Rhizobium alamii improves water stress tolerance in a non-legume.

With the increasing demand for alternative solutions to replace or optimize the use of synthetic fertilizers and pesticides, the inoculation of bacteria that can contribute to the growth and health of plants (PGPR) is essential. The properties classically sought in PGPR are the production of phytohormones and other growth-promoting molecules, and more rarely the production of exopolysaccharides. We compared the effect of two strains of exopolysaccharide-producing Rhizobium alamii on rapeseed grown in a calcareous silty-clay soil under water stress conditions or not. The effect of factors 'water stress' and 'inoculation' were evaluated on plant growth parameters and the diversity of microbiota associated to root and root-adhering soil compartments. Water stress resulted in a significant decrease in leaf area, shoot biomass and RAS/RT ratio (root-adhering soil/root tissues), as well as overall beta-diversity. Inoculation with R. alamii YAS34 and GBV030 under water-stress conditions produced the same shoot dry biomass compared to uninoculated treatment in absence of water stress, and both strains increased shoot biomass under water-stressed conditions (+7% and +15%, respectively). Only R. alamii GBV030 significantly increased shoot biomass under unstressed or water-stressed conditions compared to the non-inoculated control (+39% and +15%, respectively). Alpha-diversity of the root-associated microbiota after inoculation with R. alamii YAS34 was significantly reduced. Beta-diversity was significantly modified after inoculation with R. alamii GBV030 under unstressed conditions. LEfSe analysis identified characteristic bacterial families, Flavobacteriaceae and Comamonadaceae, in the RT and RAS compartments for the treatment inoculated by R. alamii GBV030 under unstressed conditions, as well as Halomonadaceae (RT) and several species belonging to Actinomycetales (RAS). We showed that R. alamii GBV030 had a PGPR effect on rapeseed growth, increasing its tolerance to water stress, probably involving its capacity to produce exopolysaccharides, and other plant growth-promoting (PGP) traits.

Complete Genome Sequences of Four Microbacterium Strains Isolated from Metal- and Radionuclide-Rich Soils.

Here, we present the genome sequences of four Microbacterium strains, which were isolated at different locations in Europe from metal- or radionuclide-rich soils. High-quality complete genome sequences were obtained with PacBio and Illumina data sets with an original two-step procedure.

Proteomics data for characterizing Microbacterium oleivorans A9, an uranium-tolerant actinobacterium isolated near the Chernobyl nuclear power plant.

Microbacterium oleivorans A9 cells were exposed or not to 10 µM uranyl nitrate as resting cells in sodium chloride solution. Bacteria exposed to U(VI) and controls were harvested after 0.5, 4, and 24 h of toxicant exposure. Bacteria were subjected to high-throughput proteomics analysis using a Q-Exactive HF high resolution tandem mass spectrometer incorporating an ultra-high-field orbitrap analyzer. MS/MS spectra were assigned with a protein sequence database derived from a draft genome obtained by Illumina sequencing and systematic six-reading frame translation of all the contigs. Proteins identified in bacteria exposed to U(VI) and controls at the three time points allow defining the proteome dynamics upon uranium stress. The data reported here are related to a published study regarding the proteome dynamics of M. oleivorans A9 upon uranium stress by Gallois et al. (in press) entitled "Proteogenomic insights into uranium tolerance of a Chernobyl׳s Microbacterium bacterial isolate". The data accompanying the manuscript describing the database searches and comparative analysis have been deposited to the ProteomeXchange with identifier PXD005794.

Two New Secreted Proteases Generate a Casein-Derived Antimicrobial Peptide in Bacillus cereus Food Born Isolate Leading to Bacterial Competition in Milk.

Milk and dairy products harbor a wide variety of bacterial species that compete for both limited resources and space. Under these competitive conditions, bacteria develop specialized mechanisms to protect themselves during niche colonization and nutrient acquisition processes. The bacterial antagonism mechanisms include the production of antimicrobial agents or molecules that facilitate competitor dispersal. In the present work, a bacterial strain designated RC6 was isolated from Ricotta and identified as Bacillus cereus. It generates antimicrobial peptide (AMP) when grown in the presence of casein. The AMP was active against several species of Bacillus and Listeria monocytogenes. MALDI-TOF analysis of the RP-HPLC purified fractions and amino acid sequencing revealed a molecular mass of 751 Da comprised of a 6-residue sequence, YPVEPF. BLAST analysis showed that the AMP corresponds to the fractions 114-119 of bovine ß-casein and represents the product of a specific proteolysis. Analysis of the purified proteolytic fractions from the B. cereus RC6 culture supernatant indicated that the presence of at least two different endoproteases is crucial for the generation of the AMP. Indeed, we were able to identify two new candidate endoproteases by means of genome sequencing and functional assignment using a 3D structural model and molecular docking of misannotated hypothetical proteins. In this light, the capacity of B. cereus RC6 to generate antimicrobial peptides from casein, through the production of extracellular enzymes, presents a new model of antagonistic competition leading to niche colonization. Hence, as a dairy product contaminant, this strategy may enable proteolytic B. cereus RC6 niche specialization in milk matrices.

Proteogenomic insights into uranium tolerance of a Chernobyl's Microbacterium bacterial isolate.

Microbacterium oleivorans A9 is a uranium-tolerant actinobacteria isolated from the trench T22 located near the Chernobyl nuclear power plant. This site is contaminated with different radionuclides including uranium. To observe the molecular changes at the proteome level occurring in this strain upon uranyl exposure and understand molecular mechanisms explaining its uranium tolerance, we established its draft genome and used this raw information to perform an in-depth proteogenomics study. High-throughput proteomics were performed on cells exposed or not to 10µM uranyl nitrate sampled at three previously identified phases of uranyl tolerance. We experimentally detected and annotated 1532 proteins and highlighted a total of 591 proteins for which abundances were significantly differing between conditions. Notably, proteins involved in phosphate and iron metabolisms show high dynamics. A large ratio of proteins more abundant upon uranyl stress, are distant from functionally-annotated known proteins, highlighting the lack of fundamental knowledge regarding numerous key molecular players from soil bacteria. BIOLOGICAL SIGNIFICANCE: Microbacterium oleivorans A9 is an interesting environmental model to understand biological processes engaged in tolerance to radionuclides. Using an innovative proteogenomics approach, we explored its molecular mechanisms involved in uranium tolerance. We sequenced its genome, interpreted high-throughput proteomic data against a six-reading frame ORF database deduced from the draft genome, annotated the identified proteins and compared protein abundances from cells exposed or not to uranyl stress after a cascade search. These data show that a complex cellular response to uranium occurs in Microbacterium oleivorans A9, where one third of the experimental proteome is modified. In particular, the uranyl stress perturbed the phosphate and iron metabolic pathways. Furthermore, several transporters have been identified to be specifically associated to uranyl stress, paving the way to the development of biotechnological tools for uranium decontamination.

Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide.

The sulfate reducing bacterium Desulfovibrio desulfuricans inhabits both the human gut and external environments. It can reduce nitrate and nitrite as alternative electron acceptors to sulfate to support growth. Like other sulphate reducing bacteria, it can also protect itself against nitrosative stress caused by NO generated when nitrite accumulates. By combining in vitro experiments with bioinformatic and RNA-seq data, metabolic responses to nitrate or NO and how nitrate and nitrite reduction are coordinated with the response to nitrosative stress were revealed. Although nitrate and nitrite reduction are tightly regulated in response to substrate availability, the global responses to nitrate or NO were largely regulated independently. Multiple NADH dehydrogenases, transcription factors of unknown function and genes for iron uptake were differentially expressed in response to electron acceptor availability or nitrosative stress. Amongst many fascinating problems for future research, the data revealed a YtfE orthologue, Ddes_1165, that is implicated in the repair of nitrosative damage. The combined data suggest that three transcription factors coordinate this regulation in which NrfS-NrfR coordinates nitrate and nitrite reduction to minimize toxicity due to nitrite accumulation, HcpR1 serves a global role in regulating the response to nitrate, and HcpR2 regulates the response to nitrosative stress.

Draft Genome Sequence of Microbacterium oleivorans Strain A9, a Bacterium Isolated from Chernobyl Radionuclide-Contaminated Soil.

Here, we present the draft genome sequence of Microbacterium oleivorans strain A9, a uranium-tolerant actinobacterium which has been isolated from radionuclide-contaminated soil from the Chernobyl exclusion zone. It is composed of 22 contigs totaling 2,954,335 bp and contains 2,813 coding DNA sequences, one cluster of rRNA genes, and 45 tRNA genes.