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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., Instituto de Biotecnologia y Biologia Molecular

To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe&ndash, plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant&ndash, growth&ndash, promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.

Increasing food and energy demands have resulted in a considerable intensification of farming practices, whichbrought about severe consequences for agricultural soils during last decades. In order to maintain soil quality andhealth for the future, the development of more extensive and sustainable farming strategies is urgently needed.The soil and rhizosphere microbiome play an integral role in virtually all soil processes and are intimately linkedto plant performance. Various studies indicated that agricultural management practices affect soil microbiomes.We therefore hypothesized that this external impact is conveyed by the microbial communities to the currentcrops at the time of their establishment. We used twelve differently managed soils from three long-term fieldtrials established in 1978 (Therwil, Switzerland), 1992 (Bernburg, Germany), and 2006 (Thyrow, Germany) toanalyze the impact of various management strategies (crop rotation, fertilization, tillage) on soil and its associatedrhizosphere microbiomes under consideration of plant productivity, plant health, and the ability of the soils tosuppress soil-borne phytopathogens. The model plant lettuce (Lactuca sativa L.) was cultivated for ten weeks undergrowth-chamber conditions in these soils. High-throughput sequencing of bacterial 16S rRNA genes or fungalITS fragments, respectively, PCR- amplified from total community DNA of rhizosphere and soil samples showedsignificant differences in microbial community compositions between soils that originated from the different fieldsites and long-term farming practices. Moreover, differences depending on long-term agricultural managementin plant productivity and health as measured by RT-qPCR of stress-related plant genes were observed. Localizedanalysis of rhizosphere soil solution was performed using non-invasive sampling techniques with sorption filtersplaced onto the surface of soil-grown roots along the root observation windows with subsequent HPLC-MSprofiling. Amino acids, sugars and antifungal organic acids such as benzoic acid detected in the rhizosphere soilsolutions confirmed variations in concentrations depending on the site and management practice indicating differ-ent stress potentials of farming practices for plants. Agricultural management also affected soil suppressiveness tothe soil-borne model pathogen Rhizoctonia solani.Under controlled growth chamber conditions, we could show the legacy of long-term agricultural managementpractices on the establishment and performance of a subsequent plant generation and its associated rhizospheremicrobiome.