In disease-suppressive soils, microbiota protect plants from root infections. Bacterial members of this microbiota have been shown to produce specific molecules that mediate this phenotype. To date, however, studies have focused on individual suppressive soils and the degree of natural variability of soil suppressiveness remains unclear. Here, we screened a large collection of field soils for suppressiveness to Fusarium culmorum using wheat ( Triticum aestivum ) as a model host plant. A high variation of disease suppressiveness was observed, with 14% showing a clear suppressive phenotype. The microbiological basis of suppressiveness to F. culmorum was confirmed by gamma sterilization and soil transplantation. Amplicon sequencing revealed diverse bacterial taxonomic compositions and no specific taxa were found exclusively enriched in all suppressive soils. Nonetheless, co-occurrence network analysis revealed that two suppressive soils shared an overrepresented bacterial guild dominated by various Acidobacteria. In addition, our study revealed that volatile emission may contribute to suppression, but not for all suppressive soils. Our study raises new questions regarding the possible mechanistic variability of disease-suppressive phenotypes across physico-chemically different soils. Accordingly, we anticipate that larger-scale soil profiling, along with functional studies, will enable a deeper understanding of disease-suppressive microbiomes.

The gene encoding factor C (facC), an extracellular signal protein involved in cellular differentiation, was cloned from Streptomyces griseus 45H, and the complete nucleotide sequence was determined. The deduced amino acid sequence was confirmed by HPLC/electrospray ionization-mass spectrometry analysis. The full-length protein consists of 324 amino acids and has a predicted molecular mass of 34 523 Da. The mature extracellular 286 amino acid protein (31 038 Da) is probably produced by cleaving off a 38 amino acid secretion signal sequence. Southern hybridization detected facC in several other Streptomyces strains, but database searches failed to identify a protein with significant homology to factor C. Expression of facC from a low-copynumber vector in S. griseus 52-1 resulted in a phenotypic effect similar to that given by exogenously added factor C protein.

In the era that huge numbers of microbial genomes are being released in the databases, it becomes increasingly important to rapidly mine genes as well as predict the regulatory networks that control their expression. To this end, we have developed an improved and online version of the PREDetector software aimed at identifying putative transcription factor-binding sites (TFBS) in bacterial genomes.The original philosophy of PREDetector 1.0 is maintained, i.e. to allow users to freely fix the DNA-motif screening parameters, and to provide a statistical means to estimate the reliability of the prediction output. This new version offers an interactive table as well as graphics to dynamically alter the main screening parameters with automatic update of the list of identified putative TFBS. PREDetector 2.0 also has the following additional options: (i) access to genome sequences from different databases, (ii) access to weight matrices from public repositories, (iii) visualization of the predicted hits in their genomic context, (iv) grouping of hits identified in the same upstream region, (v) possibility to store the performed jobs, and (vi) automated export of the results in various formats. PREDetector 2.0 is available at

22The bacterial cell wall maintains cell shape and protects against bursting by the 23 turgor. A major constituent of the cell wall is peptidoglycan (PG), which is 24 continuously modified to allow cell growth and differentiation through the concerted 25 activity of biosynthetic and hydrolytic enzymes. Streptomycetes are Gram-positive 26 bacteria with a complex multicellular life style alternating between mycelial growth 27 and the formation of reproductive spores. This involves cell-wall remodeling at apical 28 sites of the hyphae during cell elongation and autolytic degradation of the vegetative 29 mycelium during the onset of development and antibiotic production. Here, we show 30 that there are distinct differences in the cross-linking and maturation of the PG 31 between exponentially growing vegetative hyphae and the aerial hyphae that 32 undergo sporulation. LC-MS/MS analysis identified over 80 different muropeptides, 33 revealing that major PG hydrolysis takes place over the course of mycelial growth. 34 Half of the dimers lack one of the disaccharide units in transition-phase cells, most 35 likely due to autolytic activity. De-acetylation of MurNAc to MurN was particularly 36 pronounced in spores, suggesting that MurN plays a role in spore development. 37 Taken together, our work highlights dynamic and growth phase-dependent 38 construction and remodeling of PG in Streptomyces. 39 40 IMPORTANCE 41 Streptomycetes are bacteria with a complex lifestyle, which are model organisms for 42 bacterial multicellularity. From a single spore a large multigenomic, multicellular 43 mycelium is formed, which differentiates to form spores. Programmed cell death is an 44 important event during the onset of morphological differentiation. In this work we 45 3 provide new insights into the changes in the peptidoglycan architecture over time, 46 highlighting changes over the course of development and between growing mycelia 47 56 Peptidoglycan (PG) is a major component of the bacterial cell wall. It forms a physical 57boundary that maintains cell shape, protects cellular integrity against the osmotic 58 pressure and acts as a scaffold for large protein assemblies and exopolymers (66). 59The cell wall is a highly dynamic macromolecule that is continuously constructed and 60 deconstructed to allow for cell growth and to meet environmental demands (27). PG 61 is built up of glycan strands of alternating N-acetylglucosamine (GlcNAc) and N-62 acetylmuramic acid (MurNAc) residues that are connected by short peptides to form 63 a mesh-like polymer. PG biosynthesis starts with the synthesis of PG precursors by 64 the Mur enzymes in the cytoplasm and cell membrane, resulting in lipid II precursor, 65 undecaprenylpyrophosphoryl-MurNAc(GlcNAc)-pentapeptide. Lipid II is transported 66 across the cell membrane by MurJ and/or FtsW/SEDS proteins and the PG is 67 polymerized and incorporated into the existing cell wall by the activities of 68 glycosyltransferases and transpeptidases (9, 30, 57). 69 The Gram-positive model bacterium Bacillus ...

Horizontal gene transfer in bacteria is widely believed to occur via three main mechanisms: conjugation, transduction and transformation. These mechanisms facilitate the passage of DNA across the protective cell wall using sophisticated machinery. We present here a new mechanism of DNA uptake that is independent of canonical DNA uptake machineries and is used by bacteria that live without a cell wall. We show that the cell wall-deficient bacteria engulf extracellular material, whereby intracellular vesicles are formed, and DNA is internalized. This mechanism is not specific to DNA, and allows uptake of other macromolecules and even 125 nm lipid nanoparticles (LNPs). Uptake was prevented by molecules known to inhibit eukaryotic endocytosis, suggesting this to be an energy-dependent process. Given that cell wall-deficient bacteria are considered a model for early life forms, our work provides a possible mechanism for primordial cells to acquire new genetic material or food before invention of the bacterial cell wall.