Endophytic PGPR from Tomato Roots: Isolation, In Vitro Characterization and In Vivo Evaluation of Treated Tomatoes (Solanum lycopersicum L.).

Plant-growth-promoting rhizobacteria (PGPR) are soil bacteria colonizing the rhizosphere and the rhizoplane which have an effect on plant growth through multiple chemical compounds. Rhizobacteria with beneficial effects for plants could therefore be used to reduce the dependence on synthetic chemical fertilizers in conventional agriculture. Within this study, 67 endophytic fungi and 49 bacteria were isolated from root samples from 3 different commercial productions: an off-ground tomato production in a greenhouse, an organic production and a conventional production, both in a soil tunnel. Following morphological selection, 12 fungal and 33 bacterial isolates were genetically identified. Thirteen bacterial isolates belonging to nine potential PGPR species were then applied to tomato seedlings established in sterile substrate. The ability of these bacteria to produce indole acetic acid (IAA) and solubilize phosphate was also evaluated. They all were IAA producers and solubilized phosphate. The most interesting strains for growth promotion were found to be the isolates Pseudomonas palleroniana B10, Bacillus subtilis B25, Bacillus aryabhattai B29 and Pseudomonas fluorescens B17. The isolates P. fluorescens B17, B. aryabhattai B29, B. subtilis B18 and Pseudomonas moraviensis B6 also increased root growth. This study proposed a quick protocol for isolating and testing potential endophytic PGPR that should be characterized further for the direct and indirect mechanisms of growth promotion.

From Strain Characterization to Field Authorization: Highlights on Bacillus velezensis Strain B25 Beneficial Properties for Plants and Its Activities on Phytopathogenic Fungi.

Agriculture is in need of alternative products to conventional phytopharmaceutical treatments from chemical industry. One solution is the use of natural microorganisms with beneficial properties to ensure crop yields and plant health. In the present study, we focused our analyses on a bacterium referred as strain B25 and belonging to the species Bacillus velezensis (synonym B. amyloliquefaciens subsp. plantarum or B. methylotrophicus), a promising plant growth promoting rhizobacterium (PGPR) and an inhibitor of pathogenic fungi inducing crops diseases. B25 strain activities were investigated. Its genes are well preserved, with their majority being common with other Bacillus spp. strains and responsible for the biosynthesis of secondary metabolites known to be involved in biocontrol and plant growth-promoting activities. No antibiotic resistance genes were found in the B25 strain plasmid. In vitro and in planta tests were conducted to confirm these PGPR and biocontrol properties, showing its efficiency against 13 different pathogenic fungi through antibiosis mechanism. B25 strain also showed good capacities to quickly colonize its environment, to solubilize phosphorus and to produce siderophores and little amounts of auxin-type phytohormones (around 13,051 µg/mL after 32 h). All these findings combined to the fact that B25 demonstrated good properties for industrialization of the production and an environmental-friendly profile, led to its commercialization under market authorization since 2018 in several biostimulant preparations and opened its potential use as a biocontrol agent.

Draft Genome Sequences of 3 Strains of Apilactobacillus kunkeei Isolated from the Bee Gut Microbial Community.

Apilactobacillus kunkeei is a fructophilic lactic acid bacterium found in fructose-rich environments such as flowers, fruits, fermented food, honey, and honeydew, as well as in the guts of fructose-feeding insects. We report here the draft genome sequences of three Apilactobacillus kunkeei strains isolated from the gut microbial community of three honeybees.

Draft Genome Sequence of Bacillus licheniformis Strain UASWS1606, a Plant Biostimulant for Agriculture.

Bacillus licheniformis is a well-known industrial bacterium. New strains show interesting properties of biostimulants and biological control agents for agriculture. Here, we report the draft genome sequence, obtained with an Illumina MiniSeq system, of strain UASWS1606 of the bacterium Bacillus licheniformis, which is being developed as an agricultural biostimulant.

Draft Genome Sequences of Pseudomonas koreensis Strain UASWS1668, Bacillus megaterium Strain UASWS1667, and Paenibacillus sp. Strain UASWS1643, Considered Potential Plant Growth-Promoting Rhizobacteria.

Plant growth-promoting rhizobacteria (PGPR) include species in the genera Bacillus, Paenibacillus, and Pseudomonas We report here the draft genome sequences of the strains Pseudomonas koreensis UASWS1668 and Bacillus megaterium UASWS1667, isolated from a horse chestnut tree, and Paenibacillus sp. strain UASWS1643, isolated from a tomato stem. Auxin production and phosphate solubilization were biochemically confirmed.

Whole-Genome Sequence of Pseudomonas putida Strain 1312, a Potential Biostimulant Developed for Agriculture.

We report the draft genome sequence of strain 1312 of Pseudomonas putida, which could be interesting to develop as a biostimulant for agriculture and soil depollution treatments.

Whole-Genome Sequence of Pseudomonas aeruginosa Strain 4014, Isolated from Soil in France.

We report here the draft genome sequence of strain 4014 of Pseudomonas aeruginosa, a common human pathogen, isolated from soil in France. This sequence predicts resistance to multiple antibiotics, including vancomycin.

Whole-Genome Sequence of Pseudomonas sp. Strain 1239, Isolated from Soil in Western France.

We report here the draft genome sequence of Pseudomonas sp. strain 1239, a bacterium that is potentially usable as a biostimulant for agriculture or in depollution. Its genome encodes resistance to mercury, heavy metals, and several antibiotics. It is potentially able to produce marinocine, a broad-spectrum antibiotic.

Whole-Genome Sequences of Two Arthrobacter sp. Strains, 4041 and 4042, Potentially Usable in Agriculture and Environmental Depollution.

We report here the draft genome sequences of Arthrobacter sp. strains 4041 and 4042, both of which possibly belong to the diverse Arthrobacter agilis species and are potentially usable as plant biostimulants for agriculture and as depolluting bacteria for the environment.

Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents.

Anaerobic digestion is a common method for reducing the amount of sludge solids in used waters and enabling biogas production. The wet oxidation process (WOX) improves anaerobic digestion by converting carbon into methane through oxidation of organic compounds. WOX produces effluents rich in ammonia, which must be removed to maintain the activity of methanogens. Ammonia removal from WOX could be biologically operated by aerobic granules. To this end, granulation experiments were conducted in 2 bioreactors containing an activated sludge (AS). For the first time, the dynamics of the microbial community structure and the expression levels of 7 enzymes of the nitrogen metabolism in such active microbial communities were followed in regard to time by metagenomics and metatranscriptomics. It was shown that bacterial communities adapt to the wet oxidation effluent by increasing the expression level of the nitrogen metabolism, suggesting that these biological activities could be a less costly alternative for the elimination of ammonia, resulting in a reduction of the use of chemicals and energy consumption in sewage plants. This study reached a strong sequencing depth (from 4.4 to 7.6 Gb) and enlightened a yet unknown diversity of the microorganisms involved in the nitrogen pathway. Moreover, this approach revealed the abundance and expression levels of specialised enzymes involved in nitrification, denitrification, ammonification, dissimilatory nitrate reduction to ammonium (DNRA) and nitrogen fixation processes in AS.

Whole-Genome Sequences of 14 Strains of Bradyrhizobium canariense and 1 Strain of Bradyrhizobium japonicum Isolated from Lupinus spp. in Algeria.

We report here the whole-genome sequences of 14 strains of Bradyrhizobium canariense, isolated from root nodules of Lupinus microanthus and Lupinus angustifolius, and 1 strain of Bradyrhizobium japonicum isolated from root nodules from Lupinus angustifolius in Algeria. These sequences add to the known diversity of this agronomically important genus.

Metagenomes of Soil Samples from an Established Perennial Cropping System of Asparagus Treated with Biostimulants in Southern France.

We report here the metagenomes of soil samples from a perennial cropping system of asparagus that was treated with two biostimulants. Two treatments were compared to an untreated control. Control soil samples were taken at the beginning and at end of the experiment.

Deeper Insight in Beehives: Metagenomes of Royal Jelly, Pollen, and Honey from Lavender, Chestnut, and Fir Honeydew and Epiphytic and Endophytic Microbiota of Lavender and Rose Flowers.

Microbiota of beehive products are very little known. We report here for the first time six metagenomes of royal jelly, pollen, and different types of honey from wild and cultivated lavender, chestnut, and fir honeydew. Four metagenomes of epiphytic and endophytic microbiota of lavender and rose flowers are also reported.

Metagenome-Assembled Genome Sequence of Rhodopseudomonas palustris Strain ELI 1980, Commercialized as a Biostimulant.

We report here the draft genome sequence of strain ELI 1980 of Rhodopseudomonas palustris, commercialized as a biostimulant for agriculture. The genome was reconstructed from the metagenome of a commercial product containing this strain as its major component.

Metagenomes and Metatranscriptomes of Activated Sludge from a Sewage Plant, with or without Aerobic Granule Enrichment.

We report here the metagenomes and metatranscriptomes of activated sludge bioreactors, enriched or not enriched with aerobic granules, at an initial state and after 1 month of incubation. Data showed that the added granular biomass expressed higher levels of expression of genes involved in ammonia elimination.

Whole-Genome Sequence of Bradyrhizobium elkanii Strain UASWS1016, a Potential Symbiotic Biofertilizer for Agriculture.

Bradyrhizobium elkanii UASWS1016 has been isolated from a wet oxidation sewage plant in Italy. Fully equipped for ammonia assimilation, heavy metal resistances, and aromatic compounds degradation, it carries a large type IV secretion system, specific of plant-associated microbes. Deprived of toxins, it could be considered for agricultural and environmental uses.

Whole-Genome Sequence of Pseudomonas graminis Strain UASWS1507, a Potential Biological Control Agent and Biofertilizer Isolated in Switzerland.

We report here the whole-genome shotgun sequence of the strain UASWS1507 of the species Pseudomonas graminis, isolated in Switzerland from an apple tree. This is the first genome registered for this species, which is considered as a potential and valuable resource of biological control agents and biofertilizers for agriculture.

Whole-Genome Sequence of Pseudomonas xanthomarina Strain UASWS0955, a Potential Biological Agent for Agricultural and Environmental Uses.

We report here the whole-genome shotgun sequence of the strain UASWS0955 of the species Pseudomonas xanthomarina, isolated from sewage sludge. This genome was obtained with an Illumina MiniSeq and is the second genome registered for this species, which is considered as a promising resource for agriculture and bioremediation of contaminated soils.

Whole-Genome Sequence of Mesorhizobium hungaricum sp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses.

We report here the whole-genome shotgun sequences of the strain UASWS1009 of the species Mesorhizobium hungaricum sp. nov., which are different from any other known Mesorhizobium species. This is the first genome registered for this new species, which could be considered as a potential resource for agriculture and environmental uses.

Whole-Genome Sequence of Enteractinococcus helveticum sp. nov. Strain UASWS1574 Isolated from Industrial Used Waters.

We report here the whole-genome shotgun sequences of the strain UASWS1574 of the undescribed Enteractinococcus helveticum sp. nov., isolated from used water. This is the first genome registered for the whole genus.