The “Infernaccio” Gorges: Microbial Diversity of Black Deposits and Isolation of Manganese-Solubilizing Bacteria

Isolation and characterization of cyanobacteria and microalgae from a sulfuric pond: Plant growth-promoting and soil bioconsolidation activities

Sustainable alternatives are essential to improving agriculture production to meet the growing world's critical demands. Cyanobacteria and microalgae are considered renewable resources with a wide range of potential uses in the agricultural sector. We aimed to isolate cyanobacteria and microalgae from the mud of a carbon dioxide-rich sulfur pond and to investigate their plant growth-promoting (PGP) and soil bio-consolidating ability. Mud samples were subjected to DNA extraction and 16S rRNA gene sequencing to characterize the prokaryotic community. Phototrophic culturable microbiota was isolated and evaluated for different PGP properties. The most relevant isolates were combined in a consortium and used for in vitro bioconsolidation activity. In a greenhouse experiment, the isolates were evaluated for their ability to promote salinity stress tolerance in sunflower plants. Metabarcoding results showed that most Amplicon Sequence Variants (ASV) were associated with Actinobacteriota (35%), Proteobacteria (19%), and Acidobacteriota (11%) at the phylum level and Unknown (32%) and uncultured (31%) lineages at the genus level. The culture-dependent method yielded eight isolates associated with cyanobacteria and microalgae genera. The isolates obtained showed interesting PGP activities. Isolates C1, C2, and M1 were selected based on phosphate solubilization (85.6 µg PO4 3- mL-1 on average), indoles (C1 and M1 0.54 µg mL-1 IAA equivalents on average), and ACC deaminase activity (C2 and M1 6.00 µmol α-KB mg proteins-1 h-1). The consortium efficiently consolidated sand particles in the presence of calcium carbonate by forming biomineralized aggregates. In planta results showed positive effects of the consortium on Helianthus annuus L., plant growth under normal conditions and salt stress. The positive effects on soil and plants indicated their effectiveness as bioconsolidants and biostimulant agents. Our findings highlight the interesting potential of cyanobacteria and microalgae applications in sustainable agriculture.

Characterizing Biogenic MnOx Produced by Pseudomonas putida MnB1 and Its Catalytic Activity towards Water Oxidation

Mn-oxidizing microorganisms oxidize environmental Mn(II), producing Mn(IV) oxides. Pseudomonas putida MnB1 is a widely studied organism for the oxidation of manganese(II) to manganese(IV) by a multi-copper oxidase. The biogenic manganese oxides (BMOs) produced by MnB1 and similar organisms have unique properties compared to non-biological manganese oxides. Along with an amorphous, poorly crystalline structure, previous studies have indicated that BMOs have high surface areas and high reactivities. It is also known that abiotic Mn oxides promote oxidation of organics and have been studied for their water oxidation catalytic function. MnB1 was grown and maintained and subsequently transferred to culturing media containing manganese(II) salts to observe the oxidation of manganese(II) to manganese(IV). The structures and compositions of these manganese(IV) oxides were characterized using scanning electron microscopy, energy dispersive X-ray spectroscopy, inductively coupled plasma optical emission spectroscopy, and powder X-ray diffraction, and their properties were assessed regarding catalytic functionality towards water oxidation in comparison to abiotic acid birnessite. Water oxidation was accomplished through the whole-cell catalysis of MnB1, the results for which compare favorably to the water-oxidizing ability of abiotic Mn(IV) oxides.

Preliminary indication of the role of AHL-dependent quorum sensing systems in calcium carbonate precipitation in Gram-negative bacteria

Numerous microbial species participate in precipitation of carbonates in various natural environments, including soils, geological formations, freshwater biofilms and oceans. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and adaptive aspects remain poorly known. Many Gram-negative bacteria use cell-to-cell communication systems relying on N-acylhomoserine lactone (AHLs) signal molecules to express certain phenotypic traits in a density-dependent manner, a phenomenon referred as to quorum-sensing (QS). In this work, bacterial isolates collected from cave and rhizosphere soil were analyzed to study the occurrence of the AHL-mediated QS in bacterial calcium carbonate (CaCO3) precipitation. To test the production of AHLs signal molecules, we cross-streaked Gram-negative calcifying strains, selected among the environmental strains studied, with the AHL-negative mutant Chromobacterium subtsugae strain CV026. Only Burkholderia ambifaria LMG 11351 was able to restore violacein production in CV026 among the tested strains. The constructed AHL-negative mutant of B. ambifaria LMG 11351 could not precipitate CaCO3 on B-4 agar. Scanning Electron Microscopy (SEM) analysis on CaCO3 crystals obtained in vitro shows crystals of different morphologies, calcified biofilms and bacteria in close contact with the precipitated crystals. In the inner layers of the bioliths deposited by B. ambifaria LMG 11351, a stream-like organization of the Burkholderia imprints was not detected by SEM. Our data provide preliminary evidence that the activation of AHL-regulated genes may be a prerequisite for in vitro bacterial carbonatogenesis, in some cases, confirming the specific role of bacteria as CaCO3 precipitating agents. We enhance the understanding of bacterial CaCO3 biomineralization and its potential biotechnology implications for QS-based strategies to enhance or decrease CaCO3 precipitation through specific bacterial processes. The AHL-negative mutant of B. ambifaria LMG 11351 (a well-known plant growth-promoting bacterium) could also be used to study plant-bacteria interactions. The adaptive role of bacterial CaCO3 biomineralization was also discussed.

Exploring structure, microbiota, and metagenome functions of epigean and hypogean black deposits by microscopic, molecular and bioinformatic approaches

This study revealed how Bacteria and Archaea communities and their metabolic functions differed between two groups of black deposits identified in gorge and cave environments. Scanning electron microscopy coupled with energy dispersive spectroscopy was used to analyse the presence of microbial biosignatures and the elemental composition of samples. Metabarcoding of the V3-V4 regions of 16S rRNA was used to investigate Bacteria and Archaea communities. Based on 16S rRNA sequencing results, PICRUSt software was used to predict metagenome functions. Micrographs showed that samples presented microbial biosignatures and microanalyses highlighted Mn concretions and layers on Al-Si surfaces. The 16S rRNA metabarcoding alpha-diversity metrics showed similar Simpson's and Shannon indices and different values of the Chao-1 index. The amplicon sequence variants (ASVs) analysis at the different taxonomic levels showed a diverse genera composition. However, the communities of all samples shared the presence of uncultured ASVs belonging to the Gemmatales family (Phylogenesis: Gemmataceae; Planctomycetes; Planctomycetota; Bacteria). The predicted metagenome functions analysis revealed diverse metabolic profiles of the Cave and Gorge groups. Genes coding for essential Mn metabolism were present in all samples. Overall, the findings on structure, microbiota, and predicted metagenome functions showed a similar microbial contribution to epigean and hypogean black deposits Mn metabolism.