Soil salinization is negatively affecting soils globally, and the spread of this problem is of great concern due to the loss of functions and benefits offered by the soil resource. In the present study, we explored the diversity of halophilic and halotolerant microorganisms in the arable fraction of a sodic–saline soil without agricultural practices and two soils with agricultural practices (one sodic and one saline) near the geothermal area “Los Negritos” in Villamar, Michoacán state. This was achieved through their isolation and molecular identification, as well as the characterization of their potential for the production of metabolites and enzymes of biotechnological interest under saline conditions. Using culture-dependent techniques, 62 halotolerant and moderately halophilic strains belonging to the genera Bacillus, Brachybacterium, Gracilibacillus, Halobacillus, Halomonas, Kocuria, Marinococcus, Nesterenkonia, Oceanobacillus, Planococcus, Priestia, Salibactetium, Salimicrobium, Salinicoccus, Staphylococcus, Terribacillus, and Virgibacillus were isolated. The different strains synthesized hydrolytic enzymes under 15% (w/v) of salts, as well as metabolites with plant-growth-promoting (PGP) characteristics, such as indole acetic acid (IAA), under saline conditions. Furthermore, the production of biopolymers was detected among the strains; members of Bacillus, Halomonas, Staphylococcus, and Salinicoccus showed extracellular polymeric substance (EPS) production, and the strain Halomonas sp. LNSP3E3-1.2 produced polyhydroxybutyrate (PHB) under 10% (w/v) of total salts.

Hypersaline environments are those with salt concentrations 9–10 times higher (30–35% of NaCl) than sea water (3.5% of NaCl). At high concentrations of soluble salts, cytoplasm—mainly of bacteria and archaea—is exposed to high ionic strength and achieves osmotic equilibrium by maintaining a cytoplasmic salt concentration similar to that of the surrounding media. Halophilic enzymes are extremozymes produced by halophilic microorganisms; they have similar characteristics to regular enzymes but different properties, mainly structural. Among these properties is a high requirement of salt for biological functions. Furthermore, the discovery of enzymes capable of degrading biopolymers offer a new perspective in the treatment of residues from oil deposits, under typically high conditions of salt and temperature, while giving valuable information on heterotrophic processes in saline environments.

Four Gram-positive, aerobic, catalase- and oxidase-negative, rod-shaped, motile endophytic bacterial strains, designated NM3R9T, NE1TT3, NE2TL11 and NE2HP2T, were isolated from the inner tissues (leaf and stem) of Sphaeralcea angustifolia and roots of Prosopis laevigata. They were characterized using a polyphasic approach, which revealed that they represent two novel Microbacterium species. Phylogenetic analysis based on 16S rRNA gene sequencing showed that the species closest to NE2HP2T was Microbacterium arborescens DSM 20754T (99.6 %) and that closest to NM3R9T, NE2TL11 and NE2TT3 was Microbacterium oleivorans NBRC 103075T (97.4 %). The whole-genome average nucleotide identity value between strain NM3R9T and Microbacterium imperiale DSM 20530T was 90.91 %, and that between strain NE2HP2T and M. arborecens DSM 20754T was 91.03 %. Digital DNA–DNA hybridization showed values of less than 70 % with the type strains of related species. The polar lipids present in both strains included diphosphatidylglycerol, phosphatidylglycerol, glycolipids and unidentified lipids, whereas the major fatty acids included anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. Whole-cell sugars included mannose, rhamnose and galactose. Strains NM3R9T and NE2HP2T showed physiological characteristics different from those present in closely related Microbacterium species. According to the taxonomic analysis, both strains belong to two novel species. The name Microbacterium plantarum sp. nov. is proposed for strain NE2HP2T (=LMG 30875T=CCBAU 101117T) and Microbacterium thalli sp. nov. for strains NM3R9T (=LMG 30873T=CCBAU 101116T), NE1TT3 (=CCBAU 101114) and NE2TL11 (=CCBAU 101115).