Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation

Effect of alkaline leaching of phosphogypsum on sulfate reduction activity and bacterial community composition using different sources of anaerobic microbial inoculum

Phosphogypsum (PG), a by-product of the phosphate industry, is high in sulfate, (SO42-), which makes it an excellent substrate for sulfate-reducing bacteria (SRB) to produce hydrogen sulfide. This work aimed to optimize SO42- leaching from PG to achieve a high biological reduction of SO42- and generate high sulfide concentrations for subsequent use in the biological recovery of elemental sulfur. Five SRB consortia were isolated and enriched from: IS (Industrial sludges), MS (Marine sediments), WC (Winogradsky column), SNV (petroleum industry sediments) and PG (stored Phosphogypsum). The five consortia showed reduction activity when using PG leachate (with water) as source of SO42- and lactate, acetate, or glucose as the electron donor. The highest reduction rate (81.5 %) was registered using lactate and the IS consortium (81.5 %) followed by MS (79 %) and PG (71 %). To enhance the concentration of leached SO42- from PG for future utilization with the isolated consortia, PG was treated with NaOH solutions (2 % and 5 %). SO42- release of 97 % was achieved with a 5 % concentration and the resulting leachate was further diluted to target a SO42- concentration of 12.4 g·L-1 for utilization with the isolated consortia. Compared to water leachate, a significantly higher reduction rate was registered (2 g·L-1 of SO42) using the IS consortium, demonstrating limited inhibition effect of sulfide- concentration on SRB functionalities. Moreover, metagenomic analysis of the consortia revealed that using PG as a source of SO42- increased the abundance of Deltaproteobacteria, including known SRB like Desulfovibrio, Desulfomicrobium, and Desulfosporosinus, as well as novel SRB genera (Cupidesulfovibrio, Desulfocurvus, Desulfococcus) that showed, for the first time, significant potential as novel sulfate-reducers using PG as a SO42- source.

Trajectories of soil microbial recovery in response to restoration strategies in one of the largest and oldest open-pit phosphate mine in Asia

Southwestern China has the largest geological phosphorus-rich mountain in the world, which is seriously degraded by mining activities. Understanding the trajectory of soil microbial recovery and identifying the driving factors behind such restoration, as well as conducting corresponding predictive simulations, can be instrumental in facilitating ecological rehabilitation. Here, high-throughput sequencing and machine learning-based approaches were employed to investigate restoration chronosequences under four restoration strategies (spontaneous re-vegetation with or without topsoil; artificial re-vegetation with or without the addition of topsoil) in one of the largest and oldest open-pit phosphate mines worldwide. Although soil phosphorus (P) is extremely high here (max = 68.3 mg/g), some phosphate solubilizing bacteria and mycorrhiza fungi remain as the predominant functional types. Soil stoichiometry ratios (C:P and N:P) closely relate to the bacterial variation, but soil P content contributes less to microbial dynamics. Meanwhile, as restoration age increases, denitrifying bacteria and mycorrhizal fungi significantly increased. Significantly, based on partial least squares path analysis, it was found that the restoration strategy is the primary factor that drives soil bacterial and fungal composition as well as functional types through both direct and indirect effects. These indirect effects arise from factors such as soil thickness, moisture, nutrient stoichiometry, pH, and plant composition. Moreover, its indirect effects constitute the main driving force towards microbial diversity and functional variation. Using a hierarchical Bayesian model, scenario analysis reveals that the recovery trajectories of soil microbes are contingent upon changes in restoration stage and treatment strategy; inappropriate plant allocation may impede the recovery of the soil microbial community. This study is helpful for understanding the dynamics of the restoration process in degraded phosphorus-rich ecosystems, and subsequently selecting more reasonable recovery strategies.

Effects of phosphogypsum on enzyme activity and microbial community in acid soil

Phosphogypsum (PG) is a solid waste produced from decomposition of phosphate rock in sulfuric acid. It can improve the physicochemical properties of soil. However, the application of PG will inevitably change the living environment of soil microorganisms and lead to the evolution of the soil microbial community. The effects of PG (0, 0.01%, 0.1%, 1%, 10% PG) on soil respiration, enzyme activity and microbial community were studied systematically by indoor incubation experiments. The results showed that the addition of 0.01% PG had little effect on the soil physicochemical properties and microflora. The soil respiration rate decreased with the increase of PG; The activities of catalase, urease and phosphatase were decreased and the activities of sucrase were increased by 10% PG treatment, while 0.01% or 0.1% PG treatment improve the urease activity; Soil microbial community response was significantly separated by amount of the PG amendment, and the application of 10% PG reduced the abundance, diversity and evenness of soil bacteria and fungi. Redundancy analysis (RDA) showed that soil bacterial composition was mainly driven by electrical conductivity (EC) and Ca²⁺, while fungal composition was mainly driven by F^- and NH₄⁺. In addition, the application of PG increased the abundance of salt-tolerant microorganisms and accelerated the degradation of soil organic matter. Overall, These results can help to revisit the current management of PG applications as soil amendments.

Characterization of plant growth promoting activities of indigenous bacteria of phosphate mine wastes, a first step toward revegetation

Morocco holds the vast majority of the world's phosphate reserves, but due to the processes involved in extracting and commercializing these reserves, large quantities of de-structured, nutritionally deficient mine phosphate wastes are produced each year. In a semi-arid climate, these wastes severely hamper plant growth and development leading to huge unvegetated areas. Soil indigenous Plant Growth-Promoting Bacteria (PGPB) play a pivotal role in restauration of these phosphate mining wastes by revegetation, by increasing plants development, soil functioning, and nutrient cycling. The development of a vegetative cover above the degraded phosphate wastes, could stabilize and reintegrate these wastes in the surrounding environment. The current study's objectives were to isolate, characterize, and identify indigenous bacterial strains, and test their PGP activity in vitro and, for the best-performing strains in planta, in order to assess their potential for acting as biofertilizers. A quantitative test for the synthesis of auxin and the production of siderophores as well as a qualitative test for the solubilization of phosphate were performed on all isolated bacterial strains. The production of hydrogen cyanide (HCN), exopolysaccharides (EPS), and enzymes were also examined. Three bacteria, selected among the best PGPB of this study, were tested in planta to determine whether such indigenous bacteria could aid plant growth in this de-structured and nutrient-poor mining soil. Using 16S rRNA gene sequencing, 41 bacterial strains were isolated and 11 genera were identified: Acinetobacter, Agrococcus, Bacillus, Brevibacterium, Microbacterium, Neobacillus, Paenibacillus, Peribacillus, Pseudarthrobacter, Stenotrophomonas, and Raoultella. Among the three best performing bacteria (related to Bacillus paramycoides, Brevibacterium anseongense, and Stenotrophomonas rhizophila), only Stenotrophomonas rhizophila and Brevibacterium anseongense were able to significantly enhance Lupinus albus L. growth. The best inoculation results were obtained using the strain related to Stenotrophomonas rhizophila, improving the plant's root dry weight and chlorophyll content. This is also, to our knowledge, the first study to show a PGP activity of Brevibacterium anseongense.

Long-amplicon MinION-based sequencing study in a salt-contaminated twelfth century granite-built chapel

Abstract

The irregular damp dark staining on the stonework of a salt-contaminated twelfth century granite-built chapel is thought to be related to a non-homogeneous distribution of salts and microbial communities. To enhance understanding of the role of microorganisms in the presence of salt and damp stains, we determined the salt content and identified the microbial ecosystem in several paving slabs and inner wall slabs (untreated and previously bio-desalinated) and in the exterior surrounding soil. Soluble salt analysis and culture-dependent approaches combined with archaeal and bacterial 16S rRNA and fungal ITS fragment as well as with the functional genes nirK, dsr, and soxB long-amplicon MinION-based sequencing were performed. State-of-the-art technology was used for microbial identification, providing information about the microbial diversity and phylogenetic groups present and enabling us to gain some insight into the biological cycles occurring in the community key genes involved in the different geomicrobiological cycles. A well-defined relationship between microbial data and soluble salts was identified, suggesting that poorly soluble salts (CaSO₄) could fill the pores in the stone and lead to condensation and dissolution of highly soluble salts (Ca(NO₃)₂ and Mg(NO₃)₂) in the thin layer of water formed on the stonework. By contrast, no direct relationship between the damp staining and the salt content or related microbiota was established. Further analysis regarding organic matter and recalcitrant elements in the stonework should be carried out.

Key points

• Poorly (CaSO₄) and highly (Ca(NO₃)₂, Mg(NO₃)₂) soluble salts were detected

• Halophilic and mineral weathering microorganisms reveal ecological impacts of salts

• Microbial communities involved in nitrate and sulfate cycles were detected

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-11961-8.

Exploring the microbial community inhabiting the phosphogypsum stacks of Huelva (SW SPAIN) by a high throughput 16S/18S rDNA sequencing approach

Around 100 Mt of phosphogypsum (PG) have been deposited in large stacks on the salt marshes of the Tinto River estuary in Huelva (SW Spain), covering about 1000 ha. These stacks contain extremely acidic water (pH < 2) with high concentrations of pollutants which can cause emissions into their surroundings, generating important environmental concerns. Despite many chemical, geological or hydrological studies have been conducted to characterize the PG stacks of Huelva, the microbial community inhabiting this extreme environment remains unexplored. Using a 16S/18S-rRNA-high throughput sequencing approach, we have uncovered the main taxonomic groups able to live in the acidic metal-contaminated water, which is in direct contact with the PG, demonstrating for the first time the existence of a huge diversity of microbial species in these extreme conditions. In addition, the physicochemical characteristics of the water sampled have been analyzed. These studies have revealed that the most abundant bacteria found in two different leachate samples of the PG stacks belong to the genera Acidiphilium, Pseudomonas, Leptosprillum, Acidithrix, or Acidithiobacillus, typically found in acid mine drainage (AMD) environments, which in total represent around 50% of the total bacterial community. Biodiversity of eukaryotes in PG water is lower than that of prokaryotes, especially in the water collected from the perimeter channel that surrounds the PG stacks, where the pH reaches a value of 1.5 and the activity concentrations exceed 300 Bq L^-1 for ²³⁸U or 20 Bq L^-1 for ²¹⁰Po, values which are from four to five orders of magnitude higher than those usually found in unperturbed surface waters. Even so, an unexpected diversity of algae, fungi, and ciliates have been found in the PG stacks of Huelva, where chlorophyte microalgae and basidiomycetes fungi are the most abundant eukaryotes. Additional bioinformatics tools have been used to perform a functional analysis and predict the most common metabolic pathways in the PG microbiota. The obtained data indicate that the extreme conditions of these PG stacks hide an unexpected microbial diversity, which can play an important role in the dynamics of the contaminating compounds of the PG and provide new strains with unique biotechnological applications.

Microbial transformations by sulfur bacteria can recover value from phosphogypsum: A global problem and a possible solution

Rising global population and affluence are increasing demands for food production and the phosphorus (P) fertilizers needed to grow that food. Essential are new approaches for managing the growing amount of phosphogypsum (PG) that is a by-product of phosphoric-acid production from phosphate rock. Today, only ~15% of the worldwide production of PG is recycled, mainly for agriculture and road construction. This review addresses microbial valorization of PG through strategies that apply sulfur-transforming bacteria: sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB). The focus is on recovering elemental sulfur (S⁰), which can be used to make the sulfuric acid needed to produce phosphoric acid from rock phosphate. Our review provides in-depth understanding of the microbiological, chemical, and technological bases for microbial reclamation of S⁰ from PG. The review presents the principles and practices for sulfate leaching from PG, reduction of sulfate to sulfide by SRB, and oxidation of sulfide to S⁰ by SOB. The choice of electron donor for SRB, control of oxygen delivery to SOB, and nutrient requirements are emphasized. Although microorganism-based technologies for PG reclamation are far from mature, the efficiency of such SRB- and SOB-based processes has been documented at laboratory and industrial scales. This review should spur biotechnological advances toward recovering value from PG.

Efficiency of hybrid systems enhanced with different sludge ratios in improving resistance to short-term low temperatures

Complete autotrophic nitrogen removal over nitrite (CANON) is used in wastewater treatment. However, the performance of the CANON system significantly decreases at low temperatures; thus, a new strategy to improve the resistance of the CANON system is required. To investigate the impact of sludge ratio control (high-granule, equivalent, and high-floc systems) on the resistance of CANON to low temperatures, and their recovery after restoring to normal temperature, the nitrogen removal performance of hybrid systems with different ratios was evaluated. The equivalent system had the lowest nitrite accumulation rate and highest nitrogen removal rate. Anaerobic ammonia oxidation was the rate-limiting step of each system, and hzs was the rate-limiting gene. The higher anaerobic ammonium oxidizing bacteria (AAOB) abundance and hzs expression levels resulted in an equivalent system with better resistance and recovery to short-term low temperatures at the gene level.

Description of Microbial Communities of Phosphate Mine Wastes in Morocco, a Semi-Arid Climate, Using High-Throughput Sequencing and Functional Prediction

Soil microbiota are vital for successful revegetation, as they play a critical role in nutrient cycles, soil functions, and plant growth and health. A rehabilitation scenario of the abandoned Kettara mine (Morocco) includes covering acidic tailings with alkaline phosphate mine wastes to limit water infiltration and hence acid mine drainage. Revegetation of phosphate wastes is the final step to this rehabilitation plan. However, revegetation is hard on this type of waste in semi-arid areas and only a few plants managed to grow naturally after 5 years on the store-and-release cover. As we know that belowground biodiversity is a key component for aboveground functioning, we sought to know if any structural problem in phosphate waste communities could explain the almost absence of plants. To test this hypothesis, bacterial and archaeal communities present in these wastes were assessed by 16S rRNA metabarcoding. Exploration of taxonomic composition revealed a quite diversified community assigned to 19 Bacterial and two Archaeal phyla, similar to other studies, that do not appear to raise any particular issues of structural problems. The dominant sequences belonged to Proteobacteria, Bacteroidetes, Actinobacteria, and Gemmatimonadetes and to the genera Massilia, Sphingomonas, and Adhaeribacter. LEfSe analysis identified 19 key genera, and metagenomic functional prediction revealed a broader phylogenetic range of taxa than expected, with all identified genera possessing at least one plant growth-promoting trait. Around 47% of the sequences were also related to genera possessing strains that facilitate plant development under biotic and environmental stress conditions, such as drought and heat.

Phosphogypsum Recycling: A Review of Environmental Issues, Current Trends, and Prospects

The problem of recycling and storage of phosphogypsum is topical for many countries around the world, as it is associated with environmental problems of pollution of water bodies, land, and atmosphere. Therefore, this paper analyzes the directions of phosphogypsum recycling and possible alternatives to its use. The main disadvantages of the existing methods of phosphogypsum processing were identified and trends in this waste management were also considered. Through the VOSviewer programme, a visualization of cluster interconnections was carried out in research publications of various fields of phosphogypsum utilization. Five clusters were formed: a red cluster—phosphogypsum recycling in the construction industry; green cluster—radiation pollution problem of phosphogypsum and phosphate fertilizers; yellow cluster—monitoring migration of phosphogypsum components in the ecosystem, with the mobile forms of heavy metals and their inflow into aquifers from phosphogypsum dumps; blue cluster—use of phosphogypsum in agriculture as an ameliorant and a component of fertilizer; and a purple cluster—the impact of phosphogypsum on microorganisms, particularly in bioremediation processes. Under the proposed integrated biochemical approach, the use of various bioprocesses of phosphogypsum recovery from waste dumps and implementation of new biotechnological solutions for processing phosphorus raw materials are presented.

BMT: Bioinformatics mini toolbox for comprehensive DNA and protein analysis

Background Bioinformatics tools are of great significance and are used in different spheres of life sciences. There are wide variety of tools available to perform primary analysis of DNA and protein but most of them are available on different platforms and many remain undetected. Accessing these tools separately to perform individual task is uneconomical and inefficient. Objective Our aim is to bring different bioinformatics models on a single platform to ameliorate scientific research. Hence, our objective is to make a tool for comprehensive DNA and protein analysis. Methods To develop a reliable, straight-forward and standalone desktop application we used state of the art python packages and libraries. Bioinformatics Mini Toolbox (BMT) is combination of seven tools including FastqTrimmer, Gene Prediction, DNA Analysis, Translation, Protein analysis and Pairwise and Multiple alignment. Results FastqTrimmer assists in quality assurance of NGS data. Gene prediction predicts the genes by homology from novel genome on the basis of reference sequence. Protein analysis and DNA analysis calculates physiochemical properties of nucleotide and protein sequences, respectively. Translation translates the DNA sequence into six open reading frames. Pairwise alignment performs pairwise global and local alignment of DNA and protein sequences on the basis or multiple matrices. Multiple alignment aligns multiple sequences and generates a phylogenetic tree. Conclusion We developed a tool for comprehensive DNA and protein analysis. The link to download BMT is https://github.com/nasiriqbal012/BMT_SETUP.git.