A Combination of Genomics, Transcriptomics, and Genetics Provides Insights into the Mineral Weathering Phenotype of Pseudomonas azotoformans F77

Acidification-based mineral weathering mechanism involves a glucose/methanol/choline oxidoreductase in Caballeronia mineralivorans PML1(12)

While mineral weathering (MWe) plays a key role in plant growth promotion and soil fertility, the molecular mechanisms and the genes used by bacteria to weather minerals remain poorly characterized. Acidification-based dissolution is considered the primary mechanism used by bacteria. This mechanism is historically associated with the conversion of glucose to protons and gluconic acid through the action of particular glucose dehydrogenases (GDH) dependent on the pyrroquinoline quinone (PQQ) cofactor. Recently, bacteria lacking the GDH-PQQ system have been shown to perform the same enzymatic conversion with a glucose/methanol/choline (GMC) FAD-dependent oxidoreductase. Determining whether this particular enzyme is specific or widespread is especially important in terms of ecology and evolution. Genome analysis of the effective MWe strain Caballeronia mineralivorans PML1(12) revealed the presence of both systems (i.e., GDH-PQQ and several GMC oxidoreductases). The combination of mutagenesis, functional assays, and geochemical analyses demonstrated the key role of one of these GMC oxidoreductases in the mineral weathering ability of strain PML1(12) and the importance of the carbon source metabolized. Mass spectrometry confirmed the conversion of glucose to gluconic acid. Phylogenetic analyses highlighted a good relatedness of this new GMC oxidoreductase with GMC oxidoreductases presenting a GDH activity in Burkholderia cepacia and Collimonas pratensis and conferring its mineral weathering ability to the last one. Together, our analyses expand the number of bacteria capable of weathering minerals using GMC oxidoreductases, showing that such enzymes are not restricted to Collimonas.

IMPORTANCE

This work deciphers the molecular and genetic bases used by strain PML1(12) of Caballeronia mineralivorans to weather minerals. Through bioinformatics analyses, we identified a total of four GMC-FAD oxidoreductases in the genome of strain PML1(12) and a putative PQQ-dependent glucose dehydrogenase. Through a combination of physiological and geochemical analyses, we revealed that one of them (i.e., GMC3) was the enzyme responsible for the acidification-based mineral weathering mechanism used by strain PML1(12). To date, a single representative of this enzyme family has been identified in the effective mineral-weathering bacterial strain Collimonas pratensis PMB3(1). Phylogenetic analyses revealed that this new system appeared conserved in the Collimonas genus. The new findings presented in this work demonstrate that GMC oxidoreductases can have an active role in other effective MWe bacteria outside of collimonads and that Caballeronia are capable of weathering minerals using this type of enzyme. Our findings offer relevant information for different fields of research, such as environmental genomics, microbiology, chemistry, evolutionary biology, and soil sciences.

Deletion of pyoverdine-producing pvdA increases cadmium stabilization by Pseudomonas umsongensis CR14 in cadmium-polluted solutions

In this study, the effects of the Cd-resistant and pyoverdine-producing strain Pseudomonas umsongensis CR14 on Cd stabilization and the mechanisms were investigated. Compared with the control, CR14 markedly reduced the Cd concentration in a Cd-containing solution. The genes pvdA, 4498, 4499, and pchF, which are associated with pyoverdine production, were identified in CR14. Subsequently, CR14 and the CR14ΔpvdA, CR14Δ4498, CR14Δ4499, and CR14ΔpchF mutants were characterized for their effects on Cd stabilization in solution. After 72 h of incubation, the CR14ΔpchF and CR14ΔpvdA mutants significantly decreased Cd concentrations compared with CR14. Notably, the CR14ΔpvdA mutant showed a greater impact on Cd stabilization than the other mutants. Compared with CR14, this mutant brought a lower Cd concentration in the solution, with higher levels of cell surface-adsorbed and intracellular accumulated Cd, content of lipopolysaccharide (LPS), expression of the LPS-producing genes lptD and lpxL, and cell surface particles. Additionally, compared with CR14, the CR14ΔpvdA mutant demonstrated increased interactions between the hydroxyl, carboxyl, amino, or ether groups and Cd. These results suggest that the CR14ΔpvdA mutant immobilized Cd by increasing LPS production and cell surface particle numbers, upregulating the expression of LPS-producing genes, and increasing cell surface adsorption and intracellular accumulation in Cd-polluted solutions.

The quorum sensing SinI/SinR-TraI/TraR systems promote Pb stabilization by Ensifer adhaerens S24 in the Pb-polluted aquatic environment

In this study, the Pb-resistant Ensifer adhaerens strain S24, which contains quorum sensing (QS) systems responsible for N-acyl homoserine lactone (AHL) production, was investigated for QS system-mediated Pb stabilization and the underlying mechanisms. Whole-genome sequence analysis revealed the QS SinI/R and TraI/R systems in strain S24. Subsequently, strains S24 and the S24∆sinI/R, S24∆traI/R, S24∆traI/R/sinR, and S24∆sinI/R-traI/R/sinR mutants were constructed and compared for QS SinI/SinR-TraI/TraR system-mediated Pb stabilization in the solution and the mechanisms involved. After 5 days of incubation, strain S24 significantly decreased the Pb concentration in the Pb-contaminated solution compared with the mutants. The S24∆sinI/R-traI/R/sinR mutant exhibited reduced Pb stabilization and AHL activity than the other mutants. The S24∆sinI/R-traI/R/sinR mutant had significantly greater Pb concentrations in the solution and lower cell surface-adsorbed and extracellular precipitated Pb (PbS) contents as well as lower expression of H2S-producing genes of metC and sseA than did strain S24. Furthermore, the S24∆sinI/R-traI/R/sinR mutant displayed reduced interactions between the hydroxyl, amino, carboxyl, and ether groups and Pb, compared with strain S24. These findings implied the vital role of the SinI/SinR-TraI/TraR systems in strain S24 for Pb stabilization through enhanced cell surface adsorption and extracellular precipitation in Pb-polluted aquatic environments.

A combination of physiology, metabolomics, and genetics reveals the two-component system ResS/ResR-mediated Fe and Al release from biotite by Pseudomonas pergaminensis F77

Understanding of the mechanisms on bacteria-regulated mineral dissolution functions is important for further insight into mineral-microbe interactions. The functions of the two-component system have been studied. However, the molecular mechanisms involved in bacterial two-component system-mediated mineral dissolution are poorly understood. Here, the two-component regulatory system ResS/ResR in the mineral-solubilizing bacterium Pseudomonas pergaminensis F77 was characterized for its involvement in biotite dissolution. Strain F77 and the F77ΔresS, F77ΔresR, and F77ΔresS/R mutants were constructed and compared for the ResS/ResR system-mediated Fe and Al release from biotite in the medium and the mechanisms involved. After 3 days of incubation, the F77ΔresS, F77ΔresR, and F77ΔresS/R mutants significantly decreased the Fe and Al concentrations in the medium compared with F77. The F77ΔresS/R mutant had a greater impact on Fe and Al release from biotite than did the F77ΔresS or F77ΔresR mutant. The F77∆resS/R mutant exhibited significantly reduced Fe and Al concentrations by 21-61 % between 12 h and 48 h of incubation compared with F77. Significantly increased pH values and decreased cell counts on the mineral surfaces were found in the presence of the F77∆resS/R mutant compared with those in the presence of F77 between 12 h and 48 h of incubation. Metabolomic analysis revealed that the extracellular metabolites associated with biotite dissolution were downregulated in the F77ΔresS/R mutant. These downregulated metabolites included GDP-fucose, 20-carboxyleukotriene B4, PGP (16:1(9Z)/16:0), 3',5'-cyclic AMP, and a variety of acidic metabolites involved in carbohydrate, amino acid, and lipid metabolisms, glycan biosynthesis, and cellular community function. Furthermore, the expression levels of the genes involved in the production of these metabolites were downregulated in the F77ΔresS/R mutant compared with those in F77. Our findings suggested that the ResS/ResR system in F77 contributed to mineral dissolution by mediating the production of mineral-solubilizing related extracellular metabolites and bacterial adsorption on mineral surface.

The quorum sensing SinI/R system contributes to cadmium immobilization in Ensifer adhaerens NER9 in the cadmium-contaminated solution

In this study, the cadmium (Cd)-tolerant Ensifer adhaerens strain NER9 with quorum sensing (QS) systems (responsible for N-acyl homoserine lactone (AHL) production) was characterized for QS system-mediated Cd immobilization and the underlying mechanisms involved. Whole-genome sequence analysis revealed that strain NER9 contains the QS SinI/R and TraI/R systems. Strains NER9 and the NER9∆sinI/R, NER9∆traI/R, and NER9∆sinI/R-traI/R mutants were constructed and compared for QS SinI/R and TraI/R system-mediated Cd immobilization in the solution and the mechanisms involved. After 24 h of incubation, strain NER9 significantly decreased the Cd concentration in the Cd-contaminated solution compared with the NER9∆sinI/R, NER9∆traI/R, and NER9∆sinI/R-traI/R mutants. The NER9∆sinI/R mutant had a greater impact on Cd immobilization and a lower impact on the activities of AHLs than did the NER9∆traI/R mutant. The NER9∆sinI/R mutant had significantly greater Cd concentrations and lower cell wall- and exopolysaccharide (EPS)-adsorbed Cd contents than did strain NER9. Furthermore, the NER9∆sinI/R mutant presented a decrease in the number of functional groups interacting with Cd, compared with strain NER9. These results suggested that the SinI/R system in strain NER9 contributed to Cd immobilization by mediating cell wall- and EPS-adsorption in Cd-containing solution.

Transcriptomic Analysis Reveals the Response of the Bacterium Priestia Aryabhattai SK1-7 to Interactions and Dissolution with Potassium Feldspar

Potassium feldspar (K₂O·Al₂O₃·6SiO₂) is considered to be the most important source of potash fertilizer. The use of microorganisms to dissolve potassium feldspar is a low-cost and environmentally friendly method. Priestia aryabhattai SK1-7 is a strain with a strong ability to dissolve potassium feldspar; it showed a faster pH drop and produced more acid in the medium with potassium feldspar as the insoluble potassium source than in the medium with K₂HPO₄ as the soluble potassium source. We speculated whether the cause of acid production was related to one or more stresses, such as mineral-induced generation of reactive oxygen species (ROS), the presence of aluminum in potassium feldspar, and cell membrane damage due to friction between SK1-7 and potassium feldspar, and analyzed it by transcriptome. The results revealed that the expression of the genes related to pyruvate metabolism, the two-component system, DNA repair, and oxidative stress pathways in strain SK1-7 was significantly upregulated in potassium feldspar medium. The subsequent validation experiments revealed that ROS were the stress faced by strain SK1-7 when interacting with potassium feldspar and led to a decrease in the total fatty acid content of SK1-7. In the face of ROS stress, strain SK1-7 upregulated the expression of the maeA-1 gene, allowing malic enzyme (ME2) to produce more pyruvate to be secreted outside the cell using malate as a substrate. Pyruvate is both a scavenger of external ROS and a gas pedal of dissolved potassium feldspar. IMPORTANCE Mineral-microbe interactions play important roles in the biogeochemical cycling of elements. Manipulating mineral-microbe interactions and optimizing the consequences of such interactions can be used to benefit society. It is necessary to explore the black hole of the mechanism of interaction between the two. In this study, it is revealed that P. aryabhattai SK1-7 faces mineral-induced ROS stress by upregulating a series of antioxidant genes as a passive defense, while overexpression of malic enzyme (ME2) secretes pyruvate to scavenge ROS as well as to increase feldspar dissolution, releasing K, Al, and Si into the medium. Our research provides a theoretical basis for improving the ability of microorganisms to weather minerals through genetic manipulation in the future.

Genome and transcriptome analysis of rock-dissolving Pseudomonas sp. NLX-4 strain

Microbial weathering processes can significantly promote soil properties and reduce rock-to-soil ratio. Some soil-inhabiting bacteria exhibit efficient rock-dissolution abilities by releasing organic acids and other chemical elements from the silicate rocks. However, our understanding of the molecular mechanisms involved during bacterial rock-dissolution is still limited. In this study, we performed silicate rock-dissolution experiments on a Pseudomonas sp. NLX-4 strain isolated from an over-exploited mining site. The results revealed that Pseudomonas sp. NLX-4 strain efficiently accelerates the dissolution of silicate rocks by secreting amino acids, exopolysaccharides, and organic acids. Through employing genome and transcriptome sequencing (RNA-seq), we identified the major regulatory genes. Specifically, 15 differentially expressed genes (DEGs) encoding for siderophore transport, EPS and amino acids synthesis, organic acids metabolism, and bacterial resistance to adverse environmental conditions were highly up-regulated in silicate rock cultures of NLX-4 strain. Our study reports a potential bacterial based approach for improving the ecological restoration of over-exploited rock mining sites.