Carbonate-dissolving bacteria from 'miliolite', a bioclastic limestone, from Gopnath, Gujarat, Western India

Reclamation of Calcareous Sodic Soil by Brevibacterium sp. SOTI06, a Calcite Dissolving Bacteria

Soil degradation due to sodicity is a major constraint to agricultural development in arid and semi-arid regions. The accumulation of exchangeable Na+ ions affects soil physicochemical properties, which subsequently increases pH, thus reducing crop yield and nutrient availability. Several practices have been followed for revitalizing salt-affected soils, such as the addition of inorganic or organic amendments. Since most of these soils are calcareous (CaCO3) in nature, they can serve as a cationic source to release Ca2+ to replace the Na+ from the clay-complex. Though CaCO3 is poorly soluble, dissolution can be easily achieved by calcite dissolving bacteria. The present study aimed to evaluate the efficiency of Brevibacterium sp. SOTI06, in reclaiming calcareous sodic soil, along with organic and inorganic inputs through a soil incubation study. The reduction in pH, Na+, ESP (Exchangeable sodium percent), and free CaCO3 during the incubation period confirms the efficiency of amendments. The pH was drastically reduced from 9.10 to 8.20 in gypsum-applied soils. The combined effect of bacterium and press mud reduced higher rates of CaCO3 in soil (16.6 to 14.5%), with a rise of Ca2+ ions (23.5 to 28.7 meq 100 g soil-1). The mean calcite dissolution was higher in bioinoculant and gypsum-applied soils (9.04%). The SEM (Scanning Electron Microscopy) images confirmed the colonization and calcite dissolution potential of Brevibacterium sp. SOTI06 by pit formation in calcite stones. Hence, this study revealed that the combined application of bioinoculants with organic and inorganic amendments can effectively reclaim calcareous sodic soils.

Functional Characterization of Core and Unique Calcite-Dissolving Bacteria Communities from Peanut Fields

Calcium deficiency is a leading cause of reduced peanut (Arachis hypogaea) seed quality and has been linked to increased disease susceptibility, specifically to soilborne fungal pathogens. Sufficient calcium at flowering time is critical to ensure proper pod development. Calcite-dissolving bacteria (CDB) isolated from farming fields can dissolve calcite (CaCO3) on plates and increase soluble calcium levels in soil. However, the phylogenetic diversity and geographic distribution of CDB is unclear. Here, we surveyed soil samples from 15 peanut-producing fields in three regions in southern Georgia, representing distinct soil compositions. We isolated CDB through differentiating media and identified 52 CDB strains. CDB abundance was not associated with any of the soil characteristics we evaluated. Three core genera, represented by 43 strains, were found in all three regions. Paenibacillus was the most common CDB found in all regions, making up 30 of the 52 identified strains. Six genera, represented by eight strains, are unique to one region. Members of the core and unique communities showed comparable solubilization indexes on plates. We conclude that a diversified phylogenetic population of CDB is present in Georgia peanut fields. Despite the phylogenetic diversity, as a population, they exhibit comparable functions in solubilizing calcite on plates.

A Multi-Analytical Approach to Infer Mineral–Microbial Interactions Applied to Petroglyph Sites in the Negev Desert of Israel

Petroglyph sites exist all over the world. They are one of the earliest forms of mankind’s expression and a precursor to art. Despite their outstanding value, comprehensive research on conservation and preservation of rock art is minimal, especially as related to biodeterioration. For this reason, the main objective of this study was to explore the factors involved in the degradation of petroglyph sites in the Negev desert of Israel, with a focus on biodegradation processes. Through the use of culture-independent microbiological methods (metagenomics), we characterized the microbiomes of the samples, finding they were dominated by bacterial communities, in particular taxa of Actinobacteria and Cyanobacteria, with resistance to radiation and desiccation. By means of XRF and Raman spectroscopies, we defined the composition of the stone (calcite and quartz) and the dark crust (clay minerals with Mn and Fe oxides), unveiling the presence of carotenoids, indicative of biological colonization. Optical microscopy and SEM–EDX analyses on thin sections highlighted patterns of weathering, possibly connected to the presence of biodeteriorative microorganisms that leach the calcareous matrix from the bedrock and mobilize metal cations from the black varnish for metabolic processes, slowly weathering it.

A new carbonic anhydrase identified in the Gram-negative bacterium (Chromohalobacter sp.) and the interaction of anions with the enzyme

In this study, the characterization and inhibition characteristic of α-class carbonic anhydrase from Chromohalobacter (ChCA) was documented for the first time. The carbonic anhydrase enzyme had 47.77% yield and 54.45-fold purity. The specific activity of the enzyme was determined as 318.52 U/mg proteins. Alternative substrate (4-nitrophenyl trifluoroacetate, 4-nitrophenyl phosphate, 4-nitrophenyl sulphate and 4-nitrophenyl acetate) were tested for the enzyme. K_M and V_max values for 4-nitrophenyl acetate were 4.57 mM and 4.29 EU/mL and for 4-nitrophenyl trifluoroacetate were 2.39 mM and 2.41 EU/mL. The anions, Cl^-, NO₂^-, NO₃^-, Br^-, ClO₃^-, ClO₄^-, I^-, CO₃^2- and SO₄^2-, inhibited the ChCA hydratase activity. Among nine anions, the strongest inhibitor activities were obtained with micro molar concentrations of NO₂^-, NO₃^-, Br^-, I^-, CO₃^2- (K_I values of 160-255 μM). Other four anions tested (Cl^-, ClO₃^-, ClO₄^- and SO₄^2-) showed moderate inhibitory activities (K_I values of 680-813.5 μM). The results obtained demonstrate that the anions we tested inhibit the Chromohalobacter CA (ChCA) enzyme as in other α-CAs in mammals; however, the susceptibility of ChCA resulted from anions differed significantly from that of other organism CAs.

Calcite Dissolution by Brevibacterium sp. SOTI06: A Futuristic Approach for the Reclamation of Calcareous Sodic Soils

Assessing the ability of soil microorganisms to dissolute poorly soluble native calcite to supply Ca²⁺ is a new area to be explored in reclaiming sodic soils by supplying adequate Ca²⁺ and reducing the recurrent sodicity. Hence, the present study aimed to isolate a calcite dissolving bacteria (CDB) from calcareous sodic soils and to understand the mechanism of calcite dissolution. Of the 33 CDB isolates recovered from the calcareous sodic soils of Tamil Nadu (Coimbatore, Ramnad, and Trichy), 11 isolates were screened for calcite dissolution based on titratable acidity. 16S rRNA gene sequence analysis of the three best isolates viz., SORI09, SOTI05, and SOTI06 revealed 99% similarity to Bacillus aryabhattai, 100% to B. megaterium, and 93% to Brevibacterium sp., respectively. Among them, Brevibacterium sp. SOTI06 released more Ca²⁺ (3.6 g.l^-1) by dissolving 18.6% of the native calcite. The spectral data of FTIR also showed reduction in the intensity of calcite (55.36-41.27) by the isolate at a wave number of 1636 cm^-1 which confirmed the dissolution. Besides producing organic acids (gluconic acid and acetic acid), Brevibacterium sp. SOTI06 also produced siderophore (91.6%) and extracellular polysaccharides (EPS, 13.3 μg. ml^-1) which might have enhanced the calcite dissolution.