalent to 205 fungal isolates were identified as Trichoderma, of which 87% (=179 isolates) were obtained from the fields inoculated with BMc. Gene sequence analysis showed a high similarity of the MALDI-TOF MS-identified Trichoderma, with that of the inoculated Trichoderma harzianum OMG16 confirming the re-isolation of the added beneficial fungus. This study highlighted the use of MALDI-TOF MS analysis as a quick, cost-effective detection and efficient monitoring tool for microbial-based bioinoculants in the field.

Influence of sewage sludge stabilization method on microbial community and the abundance of antibiotic resistance genes

Municipal sewage sludge (MSS) and other biosolids are of high interest for agriculture. These nutrient-rich organic materials can potentially serve as organic fertilizers. Besides an increase of organic matter in soil, other positive effects were shown after their application. Especially the positive influence on circular economy increased the attention paid to management of MSS in recent years. Unfortunately, the use of sewage sludge has some drawbacks. Biosolids are frequently polluted with heavy metals, xenobiotic organic compounds and industrial chemicals, which may be hazardous for the environment and humans. Here, we investigated the influence of stabilization method and the size of wastewater treatment plant on the structure of microbial communities as well as the abundance of antibiotic resistance genes (ARG) and mobile genetic elements (MGE). All tested ARG and MGE were detectable in almost all of the samples. Interestingly, the presence of MGE as well as particular heavy metals correlated positively with the presence of several ARG. We conclude that the distribution of ARG and MGE in biosolids originated from municipal wastewater treatment plants, cannot be explained by the size of the facility or the applied stabilization method. Moreover, we postulate that the presence of pollutants and long-term impacts should be assessed prior to a possible use of sewage sludge as fertilizer.

What Drives the Assembly of Plant-associated Protist Microbiomes? Investigating the Effects of Crop Species, Soil Type and Bacterial Microbiomes

In a field experiment we investigated the influence of the environmental filters soil type (i.e. three contrasting soils) and plant species (i.e. lettuce and potato) identity on rhizosphere community assembly of Cercozoa, a dominant group of mostly bacterivorous soil protists. Plant species (14%) and rhizosphere origin (vs bulk soil) with 13%, together explained four times more variation in cercozoan beta diversity than the three soil types (7% explained variation). Our results clearly confirm the existence of plant species-specific protist communities. Network analyses of bacteria-Cercozoa rhizosphere communities identified scale-free small world topologies, indicating mechanisms of self-organization. While the assembly of rhizosphere bacterial communities is bottom-up controlled through the resource supply from root (secondary) metabolites, our results support the hypothesis that the net effect may depend on the strength of top-down control by protist grazers. Since grazing of protists has a strong impact on the composition and functioning of bacteria communities, protists expand the repertoire of plant genes by functional traits, and should be considered as 'protist microbiomes' in analogy to 'bacterial microbiomes'.

Long-Term Fertilization Strategy Impacts Rhizoctonia solani–Microbe Interactions in Soil and Rhizosphere and Defense Responses in Lettuce

The long-term effects of agricultural management such as different fertilization strategies on soil microbiota and soil suppressiveness against plant pathogens are crucial. Therefore, the suppressiveness of soils differing in fertilization history was assessed using two Rhizoctonia solani isolates and their respective host plants (lettuce, sugar beet) in pot experiments. Further, the effects of fertilization history and the pathogen R. solani AG1-IB on the bulk soil, root-associated soil and rhizosphere microbiota of lettuce were analyzed based on amplicon sequencing of the 16S rRNA gene and ITS2 region. Organic fertilization history supported the spread of the soil-borne pathogens compared to long-term mineral fertilization. The fertilization strategy affected bacterial and fungal community composition in the root-associated soil and rhizosphere, respectively, but only the fungal community shifted in response to the inoculated pathogen. The potential plant-beneficial genus Talaromyces was enriched in the rhizosphere by organic fertilization and presence of the pathogen. Moreover, increased expression levels of defense-related genes in shoots of lettuce were observed in the soil with organic fertilization history, both in the absence and presence of the pathogen. This may reflect the enrichment of potential plant-beneficial microorganisms in the rhizosphere, but also pathogen infestation. However, enhanced defense responses resulted in retarded plant growth in the presence of R. solani (plant growth/defense tradeoff).

Role of Benzoic Acid and Lettucenin A in the Defense Response of Lettuce against Soil-Borne Pathogens

Soil-borne pathogens can severely limit plant productivity. Induced defense responses are plant strategies to counteract pathogen-related damage and yield loss. In this study, we hypothesized that benzoic acid and lettucenin A are involved as defense compounds against Rhizoctonia solani and Olpidium virulentus in lettuce. To address this hypothesis, we conducted growth chamber experiments using hydroponics, peat culture substrate and soil culture in pots and minirhizotrons. Benzoic acid was identified as root exudate released from lettuce plants upon pathogen infection, with pre-accumulation of benzoic acid esters in the root tissue. The amounts were sufficient to inhibit hyphal growth of R. solani in vitro (30%), to mitigate growth retardation (51%) and damage of fine roots (130%) in lettuce plants caused by R. solani, but were not able to overcome plant growth suppression induced by Olpidium infection. Additionally, lettucenin A was identified as major phytoalexin, with local accumulation in affected plant tissues upon infection with pathogens or chemical elicitation (CuSO₄) and detected in trace amounts in root exudates. The results suggest a two-stage defense mechanism with pathogen-induced benzoic acid exudation initially located in the rhizosphere followed by accumulation of lettucenin A locally restricted to affected root and leaf tissues.

Potato plant spheres and to a lesser extent the soil type influence the proportion and diversity of bacterial isolates with in vitro antagonistic activity towards Ralstonia solanacearum

Ralstonia solanacearum biovar2-race3 (Rs r3b2) is an epidemic soil-borne bacterial phytopathogen causing brown rot disease in potato. In this study, we assessed how three soil types stored at the same field site influenced the proportion and diversity of bacterial isolates with in vitro antagonistic activity towards Rs in bulk soil and different potato plant spheres (rhizosphere, endorhiza and endocaulosphere; ecto- and endosphere of seed and yield tubers). In general, the plate counts observed for each sample type were not significantly different. A total of 96 colonies per sample type was picked and screened for in vitro antagonistic activity against Rs. Antagonists were obtained from all bulk soils and plant spheres with the highest proportion obtained from the endorhiza and endocaulosphere of potato plants. BOX-PCR fingerprints of antagonists showed that some were specific for particular plant spheres independent of the soil type, while others originated from different plant spheres of a particular soil type. The majority of antagonists belonged to Pseudomonas. A high proportion of antagonists produced siderophores, and interestingly antagonists from potato tubers frequently carried multiple antibiotic production genes. Our data showed an enrichment of bacteria with genes or traits potentially involved in biocontrol in the rhizosphere and in endophytic compartments. We report that the proportion and diversity of in vitro antagonists towards Rs isolated from bulk soil and different spheres of potato plants grown under field conditions in three different soil types was mainly shaped by the plant sphere and to a lesser extent by the soil type. Bacteria with antagonistic activity towards Ralstonia solanacearum were isolated from all plant spheres and bulk soils but their proportion was highest in endophytic compartments.

Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories

A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.

Transcriptional Changes in Potato Sprouts upon Interaction with Rhizoctonia solani Indicate Pathogen-Induced Interference in the Defence Pathways of Potato

Rhizoctonia solani is the causer of black scurf disease on potatoes and is responsible for high economical losses in global agriculture. In order to increase the limited knowledge of the plants' molecular response to this pathogen, we inoculated potatoes with R. solani AG3-PT isolate Ben3 and carried out RNA sequencing with total RNA extracted from potato sprouts at three and eight days post inoculation (dpi). In this dual RNA-sequencing experiment, the necrotrophic lifestyle of R. solani AG3-PT during early phases of interaction with its host has already been characterised. Here the potato plants' comprehensive transcriptional response to inoculation with R. solani AG3 was evaluated for the first time based on significantly different expressed plant genes extracted with DESeq analysis. Overall, 1640 genes were differentially expressed, comparing control (-Rs) and with R. solani AG3-PT isolate Ben3 inoculated plants (+Rs). Genes involved in the production of anti-fungal proteins and secondary metabolites with antifungal properties were significantly up regulated upon inoculation with R. solani. Gene ontology (GO) terms involved in the regulation of hormone levels (i.e., ethylene (ET) and jasmonic acid (JA) at 3 dpi and salicylic acid (SA) and JA response pathways at 8 dpi) were significantly enriched. Contrastingly, the GO term "response to abiotic stimulus" was down regulated at both time points analysed. These results may support future breeding efforts toward the development of cultivars with higher resistance level to black scurf disease or the development of new control strategies.

Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root-Microbial Interactions and Plant Health of Lettuce

Fertilization management can affect plant performance and soil microbiota, involving still poorly understood rhizosphere interactions. We hypothesized that fertilization practice exerts specific effects on rhizodeposition with consequences for recruitment of rhizosphere microbiota and plant performance. To address this hypothesis, we conducted a minirhizotron experiment using lettuce as model plant and field soils with contrasting properties from two long-term field experiments (HUB-LTE: loamy sand, DOK-LTE: silty loam) with organic and mineral fertilization history. Increased relative abundance of plant-beneficial arbuscular mycorrhizal fungi and fungal pathotrophs were characteristic of the rhizospheres in the organically managed soils (HU-org; BIODYN2). Accordingly, defense-related genes were systemically expressed in shoot tissues of the respective plants. As a site-specific effect, high relative occurrence of the fungal lettuce pathogen Olpidium sp. (76-90%) was recorded in the rhizosphere, both under long-term organic and mineral fertilization at the DOK-LTE site, likely supporting Olpidium infection due to a lower water drainage potential compared to the sandy HUB-LTE soils. However, plant growth depressions and Olpidium infection were exclusively recorded in the BIODYN2 soil with organic fertilization history. This was associated with a drastic (87-97%) reduction in rhizosphere abundance of potentially plant-beneficial microbiota (Pseudomonadaceae, Mortierella elongata) and reduced concentrations of the antifungal root exudate benzoate, known to be increased in presence of Pseudomonas spp. In contrast, high relative abundance of Pseudomonadaceae (Gammaproteobacteria) in the rhizosphere of plants grown in soils with long-term mineral fertilization (61-74%) coincided with high rhizosphere concentrations of chemotactic dicarboxylates (succinate, malate) and a high C (sugar)/N (amino acid) ratio, known to support the growth of Gammaproteobacteria. This was related with generally lower systemic expression of plant defense genes as compared with organic fertilization history. Our results suggest a complex network of belowground interactions among root exudates, site-specific factors and rhizosphere microbiota, modulating the impact of fertilization management with consequences for plant health and performance.

Species-Specific Impact of Fusarium Infection on the Root and Shoot Characteristics of Asparagus

Soil-borne pathogens can have considerable detrimental effects on asparagus (Asparagus officinalis) growth and production, notably caused by the Fusarium species F. oxysporum f.sp. asparagi, F. proliferatum and F. redolens. In this study, their species-specific impact regarding disease severity and root morphological traits was analysed. Additionally, various isolates were characterised based on in vitro physiological activities and on protein extracts using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS). The response of two asparagus cultivars to the different Fusarium species was evaluated by inoculating experiments. Differences in aggressiveness were observed between Fusarium species and their isolates on roots, while no clear disease symptoms became visible in ferns eight weeks after inoculation. F. redolens isolates Fred1 and Fred2 were the most aggressive strains followed by the moderate aggressive F. proliferatum and the less and almost non-aggressive F. oxysporum isolates, based on the severity of disease symptoms. Fungal DNA in stem bases and a significant induction of pathogenesis-related gene expression was detectable in both asparagus cultivars. A significant negative impact of the pathogens on the root characteristics total root length, volume, and surface area was detected for each isolate tested, with Fred1 causing the strongest effects. No significant differences between the tested asparagus cultivars were observed.

Agricultural production systems can serve as reservoir for human pathogens

Food-borne diseases are a threat to human health and can cause severe economic losses. Nowadays, in a growing and increasingly interconnected world, food-borne diseases need to be dealt with in a global manner. In order to tackle this issue, it is essential to consider all possible entry routes of human pathogens into the production chain. Besides the post-harvest handling of the fresh produce itself, also the prevention of contamination in livestock and agricultural soils are of particular importance. While the monitoring of human pathogens and intervening measures are relatively easy to apply in livestock and post-harvest, the investigation of the prevention strategies in crop fields is a challenging task. Furthermore, crop fields are interconnected with livestock via fertilizers and feed; therefore, a poor hygiene management can cause cross-contamination. In this review, we highlight the possible contamination of crop plants by bacterial human pathogens via the rhizosphere, their interaction with the plant and possible intervention strategies. Furthermore, we discuss critical issues and questions that are still open.

Salmonella adapts to plants and their environment during colonization of tomatoes

Humans and animals are considered typical hosts for Salmonella, however, also plants can be colonized. Tomatoes were linked to salmonellosis outbreaks already on several occasions. The aim of this study was, therefore, to establish a comprehensive view on the interaction between Salmonella enterica and tomatoes, and to test the hypothesis that colonization of plants is an interactive process. We assessed the persistence of Salmonella in agricultural soil, the colonization pattern in and on tomatoes, as well as the reciprocal responses of tomatoes to different Salmonella strains and Salmonella to root exudates and tomato-related media. This study revealed that Salmonella can persist in the soil and inside the tomato plant. Additionally, we show that Salmonella strains have particular colonization pattern, although the persistence inside the plant differs between the tested strains. Furthermore, the transcriptome response of tomato showed an up-regulation of several defense-related genes. Salmonella transcriptome analysis in response to the plant-based media showed differentially regulated genes related to amino acid and fatty acid synthesis and stress response, while the response to root exudates revealed regulation of the glyoxylate cycle. Our results indicate that both organisms actively engage in the interaction and that Salmonella adapts to the plant environment.

Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics

The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.

Effect of long-term organic and mineral fertilization strategies on rhizosphere microbiota assemblage and performance of lettuce

Long-term agricultural fertilization strategies gradually change soil properties including the associated microbial communities. Cultivated crops recruit beneficial microbes from the surrounding soil environment via root exudates. In this study, we aimed to investigate the effects of long-term fertilization strategies across field sites on the rhizosphere prokaryotic (Bacteria and Archaea) community composition and plant performance. We conducted growth chamber experiments with lettuce (Lactuca sativa L.) cultivated in soils from two long-term field experiments, each of which compared organic versus mineral fertilization strategies. 16S rRNA gene amplicon sequencing revealed the assemblage of a rhizosphere core microbiota shared in all lettuce plants across soils, going beyond differences in community composition depending on field site and fertilization strategies. The enhanced expression of several plant genes with roles in oxidative and biotic stress signalling pathways in lettuce grown in soils with organic indicates an induced physiological status in plants. Lettuce plants grown in soils with different fertilization histories were visibly free of stress symptoms and achieved comparable biomass. This suggests a positive aboveground plant response to belowground plant-microbe interactions in the rhizosphere. Besides effects of fertilization strategy and field site, our results demonstrate the crucial role of the plant in driving rhizosphere microbiota assemblage.

Salmonella Establishment in Agricultural Soil and Colonization of Crop Plants Depend on Soil Type and Plant Species

Human pathogenic bacteria, such as Salmonella enterica, are able to colonize crop plants. So far, not much is known about biotic and abiotic factors influencing this colonization in field soil. This understanding, however, is imperative for the provision of safe fresh produce to the consumer. In this study, we investigated the effects of soil type, organic fertilization, plant species and the way of Salmonella entry into the plant production system, on the survival of S. enterica in soil as well as the colonization of plants. The selected S. enterica serovar Typhimurium strain 14028s, S. Typhimurium strain LT2 and S. Senftenberg were able to persist in soil for several weeks. Salmonella's persistence in soil was prolonged in loamy, if compared to sandy soil, and when applied together with organic fertilizer. The leaves of lettuce and corn salad were colonized by S. enterica providing evidence for internalization from the soil via the root. Colonization rates were affected by soil type, plant species and S. enterica strain. Overall, S. enterica was detected in leaves of 0.5-0.9% of the plants, while lettuce was more frequently colonized than corn salad. Plants grown in sandy soil were more often colonized than plants grown in loamy soil. After spray inoculation, S. enterica could be detected on and in leaves for several weeks by cultivation-depending methods, confirmed by confocal microscopy using GFP-labeled S. Typhimurium 14028s. On the one hand, transcriptome data from S. Typhimurium 14028s assessed in response to lettuce medium or lettuce root exudates showed an upregulation of genes associated with biofilm formation and virulence. On the other hand, lettuce inoculated with S. Typhimurium 14028s showed a strong upregulation of genes associated with plant immune response and genes related to stress response. In summary, these results showed that organic fertilizers can increase the persistence of Salmonella in soil and that soil type and plant species play a crucial role in the interactions between human pathogens and crop plants. This understanding is therefore a starting point for new strategies to provide safe food for the consumer.

A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani

The leafy green vegetable Lactuca sativa, L. is susceptible to the soil-born fungus Rhizoctonia solani AG1-IB. In a previous study, we reported on the transcriptional response of R. solani AG1-IB (isolate 7/3/14) during the interspecies interaction with L. sativa cv. Tizian by means of RNA sequencing. Here we present the L. sativa transcriptome and metabolome from the same experimental approach. Three distinct interaction zones were sampled and compared to a blank (non-inoculated) sample: symptomless zone 1, zone 2 showing light brown discoloration, and a dark brown zone 3 characterized by necrotic lesions. Throughout the interaction, we observed a massive reprogramming of the L. sativa transcriptome, with 9231 unique genes matching the threshold criteria for differential expression. The lettuce transcriptome of the light brown zone 2 presents the most dissimilar profile compared to the uninoculated zone 4, marking the main stage of interaction. Transcripts putatively encoding several essential proteins that are involved in maintaining jasmonic acid and auxin homeostasis were found to be negatively regulated. These and other indicator transcripts mark a potentially inadequate defence response, leading to a compatible interaction. KEGG pathway mapping and GC-MS metabolome data revealed large changes in amino acid, lignin and hemicellulose related pathways and related metabolites.

The Use of Features from Fluorescence, Thermography, and NDVI Imaging to Detect Biotic Stress in Lettuce

Fluorescence, normalized difference vegetation index, and thermal imaging are three frequently used nondestructive methods to detect biotic stress in plants. Due, in part, to the inconsistent results reported in the literature and the lack of measurements on the whole-plant scale, we tested the suitability of a wide variety of variables obtained using these three imaging methods to classify young plants into biotically stressed and nonstressed plants. To this end, we applied the model plant-pathogen system lettuce-Rhizoctonia solani. The relevant data from each image and plant (healthy and diseased) was extracted semiautomatically using sophisticated image processing algorithms. This method enabled us to identify the most appropriate variables via discriminant function and logistic regression analysis: photosystem II maximum quantum yield (Fv/Fm) and fluorescence decline ratio can be used to classify variables with an error ≤0.052. Lettuce seedlings with an Fv/Fm ratio > 0.73 were consistently healthy. In some cases, it was possible to detect infection prior to the appearance of symptoms. Possibilities to transfer the method to horticultural practice are discussed.

Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome

Lettuce (Lactuca sativa, L.) is an important annual plant of the family Asteraceae (Compositae). The commercial lettuce cultivar Tizian has been used in various scientific studies investigating the interaction of the plant with phytopathogens or biological control agents. Here, we present the de novo draft genome sequencing and gene prediction for this specific cultivar derived from transcriptome sequence data. The assembled scaffolds amount to a size of 2.22 Gb. Based on RNAseq data, 31,112 transcript isoforms were identified. Functional predictions for these transcripts were determined within the GenDBE annotation platform. Comparison with the cv. Salinas reference genome revealed a high degree of sequence similarity on genome and transcriptome levels, with an average amino acid identity of 99%. Furthermore, it was observed that two large regions are either missing or are highly divergent within the cv. Tizian genome compared to cv. Salinas. One of these regions covers the major resistance complex 1 region of cv. Salinas. The cv. Tizian draft genome sequence provides a valuable resource for future functional and transcriptome analyses focused on this lettuce cultivar.

Rhizosphere Competence and Biocontrol Effect of Pseudomonas sp. RU47 Independent from Plant Species and Soil Type at the Field Scale

Biocontrol inoculants often show inconsistency in their efficacy at field scale and the reason for this remains often unclear. A high rhizosphere competence of inoculant strains is assumed to be a key factor for successful biocontrol effects as the biocontrol strain has to compete with the indigenous microbial community in the rhizosphere. It is known that many factors, among them plant species and soil type shape the rhizosphere microbial community composition. However, microbial community composition in the rhizosphere can also be influenced by the presence of a pathogen. We hypothesized that plant species, soil type, and a pathogen affect the rhizosphere competence of a biocontrol strain and its biocontrol effect against a soil-borne pathogen. To test the hypothesis, we used an experimental plot system with three soil types (diluvial sand, alluvial loam, loess loam) kept under similar agricultural management at the same field site for 12 years. We investigate the rhizosphere competence of Pseudomonas sp. RU47 in two plant species (potato and lettuce) and its biocontrol effect against Rhizoctonia diseases. The colonization density of a rifampicin resistant mutant of RU47 in the rhizosphere of both crops was evaluated by plate counts. Bacterial community compositions were analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments amplified from total community DNA. The inoculant RU47 was able to colonize the rhizosphere of both model crops in a sufficient density and to reduce disease severity of black scurf on potato and bottom rot on lettuce in all three soils. DGGE indicated that RU47 affected the bacterial community composition stronger in the rhizosphere of lettuce than in the potato rhizosphere. In contrast, the effect of the pathogen Rhizoctonia solani on the bacterial community was much stronger in the rhizosphere of potato than in the lettuce rhizosphere. A significant effect of RU47 on the Pseudomonas-specific gacA fingerprints of the rhizosphere was only observed in lettuce in alluvial soil. The soil type and plant species independent biocontrol effects of RU47 and its minor influence on the indigenous bacterial community composition might be important criteria for the registration and use of RU47 as biocontrol strain.

Plant microbial diversity is suggested as the key to future biocontrol and health trends

The microbiome of plants plays a crucial role in both plant and ecosystem health. Rapid advances in multi-omics tools are dramatically increasing access to the plant microbiome and consequently to the identification of its links with diseases and to the control of those diseases. Recent insights reveal a close, often symbiotic relationship between microorganisms and plants. Microorganisms can stimulate germination and plant growth, prevent diseases, and promote stress resistance and general fitness. Plants and their associated microorganisms form a holobiont and have to be considered as co-evolved species assemblages consisting of bacterial, archaeal and diverse eukaryotic species. The beneficial interplay of the host and its microbiome is responsible for maintaining the health of the holobiont, while diseases are often correlated with microbial dysbioses. Microbial diversity was identified as a key factor in preventing diseases and can be implemented as a biomarker in plant protection strategies. Targeted and predictive biocontrol approaches are possible by developing microbiome-based solutions. Moreover, combined breeding and biocontrol strategies maintaining diversity and ecosystem health are required. The analysis of plant microbiome data has brought about a paradigm shift in our understanding of its role in health and disease and has substantial consequences for biocontrol and health issues.

The Rhizoctonia solani AG1-IB (isolate 7/3/14) transcriptome during interaction with the host plant lettuce (Lactuca sativa L.)

The necrotrophic pathogen Rhizoctonia solani is one of the most economically important soil-borne pathogens of crop plants. Isolates of R. solani AG1-IB are the major pathogens responsible for bottom-rot of lettuce (Lactuca sativa L.) and are also responsible for diseases in other plant species. Currently, there is lack of information regarding the molecular responses in R. solani during the pathogenic interaction between the necrotrophic soil-borne pathogen and its host plant. The genome of R. solani AG1-IB (isolate 7/3/14) was recently established to obtain insights into its putative pathogenicity determinants. In this study, the transcriptional activity of R. solani AG1-IB was followed during the course of its pathogenic interaction with the host plant lettuce under controlled conditions. Based on visual observations, three distinct pathogen-host interaction zones on lettuce leaves were defined which covered different phases of disease progression on tissue inoculated with the AG1-IB (isolate 7/3/14). The zones were defined as: Zone 1-symptomless, Zone 2-light brown discoloration, and Zone 3-dark brown, necrotic lesions. Differences in R. solani hyphae structure in these three zones were investigated by microscopic observation. Transcriptional activity within these three interaction zones was used to represent the course of R. solani disease progression applying high-throughput RNA sequencing (RNA-Seq) analysis of samples collected from each Zone. The resulting three transcriptome data sets were analyzed for their highest expressed genes and for differentially transcribed genes between the respective interaction zones. Among the highest expressed genes was a group of not previously described genes which were transcribed exclusively during early stages of interaction, in Zones 1 and 2. Previously described importance of up-regulation in R. solani agglutinin genes during disease progression could be further confirmed; here, the corresponding genes exhibited extremely high transcription levels. Most differentially higher expressed transcripts were found within Zone 2. In Zone 3, the zone with the strongest degree of interaction, gene transcripts indicative of apoptotic activity were highly abundant. The transcriptome data presented in this work support previous models of the disease and interaction cycle of R. solani and lettuce and may influence effective techniques for control of this pathogen.

Persistence of Salmonella Typhimurium LT2 in Soil Enhanced after Growth in Lettuce Medium

The persistence of Salmonella in the environment is influenced by a multitude of biotic and abiotic factors. In addition, its persistence can be influenced by preadaptation before the introduction into the environment. In order to study how preadaptation changes the survival of Salmonella in soil and therefore its potential to colonize the phytosphere, we developed a new medium based on lettuce material [lettuce medium (LM)]. Salmonella enterica serovar Typhimurium strain LT2 was used as a model for Salmonella in this study. LT2 was inoculated into soil microcosms after pregrowth in Luria Bertani (LB) broth or in LM. Survival of LT2 in soil was monitored over 56 days by plate counts and quantification of the Typhimurium-specific gene STM4497 using qPCR in total community DNA for which primers and TaqMan probe were designed in this study. Significantly enhanced persistence was observed for LT2 pregrown in LM compared to LT2 pregrown in LB, indicating a preadaptation effect. Surprisingly, no improved survival could be observed for S. Typhimurium strain 14028s and S. enterica serovar Senftenberg after pregrowth on LM. This indicates a high strain specificity of preadaptation. Results from previous studies suggested that biofilm formation could enhance the survival of human pathogens in various environments and might contribute to enhanced survival on plants. In vitro biofilm assays with several Salmonella strains revealed a strain-specific effect of LM on the biofilm formation. While LM significantly improved the biofilm formation of S. Senftenberg, the biofilm formation of LT2 was better in LB. This indicates that the better survival of LM-pregrown LT2 in soil was not linked to an improved ability to form biofilms but was likely due to other factors. Most importantly, this study showed that the medium used to pregrow Salmonella can influence its survival in soil and its biofilm formation which might influence the fate of Salmonella in soil.

A Proteomic Approach Suggests Unbalanced Proteasome Functioning Induced by the Growth-Promoting Bacterium Kosakonia radicincitans in Arabidopsis

Endophytic plant growth-promoting bacteria have significant impact on the plant physiology and understanding this interaction at the molecular level is of particular interest to support crop productivity and sustainable production systems. We used a proteomics approach to investigate the molecular mechanisms underlying plant growth promotion in the interaction of Kosakonia radicincitans DSM 16656 with Arabidopsis thaliana. Four weeks after the inoculation, the proteome of roots from inoculated and control plants was compared using two-dimensional gel electrophoresis and differentially abundant protein spots were identified by liquid chromatography tandem mass spectrometry. Twelve protein spots were responsive to the inoculation, with the majority of them being related to cellular stress reactions. The protein expression of 20S proteasome alpha-3 subunit was increased by the presence of K. radicincitans. Determination of proteasome activity and immuno blotting analysis for ubiquitinated proteins revealed that endophytic colonization interferes with ubiquitin-dependent protein degradation. Inoculation of rpn12a, defective in a 26S proteasome regulatory particle, enhanced the growth-promoting effect. This indicates that the plant proteasome, besides being a known target for plant pathogenic bacteria, is involved in the establishment of beneficial interactions of microorganisms with plants.

Temporal impact of the vascular wilt pathogen Verticillium dahliae on tomato root proteome

The soil-borne fungus Verticillium dahliae is the causal agent of wilting disease and affects a wide range of plant species worldwide. Here, we report on the time-resolved analysis of the tomato root proteome in response to fungal colonization. Tomato (Solanum lycopersicum cv. Hildares) was inoculated with V. dahliae at the two-leaf stage and roots were harvested at 7, 14 and 21 days post inoculation (dpi). In order to identify proteins related to the fungal spread at the different time points, a subsequent proteome analysis by two-dimensional differential gel electrophoresis (2D-DIGE) was conducted on samples from three independent experiments. Hierarchical clustering and k-means clustering of identified proteins distinguished early and late responses to fungal colonization. The results underline that plant defense and adaptation responses are timely coordinated. Proteins involved in oxidative stress were down-regulated at 7 dpi but induced 21 dpi indicating versatile reactive oxygen species signaling interacting with salicylic acid defence signaling at that stage of infection. Drought-stress proteins were induced at 21 dpi, reflecting the beginning of wilting symptoms. Notably, two proteins involved in energy-generating pathways were induced throughout all sampling dates and may reflect the increase in metabolic activity to maintain root growth and, concurrently, activate defense responses.

BIOLOGICAL SIGNIFICANCE

Mounting of defense responses requires a substantial flux of carbon and nitrogen from primary to secondary metabolites. In-depth understanding of these key metabolic pathways required for growth and defense responses, especially at proteome level, will allow the development of breeding strategies for crops where Verticillium tolerance is absent. Our data show early and late responses of tomato root proteins towards pathogen infection and identify primary metabolism enzymes affected by V. dahliae. Those proteins represent candidates for plant improvement.

Statistical test for tolerability of effects of an antifungal biocontrol strain on fungal communities in three arable soils

A statistical method was developed to test for equivalence of microbial communities analysed by next-generation sequencing of amplicons. The test uses Bray-Curtis distances between the microbial community structures and is based on a two-sample jackknife procedure. This approach was applied to investigate putative effects of the antifungal biocontrol strain RU47 on fungal communities in three arable soils which were analysed by high-throughput ITS amplicon sequencing. Two contrasting workflows to produce abundance tables of operational taxonomic units from sequence data were applied. For both, the developed test indicated highly significant equivalence of the fungal communities with or without previous exposure to RU47 for all soil types, with reference to fungal community differences in conjunction with field site or cropping history. However, minor effects of RU47 on fungal communities were statistically significant using highly sensitive multivariate tests. Nearly all fungal taxa responding to RU47 increased in relative abundance indicating the absence of ecotoxicological effects. Use of the developed equivalence test is not restricted to evaluate effects on soil microbial communities by inoculants for biocontrol, bioremediation or other purposes, but could also be applied for biosafety assessment of compounds like pesticides, or genetically engineered plants.

Development of a Rhizoctonia solani AG1-IB Specific Gene Model Enables Comparative Genome Analyses between Phytopathogenic R. solani AG1-IA, AG1-IB, AG3 and AG8 Isolates

Rhizoctonia solani, a soil-born plant pathogenic basidiomycetous fungus, affects various economically important agricultural and horticultural crops. The draft genome sequence for the R. solani AG1-IB isolate 7/3/14 as well as a corresponding transcriptome dataset (Expressed Sequence Tags—ESTs) were established previously. Development of a specific R. solani AG1-IB gene model based on GMAP transcript mapping within the eukaryotic gene prediction platform AUGUSTUS allowed detection of new genes and provided insights into the gene structure of this fungus. In total, 12,616 genes were recognized in the genome of the AG1-IB isolate. Analysis of predicted genes by means of different bioinformatics tools revealed new genes whose products potentially are involved in degradation of plant cell wall components, melanin formation and synthesis of secondary metabolites. Comparative genome analyses between members of different R. solani anastomosis groups, namely AG1-IA, AG3 and AG8 and the newly annotated R. solani AG1-IB genome were performed within the comparative genomics platform EDGAR. It appeared that only 21 to 28% of all genes encoded in the draft genomes of the different strains were identified as core genes. Based on Average Nucleotide Identity (ANI) and Average Amino-acid Identity (AAI) analyses, considerable sequence differences between isolates representing different anastomosis groups were identified. However, R. solani isolates form a distinct cluster in relation to other fungi of the phylum Basidiomycota. The isolate representing AG1-IB encodes significant more genes featuring predictable functions in secondary metabolite production compared to other completely sequenced R. solani strains. The newly established R. solani AG1-IB 7/3/14 gene layout now provides a reliable basis for post-genomics studies.

Cyclic Lipopeptides of Bacillus amyloliquefaciens subsp. plantarum Colonizing the Lettuce Rhizosphere Enhance Plant Defense Responses Toward the Bottom Rot Pathogen Rhizoctonia solani

The commercially available inoculant Bacillus amyloliquefaciens FZB42 is able to considerably reduce lettuce bottom rot caused by Rhizoctonia solani. To understand the interaction between FZB42 and R. solani in the rhizosphere of lettuce, we used an axenic system with lettuce bacterized with FZB42 and inoculated with R. solani. Confocal laser scanning microscopy showed that FZB42 could delay the initial establishment of R. solani on the plants. To show which secondary metabolites of FZB42 are produced under these in-situ conditions, we developed an ultra-high performance liquid chromatography coupled to time of flight mass spectrometry-based method and identified surfactin, fengycin, and bacillomycin D in the lettuce rhizosphere. We hypothesized that lipopeptides and polyketides play a role in enhancing the plant defense responses in addition to the direct antagonistic effect toward R. solani and used a quantitative real-time polymerase chain reaction-based assay for marker genes involved in defense signaling pathways in lettuce. A significant higher expression of PDF 1.2 observed in the bacterized plants in response to subsequent pathogen challenge showed that FZB42 could enhance the lettuce defense response toward the fungal pathogen. To identify if surfactin or other nonribosomally synthesized secondary metabolites could elicit the observed enhanced defense gene expression, we examined two mutants of FZB42 deficient in production of surfactin and the lipopetides and polyketides, by expression analysis and pot experiments. In the absence of surfactin and other nonribosomally synthesized secondary metabolites, there was no enhanced PDF 1.2-mediated response to the pathogen challenge. Pot experiment results showed that the mutants failed to reduce disease incidence in lettuce as compared with the FZB42 wild type, indicating, that surfactin as well as other nonribosomally synthesized secondary metabolites play a role in the actual disease suppression and on lettuce health. In conclusion, our study showed that nonribosomally synthesized secondary metabolites of FZB42 are actually produced in the lettuce rhizosphere and contribute to the disease suppression by mediating plant defense gene expression toward the pathogen R. solani.

Verticillium longisporum infection induces organ-specific glucosinolate degradation in Arabidopsis thaliana

The species Verticillium represents a group of highly destructive fungal pathogens, responsible for vascular wilt in a number of crops. The host response to infection by Verticillium longisporum at the level of secondary plant metabolites has not been well explored. Natural variation in the glucosinolate (GLS) composition of four Arabidopsis thaliana accessions was characterized: the accessions Bur-0 and Hi-0 accumulated alkenyl GLS, while 3-hydroxypropyl GLS predominated in Kn-0 and Ler-0. With respect to GLS degradation products, Hi-0 and Kn-0 generated mainly isothiocyanates, whereas Bur-0 released epithionitriles and Ler-0 nitriles. An analysis of the effect on the composition of both GLS and its breakdown products in the leaf and root following the plants' exposure to V. longisporum revealed a number of organ- and accession-specific alterations. In the less disease susceptible accessions Bur-0 and Ler-0, colonization depressed the accumulation of GLS in the rosette leaves but accentuated it in the roots. In contrast, in the root, the level of GLS breakdown products in three of the four accessions fell, suggestive of their conjugation or binding to a fungal target molecule(s). The plant-pathogen interaction influenced both the organ- and accession-specific formation of GLS degradation products.

Improved genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 as established by deep mate-pair sequencing on the MiSeq (Illumina) system

The phytopathogenic fungus Rhizoctonia solani AG1-IB of the phylum Basidiomycota affects various economically important crops comprising bean, rice, soybean, figs, cabbage and lettuce. The R. solani isolate 7/3/14 of the anastomosis group AG1-IB was deeply resequenced on the Illumina MiSeq system applying the mate-pair mode to improve its genome sequence. Assembly of obtained sequence reads significantly reduced the amount of scaffolds and improved the genome sequence of the isolate compared to the previous sequencing approach. The genome sequence of the AG1-IB isolate 7/3/14 now provides an up-graded basis to analyze genome features predicted to play a role in pathogenesis and for the development of strategies to antagonize the pathogenic impact of this fungus.

Soil type-dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce

Bacterial biocontrol strains used as an alternative to chemical fungicides may influence bacterial communities in the rhizosphere and effects might differ depending on the soil type. Here we present baseline data on the effects of Pseudomonas jessenii RU47 on the bacterial community composition in the rhizosphere of lettuce grown in diluvial sand, alluvial loam and loess loam at the same field site. 16S rRNA gene fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. DGGE fingerprints revealed that in three consecutive years (2010-2012) RU47 had a slight but statistically significant effect on the bacterial community composition in one (2010), two (2011) or all the three soils (2012). However, these effects were much less pronounced compared with the influence of soil types. Additional pyrosequence analysis of samples from 2011 showed that significant changes in bacterial community compositions in response to RU47 inoculation occurred only in alluvial loam. Different taxonomic groups responded to the RU47 application depending on the soil type. Most remarkable was the increased relative abundance of OTUs belonging to the genera Bacillus and Paenibacillus in alluvial loam. Pyrosequencing allowed side-effects of the application of bacterial inoculants into the rhizosphere to be identified.

Soil type dependent rhizosphere competence and biocontrol of two bacterial inoculant strains and their effects on the rhizosphere microbial community of field-grown lettuce

Rhizosphere competence of bacterial inoculants is assumed to be important for successful biocontrol. Knowledge of factors influencing rhizosphere competence under field conditions is largely lacking. The present study is aimed to unravel the effects of soil types on the rhizosphere competence and biocontrol activity of the two inoculant strains Pseudomonas jessenii RU47 and Serratia plymuthica 3Re4-18 in field-grown lettuce in soils inoculated with Rhizoctonia solani AG1-IB or not. Two independent experiments were carried out in 2011 on an experimental plot system with three soil types sharing the same cropping history and weather conditions for more than 10 years. Rifampicin resistant mutants of the inoculants were used to evaluate their colonization in the rhizosphere of lettuce. The rhizosphere bacterial community structure was analyzed by denaturing gradient gel electrophoresis of 16S rRNA gene fragments amplified from total community DNA to get insights into the effects of the inoculants and R. solani on the indigenous rhizosphere bacterial communities. Both inoculants showed a good colonization ability of the rhizosphere of lettuce with more than 10(6) colony forming units per g root dry mass two weeks after planting. An effect of the soil type on rhizosphere competence was observed for 3Re4-18 but not for RU47. In both experiments a comparable rhizosphere competence was observed and in the presence of the inoculants disease symptoms were either significantly reduced, or at least a non-significant trend was shown. Disease severity was highest in diluvial sand followed by alluvial loam and loess loam suggesting that the soil types differed in their conduciveness for bottom rot disease. Compared to effect of the soil type of the rhizosphere bacterial communities, the effects of the pathogen and the inoculants were less pronounced. The soil types had a surprisingly low influence on rhizosphere competence and biocontrol activity while they significantly affected the bottom rot disease severity.

Transcriptome analysis of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 applying high-throughput sequencing of expressed sequence tags (ESTs)

Rhizoctonia solani is a soil-borne plant pathogenic fungus of the phylum Basidiomycota. It affects a wide range of agriculturally important crops and hence is responsible for economically relevant crop losses. Transcriptome analysis of the bottom rot pathogen R. solani AG1-1B (isolate 7/3/14) by applying high-throughput sequencing and bioinformatics methods addressing Expressed Sequence Tag (EST) data interpretation provided new insights in expressed genes of this fungus. Two normalized cDNA libraries representing different cultivation conditions of the fungus were sequenced on the 454 FLX (Roche) system. Subsequent to cDNA sequence assembly and quality control, ESTs were analysed applying advanced bioinformatics methods. More than 14 000 transcript isoforms originating from approximately 10 000 predictable R. solani AG1-IB 7/3/14 genes are represented in each dataset. Comparative analyses revealed several differentially expressed genes depending on the growth conditions applied. Determinants with predicted functions in recognition processes between the fungus and the host plant were identified. Moreover, many R. solani AG1-IB ESTs were predicted to encode putative cellulose, pectin, and lignin degrading enzymes. Furthermore, genes playing a possible role in mitogen-activated protein (MAP) kinase cascades, 4-aminobutyric acid (GABA) metabolism, melanin synthesis, plant defence antagonism, phytotoxin, and mycotoxin synthesis were detected.

Effect of the strain Bacillus amyloliquefaciens FZB42 on the microbial community in the rhizosphere of lettuce under field conditions analyzed by whole metagenome sequencing

Application of the plant associated bacterium Bacillus amyloliquefaciens FZB42 on lettuce (Lactuca sativa) confirmed its capability to promote plant growth and health by reducing disease severity (DS) caused by the phytopathogenic fungus Rhizoctonia solani. Therefore this strain is commercially applied as an eco-friendly plant protective agent. It is able to produce cyclic lipopeptides (CLP) and polyketides featuring antifungal and antibacterial properties. Production of these secondary metabolites led to the question of a possible impact of strain FZB42 on the composition of microbial rhizosphere communities after its application. Rating of DS and lettuce growth during a field trial confirmed the positive impact of strain FZB42 on the health of the host plant. To verify B. amyloliquefaciens as an environmentally compatible plant protective agent, its effect on the indigenous rhizosphere community was analyzed by metagenome sequencing. Rhizosphere microbial communities of lettuce treated with B. amyloliquefaciens FZB42 and non-treated plants were profiled by high-throughput metagenome sequencing of whole community DNA. Fragment recruitments of metagenome sequence reads on the genome sequence of B. amyloliquefaciens FZB42 proved the presence of the strain in the rhizosphere over 5 weeks of the field trial. Comparison of taxonomic community profiles only revealed marginal changes after application of strain FZB42. The orders Burkholderiales, Actinomycetales and Rhizobiales were most abundant in all samples. Depending on plant age a general shift within the composition of the microbial communities that was independent of the application of strain FZB42 was observed. In addition to the taxonomic profiling, functional analysis of annotated sequences revealed no major differences between samples regarding application of the inoculant strain.

The impact of the pathogen Rhizoctonia solani and its beneficial counterpart Bacillus amyloliquefaciens on the indigenous lettuce microbiome

Lettuce belongs to the most commonly raw eaten food worldwide and its microbiome plays an important role for both human and plant health. Yet, little is known about the impact of potentially occurring pathogens and beneficial inoculants of the indigenous microorganisms associated with lettuce. To address this question we studied the impact of the phytopathogenic fungus Rhizoctonia solani and the biological control agent Bacillus amyloliquefaciens FZB42 on the indigenous rhizosphere and phyllosphere community of greenhouse-grown lettuce at two plant stages. The rhizosphere and phyllosphere gammaproteobacterial microbiomes of lettuce plants showed clear differences in their overall and core microbiome composition as well as in corresponding diversity indices. The rhizosphere was dominated by Xanthomonadaceae (48%) and Pseudomonadaceae (37%) with Rhodanobacter, Pseudoxanthomonas, Dokdonella, Luteimonas, Steroidobacter, Thermomonas as core inhabitants, while the dominating taxa associated to phyllosphere were Pseudomonadaceae (54%), Moraxellaceae (16%) and Enterobacteriaceae (25%) with Alkanindiges, Pantoea and a group of Enterobacteriaceae unclassified at genus level. The preferential occurrence of enterics in the phyllosphere was the most significant difference between both habitats. Additional enhancement of enterics on the phyllosphere was observed in bottom rot diseased lettuce plants, while Acinetobacter and Alkanindiges were identified as indicators of healthy plants. Interestingly, the microbial diversity was enhanced by treatment with both the pathogen, and the co-inoculated biological control agent. The highest impact and bacterial diversity was found by Rhizoctonia inoculation, but FZB42 lowered the impact of Rhizoctonia on the microbiome. This study shows that the indigenous microbiome shifts as a consequence to pathogen attack but FZB42 can compensate these effects, which supports their role as biocontrol agent and suggests a novel mode of action.

Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce

The complex and enormous diversity of microorganisms associated with plant roots is important for plant health and growth and is shaped by numerous factors. This study aimed to unravel the effects of the soil type on bacterial communities in the rhizosphere of field-grown lettuce. We used an experimental plot system with three different soil types that were stored at the same site for 10 years under the same agricultural management to reveal differences directly linked to the soil type and not influenced by other factors such as climate or cropping history. Bulk soil and rhizosphere samples were collected 3 and 7 weeks after planting. The analysis of 16S rRNA gene fragments amplified from total community DNA by denaturing gradient gel electrophoresis and pyrosequencing revealed soil type dependent differences in the bacterial community structure of the bulk soils and the corresponding rhizospheres. The rhizosphere effect differed depending on the soil type and the plant growth developmental stage. Despite the soil type dependent differences in the bacterial community composition several genera such as Sphingomonas, Rhizobium, Pseudomonas, and Variovorax were significantly increased in the rhizosphere of lettuce grown in all three soils. The number of rhizosphere responders was highest 3 weeks after planting. Interestingly, in the soil with the highest numbers of responders the highest shoot dry weights were observed. Heatmap analysis revealed that many dominant operational taxonomic units were shared among rhizosphere samples of lettuce grown in diluvial sand, alluvial loam, and loess loam and that only a subset was increased in relative abundance in the rhizosphere compared to the corresponding bulk soil. The findings of the study provide insights into the effect of soil types on the rhizosphere microbiome of lettuce.

Root exudation and root development of lettuce (Lactuca sativa L. cv. Tizian) as affected by different soils

Development and activity of plant roots exhibit high adaptive variability. Although it is well-documented, that physicochemical soil properties can strongly influence root morphology and root exudation, particularly under field conditions, a comparative assessment is complicated by the impact of additional factors, such as climate and cropping history. To overcome these limitations, in this study, field soils originating from an unique experimental plot system with three different soil types, which were stored at the same field site for 10 years and exposed to the same agricultural management practice, were used for an investigation on effects of soil type on root development and root exudation. Lettuce (Lactuca sativa L. cv. Tizian) was grown as a model plant under controlled environmental conditions in a minirhizotrone system equipped with root observation windows (rhizoboxes). Root exudates were collected by placing sorption filters onto the root surface followed by subsequent extraction and GC-MS profiling of the trapped compounds. Surprisingly, even in absence of external stress factors with known impact on root exudation, such as pH extremes, water and nutrient limitations/toxicities or soil structure effects (use of sieved soils), root growth characteristics (root length, fine root development) as well as profiles of root exudates were strongly influenced by the soil type used for plant cultivation. The results coincided well with differences in rhizosphere bacterial communities, detected in field-grown lettuce plants cultivated on the same soils (Schreiter et al., this issue). The findings suggest that the observed differences may be the result of plant interactions with the soil-specific microbiomes.

Verticillium suppression is associated with the glucosinolate composition of Arabidopsis thaliana leaves

The soil-borne fungal pathogen Verticillium longisporum is able to penetrate the root of a number of plant species and spread systemically via the xylem. Fumigation of Verticillium contaminated soil with Brassica green manure is used as an environmentally friendly method for crop protection. Here we present a study focused on the potential role of glucosinolates and their breakdown products of the model plant Arabidopsis thaliana in suppressing growth of V. longisporum. For this purpose we analysed the glucosinolate composition of the leaves and roots of a set of 19 key accessions of A. thaliana. The effect of volatile glucosinolate hydrolysis products on the in vitro growth of the pathogen was tested by exposing the fungus to hydrated lyophilized plant tissue. Volatiles released from leaf tissue were more effective than from root tissue in suppressing mycelial growth of V. longisporum. The accessions varied in their efficacy, with the most effective suppressing mycelial growth by 90%. An analysis of glucosinolate profiles and their enzymatic degradation products revealed a correlation between fungal growth inhibition and the concentration of alkenyl glucosinolates, particularly 2-propenyl (2Prop) glucosinolate, respectively its hydrolysis products. Exposure of the fungus to purified 2Prop glucosinolate revealed that its suppressive activity was correlated with its concentration. Spiking of 2Prop glucosinolate to leaf material of one of the least effective A. thaliana accessions led to fungal growth suppression. It is suggested that much of the inhibitory effect observed for the tested accessions can be explained by the accumulation of 2Prop glucosinolate.

Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14

Anastomosis group AG1-IB isolates of the anamorphic basidiomycetous fungus Rhizoctonia solani Kühn affect various agricultural and horticultural important crops including bean, rice, soybean, figs, hortensia, cabbage and lettuce. To gain insights into the genome structure and content, the first draft genome sequence of R. solani AG1-IB isolate 7/3/14 was established. Four complete runs on the Genome Sequencer (GS) FLX platform (Roche Applied Science) yielding approx. a 25-fold coverage of the R. solani genome were accomplished. Assembly of the sequence reads by means of the gsAssembler software version 2.6 applying the heterozygotic mode resulted in numerous contigs and scaffolds and a predicted size of 87.1 Mb for the diploid status of the genome. 'Contig-length vs. read-count' analysis revealed that the assembled contigs can be classified into five different groups. Detailed BLAST-analysis revealed that most contigs of group II feature high-scoring matches to other contigs of the same group suggesting that distinguishable allelic variants exist for many genes. Due to the supposed diploid and heterokaryotic nature of R. solani AG1-IB 7/3/14, this result has been anticipated. However, the heterokaryotic character of the isolate is not really supported by sequencing data obtained for the isolate R. solani AG1-IB 7/3/14. Coverage of group III contigs is twice as high as for group II contigs which can also be explained by the diploid status of the genome and indistinguishable alleles on homologous chromosomes. Assembly of sequence data led to the identification of the rRNA unit (group V contigs) and the mitochondrial (mt) genome (group IV contigs) which is a circular molecule of 162,751 bp in size featuring a GC-content of 36.4%. The R. solani 7/3/14 mt-genome is one of the largest fungal mitochondrial genomes known to date. Its large size essentially is due to the presence of numerous non-conserved hypothetical ORFs and introns. Gene prediction for the R. solani AG1-IB 7/3/14 genome was conducted by the Augustus Gene Prediction Software for Eukaryotes (version 2.6.) applying the parameter set for the fungus Coprinopsis cinerea okayama 7#130. Gene prediction and annotation provided first insights into the R. solani AG1-IB 7/3/14 gene structure and content. In total, 12,422 genes were predicted. The average number of exons per gene is five. Exons have a mean length of 214 bp, whereas introns on average are 66 bp in length. Annotation of the genome revealed that 4169 of 12,422 genes could be assigned to KOG functional categories.

Effects of Bacillus amyloliquefaciens FZB42 on lettuce growth and health under pathogen pressure and its impact on the rhizosphere bacterial community

The soil-borne pathogen Rhizoctonia solani is responsible for crop losses on a wide range of important crops worldwide. The lack of effective control strategies and the increasing demand for organically grown food has stimulated research on biological control. The aim of the present study was to evaluate the rhizosphere competence of the commercially available inoculant Bacillus amyloliquefaciens FZB42 on lettuce growth and health together with its impact on the indigenous rhizosphere bacterial community in field and pot experiments. Results of both experiments demonstrated that FZB42 is able to effectively colonize the rhizosphere (7.45 to 6.61 Log 10 CFU g(-1) root dry mass) within the growth period of lettuce in the field. The disease severity (DS) of bottom rot on lettuce was significantly reduced from severe symptoms with DS category 5 to slight symptom expression with DS category 3 on average through treatment of young plants with FZB42 before and after planting. The 16S rRNA gene based fingerprinting method terminal restriction fragment length polymorphism (T-RFLP) showed that the treatment with FZB42 did not have a major impact on the indigenous rhizosphere bacterial community. However, the bacterial community showed a clear temporal shift. The results also indicated that the pathogen R. solani AG1-IB affects the rhizosphere microbial community after inoculation. Thus, we revealed that the inoculant FZB42 could establish itself successfully in the rhizosphere without showing any durable effect on the rhizosphere bacterial community.

Effects of dark septate endophytes on tomato plant performance

Non-mycorrhizal fungal root endophytes can be found in all natural and cultivated ecosystems, but little is known about their impact on plant performance. The impact of three mitosporic dark septate endophytes (DSE48, DSE49 and Leptodontidium orchidicola) on tomato plant characteristics was studied. Their effects on root and shoot growth, their influence on fruit yield and fruit quality parameters and their ability to diminish the impact of the pathogen Verticillium dahliae were investigated. While shoot biomass of young plants was enhanced between 10% and 20% by the endophytes DSE48 and L. orchidicola in one of two experiments and by DSE49 in both experiments, vegetative growth parameters of 24-week-old plants were not affected except a reproducible increase of root diameter by the isolate DSE49. Concerning fruit yield and quality, L. orchidicola could double the biomass of tomatoes and increased glucose content by 17%, but this was dependent on date of harvest and on root colonisation density. Additionally, the endophytes DSE49 and L. orchidicola decreased the negative effect of V. dahliae on tomato, but only at a low dosage of the pathogen. This indicates that the three dark septate endophytes can have a significant impact on tomato characters, but that the effects are only obvious at early stages of vegetative and generative development and currently too inconsistent to recommend the application of these DSEs in horticultural practice.

Impact of biotic and a-biotic parameters on structure and function of microbial communities living on sclerotia of the soil-borne pathogenic fungus Rhizoctonia solani

The plant pathogen Rhizoctonia solani is very difficult to control due to its persistent, long-living sclerotial structures in soil. Sclerotia are the main source of infection for Rhizoctonia diseases, which cause high yield losses on a broad host range world-wide. Little is known about micro-organisms associated with sclerotia in soil. Therefore, microbial communities of greenhouse and field incubated Rhizoctonia sclerotia were analysed by a multiphasic approach. Using microbial fingerprints performed by PCR-SSCP, sclerotia-associated bacterial communities showed a high diversity, whereas only a few fungi could be detected. Statistical analysis of fingerprints revealed the influence of soil types, incubation conditions (greenhouse, field), and incubation time (5 and 12 weeks) on the bacterial as well as fungal community. No significant differences were found for the microbial community associated with different Rhizoctonia anastomosis sub-groups (AG 1-IB and AG 1-IC). Rhizoctonia sclerotia are an interesting bio-resource: high proportions of fungal cell-wall degrading isolates as well as those with antagonistic activity towards R. solani were found. While a fraction of 28.4% of sclerotia-associated bacteria (=40 isolates) with antagonistic properties was determined, only 4.4% (=6 isolates) of the fungal isolates were antagonistic. We identified strong antagonists of the genera Bacillus, Enterobacter, Pseudomonas, and Stenotrophomonas, which can be used as biological control agents incorporated in soil or applied to Rhizoctonia host plants.

Colonization of roots of cultivated Solanum lycopersicum by dark septate and other ascomycetous endophytes

Tomato (Solanum lycopersicum L.) roots from four different crop sites in Colombia were surface sterilized and 51 fungal isolates were obtained and conserved for further analysis. Based on microscopical observations and growth characteristics, 20 fungal isolates corresponded to genus Fusarium, six presented asexual conidia different from Fusarium, eight were sterile mycelia, seven of which had dark septate hyphae and 17 did not continue to grow on plates after being recovered from conservation. Growth on different media, detailed morphological characterization and ITS region sequencing of the six sporulating and eight sterile isolates revealed that they belonged to different orders of Ascomycota and that the sterile dark septate endophytes did not correspond to the well known Phialocephala group. Interactions of nine isolates with tomato plantlets were assessed in vitro. No effect on shoot development was revealed, but three isolates caused brown spots in roots. Colonization patterns as analyzed by confocal microscopy differed among the isolates and ranged from epidermal to cortical penetration. Altogether 11 new isolates from root endophytic fungi were obtained, seven of which showed features of dark septate endophytes. Four known morphotypes were represented by five isolates, while six isolates belonged to five morphotypes of putative new unknown species.

Impact of Piriformospora indica on tomato growth and on interaction with fungal and viral pathogens

Piriformospora indica is a root endophytic fungus with plant-promoting properties in numerous plant species and induces resistance against root and shoot pathogens in barley, wheat, and Arabidopsis. A study over several years showed that the endophyte P. indica colonised the roots of the most consumed vegetable crop tomato. P. indica improved the growth of tomato resulting in increased biomass of leaves by up to 20%. Limitation of disease severity caused by Verticillium dahliae by more than 30% was observed on tomato plants colonised by the endophyte. Further experiments were carried out in hydroponic cultures which are commonly used for the indoor production of tomatoes in central Europe. After adaptation of inoculation techniques (inoculum density, plant stage), it was shown that P. indica influences the concentration of Pepino mosaic virus in tomato shoots. The outcome of the interaction seems to be affected by light intensity. Most importantly, the endophyte increases tomato fruit biomass in hydroponic culture concerning fresh weight (up to 100%) and dry matter content (up to 20%). Hence, P. indica represents a suitable growth promoting endophyte for tomato which can be applied in production systems of this important vegetable plant not only in soil, but also in hydroponic cultures.

In vitro antagonists of Rhizoctonia solani tested on lettuce: rhizosphere competence, biocontrol efficiency and rhizosphere microbial community response

The rhizosphere competence of 15 in vitro antagonists of Rhizoctonia solani was determined 4 weeks after sowing inoculated lettuce seeds into nonsterile soil. Based on the colonization ability determined by selective plating, eight strains were selected for growth chamber experiments to determine their efficacy in controlling bottom rot caused by R. solani on lettuce. Although in the first experiment all antagonists colonized the rhizosphere of lettuce with CFU counts above 2 x 10(6) g(-1) of root fresh weight, only four isolates significantly reduced disease severity. In subsequent experiments involving these four antagonists, only Pseudomonas jessenii RU47 showed effective and consistent disease suppression. Plate counts and denaturing gradient gel electrophoresis (DGGE) fingerprints of Pseudomonas-specific gacA genes amplified from total community DNA confirmed that RU47 established as the dominant Pseudomonas population in the rhizosphere of inoculated lettuce plants. Furthermore, the DGGE fingerprint revealed that R. solani AG1-IB inoculation severely affected the bacterial and fungal community structure in the rhizosphere of lettuce and that these effects were much less pronounced in the presence of RU47. Although the exact mechanism of antagonistic activity and the ecology of RU47 remain to be further explored, our results suggest that RU47 is a promising agent to control bottom rot of lettuce.

Effect of bacterial antagonists on lettuce: active biocontrol of Rhizoctonia solani and negligible, short-term effects on nontarget microorganisms

The aim of this study was to assess the biocontrol efficacy against Rhizoctonia solani of three bacterial antagonists introduced into naturally Rhizoctonia-infested lettuce fields and to analyse their impact on the indigenous plant-associated bacteria and fungi. Lettuce seedlings were inoculated with bacterial suspensions of two endophytic strains, Serratia plymuthica 3Re4-18 and Pseudomonas trivialis 3Re2-7, and with the rhizobacterium Pseudomonas fluorescens L13-6-12 7 days before and 5 days after planting in the field. Similar statistically significant biocontrol effects were observed for all applied bacterial antagonists compared with the uninoculated control. Single-strand conformation polymorphism analysis of 16S rRNA gene or ITS1 fragments revealed a highly diverse rhizosphere and a less diverse endophytic microbial community for lettuce. Representatives of several bacterial (Alpha-, Beta- and Gammaproteobacteria, Firmicutes, Bacteriodetes), fungal (Ascomycetes, Basidiomycetes) and protist (Oomycetes) groups were present inside or on lettuce plants. Surprisingly, given that lettuce is a vegetable that is eaten raw, species of genera such as Flavobacterium, Burkholderia, Staphylococcus, Cladosporium and Aspergillus, which contain potentially human pathogenic strains, were identified. Analysis of the indigenous bacterial and endophytic fungal populations revealed only negligible, short-term effects resulting from the bacterial treatments, and that they were more influenced by field site, plant growth stage and microenvironment.