Bacterial tolerance to host-exuded specialized metabolites structures the maize root microbiome.

Plants exude specialized metabolites from their roots, and these compounds are known to structure the root microbiome. However, the underlying mechanisms are poorly understood. We established a representative collection of maize root bacteria and tested their tolerance against benzoxazinoids (BXs), the dominant specialized and bioactive metabolites in the root exudates of maize plants.

A Novel Robust Screening Assay Identifies Strains as Reliable Antagonists of the Root-Knot Nematode .

Forty-four bacterial strains isolated from greenhouse soil and beetroots were tested for their antagonistic activity against the plant-parasitic root-knot nematode (RKN) , which causes significant yield losses in a number of important crops worldwide. Through a novel combination of in vitro and on planta screening assays, spp. 105 and 108 were identified as the most promising bacterial isolates.

Elucidation of the Bovine Intramammary Bacteriome and Resistome from healthy cows of Swiss dairy farms in the Canton Tessin.

Healthy, untreated cows of nine dairy herds from the Swiss Canton Tessin were analyzed three times within one year to identify the most abundant species of the intramammary bacteriome. Aseptically collected milk samples were cultured and bacteria identified using MALDI-TOF. Of 256 cows analyzed, 96% were bacteriologically positive and 80% of the 1,024 quarters were positive for at least one bacterial species.

Detection of Known and Novel Small Proteins in Using a Combination of Bottom-Up and Digest-Free Proteomics and Proteogenomics.

Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing them. Recent discoveries of their critical roles in many biological processes have led to an increased recognition of the importance of small proteins for basic research and as potential new drug targets. One example is CcoM, a 36 aa subunit of the -type oxidase that plays an essential role in adaptation to oxygen-limited conditions in , a model for the clinically relevant, opportunistic pathogen .

Genome sequence data of the strongly antagonistic yeast isolate APC 11.10 B as a foundation for analysing biocontrol mechanisms.

strain APC 11.10 B was isolated from apple bark in Switzerland and exhibited strong antagonistic activity against plant pathogenic fungi (e.g.

Uses One Type VI Secretion System (T6SS-1) as a Powerful Weapon against Notorious Plant Pathogens.

Paraburkholderia sabiae LMG24235 is a nitrogen-fixing betaproteobacterium originally isolated from a root nodule of Mimosa caesalpiniifolia in Brazil. We show here that this strain effectively kills strains from several bacterial families (, , ) which include important plant pathogens in a contact-dependent manner. assembly of the first complete genome of using long sequencing reads and subsequent annotation revealed two gene clusters predicted to encode type VI secretion systems (T6SS), which we named T6SS-1 and T6SS-3 according to previous classification methods (G.

Pantothenate Auxotrophy in a Naturally Occurring Biocontrol Yeast.

The genus is characterized by some of the smallest genomes among budding yeasts. These fungi are primarily found on plant surfaces and in fermented products and represent promising biocontrol agents against notorious fungal plant pathogens. In this work, we identify pantothenate auxotrophy of a Hanseniaspora meyeri isolate that shows strong antagonism against the plant pathogen Fusarium oxysporum.

Unraveling the small proteome of the plant symbiont by ribosome profiling and proteogenomics.

The soil-dwelling plant symbiont is a major model organism of Alphaproteobacteria. Despite numerous detailed OMICS studies, information about small open reading frame (sORF)-encoded proteins (SEPs) is largely missing, because sORFs are poorly annotated and SEPs are hard to detect experimentally. However, given that SEPs can fulfill important functions, identification of translated sORFs is critical for analyzing their roles in bacterial physiology.

Identification of Potential Antimicrobial Targets of Pseudomonas aeruginosa Biofilms through a Novel Screening Approach.

Pseudomonas aeruginosa is an opportunistic pathogen of considerable medical importance, owing to its pronounced antibiotic tolerance and association with cystic fibrosis and other life-threatening diseases. The aim of this study was to highlight the genes responsible for P. aeruginosa biofilm tolerance to antibiotics and thereby identify potential new targets for the development of drugs against biofilm-related infections.

A novel function of the key nitrogen-fixation activator NifA in beta-rhizobia: Repression of bacterial auxin synthesis during symbiosis.

Rhizobia fix nitrogen within root nodules of host plants where nitrogenase expression is strictly controlled by its key regulator NifA. We recently discovered that in nodules infected by the beta-rhizobial strain STM815, NifA controls expression of two bacterial auxin synthesis genes. Both the and transcripts, as well as the metabolites indole-acetamide (IAM) and indole-3-acetic acid (IAA) showed increased abundance in nodules occupied by a mutant compared to wild-type nodules.

Adaptation and Resistance: How Copes with the Bisphenol A Substitute Bisphenol F.

Bisphenols are used in the process of polymerization of polycarbonate plastics and epoxy resins. Bisphenols can easily migrate out of plastic products and enter the gastrointestinal system. By increasing colonic inflammation in mice, disrupting the intestinal bacterial community structure and altering the microbial membrane transport system in zebrafish, bisphenols seem to interfere with the gut microbiome.

Salt- and Osmo-Responsive Sensor Histidine Kinases Activate the General Stress Response to Initiate Functional Symbiosis.

The general stress response (GSR) enables bacteria to sense and overcome a variety of environmental stresses. In alphaproteobacteria, stress-perceiving histidine kinases of the HWE and HisKA_2 families trigger a signaling cascade that leads to phosphorylation of the response regulator PhyR and, consequently, to activation of the GSR σ factor σ. In the nitrogen-fixing bacterium , PhyR and σ are crucial for tolerance against a variety of stresses under free-living conditions and also for efficient infection of its symbiotic host soybean.

Genome sequence data of the antagonistic soil-borne yeast (SHA 17.2).

strain SHA 17.2, isolated from a Swiss soil sample, exhibited strong antagonistic activity against several plant pathogenic fungi and was highly competitive against other yeasts in soil As a basis for identifying the mechanisms underlying its strong antagonistic activity, we have sequenced the genome of (SHA 17.2) by long- and short read sequencing, assembled them into seven contigs/chromosomes and a mitogenome (total genome size 11.

A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.

Small proteins of up to ∼50 amino acids are an abundant class of biomolecules across all domains of life. Yet due to the challenges inherent in their size, they are often missed in genome annotations, and are difficult to identify and characterize using standard experimental approaches. Consequently, we still know few small proteins even in well-studied prokaryotic model organisms.

Indicative bacterial communities and taxa of disease-suppressing and growth-promoting composts and their associations to the rhizoplane.

Compost applications vary in their plant growth promotion and plant disease suppression, likely due to differences in physico-chemical and biological parameters. Our hypothesis was that bacteria are important for plant growth promotion and disease suppression of composts and, therefore, composts having these traits would contain similar sets of indicative bacterial taxa. Seventeen composts prepared from five different commercial providers and different starting materials were classified accordingly with bioassays using cress plants and the pathogen Pythium ultimum.

Differential Expression of Type VI Secretion Systems (T6SS) Suggests a Role of T6SS-b in Early Symbiotic Interaction.

STM815, a rhizobial strain of the family, is able to nodulate a broad range of legumes including the agriculturally important (common bean). harbors two type VI Secretion Systems (T6SS-b and T6SS-3) in its genome that contribute to its high interbacterial competitiveness and in infecting the roots of several legumes. In this study, we show that T6SS-b is found in the genomes of several soil-dwelling plant symbionts and that its expression is induced by the presence of citrate and is higher at 20/28°C compared to 37°C.

Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach.

Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy and reliability of genome annotations, particularly for small open reading frames (sORFs), can be significantly improved by integrating protein evidence from experimental approaches. Here we present a highly optimized and flexible bioinformatics workflow for bacterial proteogenomics covering all steps from (i) generation of protein databases, (ii) database searches and (iii) peptide-to-genome mapping to (iv) visualization of results.

Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome.

Background: The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities.

Author Correction: Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode.

A Correction to this paper has been published: https://doi.org/10.1038/s41597-020-00747-0.

An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1.

Pseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and biofilm-associated antibiotic resistance. Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome, identify unique and conserved genes by comparative genomics with the PAO1 reference strain and genes missed within existing assemblies by proteogenomics.

Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode.

Root-knot nematodes (genus Meloidogyne) are plant parasites causing huge economic loss in the agricultural industry and affecting severely numerous developing countries. Control methods against these plant pests are sparse, the preferred one being the deployment of plant cultivars bearing resistance genes against Meloidogyne species. However, M.

Harnessing the Microbiomes of Suppressive Composts for Plant Protection: From Metagenomes to Beneficial Microorganisms and Reliable Diagnostics.

Soil-borne diseases cause significant yield losses worldwide, are difficult to treat and often only limited options for disease management are available. It has long been known that compost amendments, which are routinely applied in organic and integrated farming as a part of good agricultural practice to close nutrient cycles, can convey a protective effect. Yet, the targeted use of composts against soil-borne diseases is hampered by the unpredictability of the efficacy.

Optimized Proteomics Workflow for the Detection of Small Proteins.

Small open reading frame encoded proteins (SEPs) gained increasing interest during the last few years because of their broad range of important functions in both prokaryotes and eukaryotes. In bacteria, signaling, virulence, and regulation of enzyme activities have been associated with SEPs. Nonetheless, the number of SEPs detected in large-scale proteome studies is often low as classical methods are biased toward the identification of larger proteins.