Dissimilatory reduction of sulfate and zero-valent sulfur at low pH and its significance for bioremediation and metal recovery

Biological S0 reduction at neutral and acidic conditions: Performance and microbial community shifts in a H2/CO2-fed bioreactor

Sulfidogenesis is a promising technology for the selective recovery of chalcophile bulk metals (e.g. Cu, Zn, and Co) from metal-contaminated waters such as acid mine drainage (AMD) and metallurgy waste streams. The use of elemental sulfur (S0) instead of sulfate (SO42-) as electron acceptor reduces electron donor requirements four-fold, lowering process costs, and expanding the range of operating conditions to a more acidic pH. We previously reported autotrophic S0 reduction using an industrial mesophilic granular sludge as inoculum under thermoacidophilic conditions. Here, we examined the effect of pH on the S0 reduction performance of the same inoculum, in a gas-lift reactor run at 30°C under neutral (pH 6.9) and acidic (pH 3.8) conditions, continuously fed with mineral media and H2 and CO2. Steady-state volumetric sulfide production rates (VSPR) dropped 2.5-fold upon transition to acidic pH, from 1.79 ± 0.18 g S2-·L-1·d-1 to 0.71 ± 0.07 g S2-·L-1·d-1. Microbial community composition was analyzed using 16S rRNA gene amplicon sequencing. At neutral pH (6.9), the high relative abundance of the S0-reducing genus Sulfurospirillum, previously known only for heterotrophic members, combined with the presence of Acetobacterium and detection of acetate, suggests an important role for heterotrophic S0 reduction facilitated by acetogenesis. Conversely, at acidic pH (3.9), S0 reduction appeared autotrophic, as indicated by the high relative abundance of Desulfurella.

Harnessing the potential of the microbial sulfur cycle for environmental biotechnology

The sulfur cycle is a complex biogeochemical cycle characterized by the high variability in the oxidation states of sulfur. While sulfur is essential for life processes, certain sulfur compounds, such as hydrogen sulfide, are toxic to all life forms. Micro-organisms facilitate the sulfur cycle, playing a prominent role even in extreme environments, such as soda lakes, acid mine drainage sites, hot springs, and other harsh habitats. The activity of these micro-organisms presents unique opportunities for mitigating sulfur-based pollution and enhancing the recovery of sulfur and metals. This review highlights the application of sulfur-oxidizing and -reducing micro-organisms in environmental biotechnology through three illustrative examples. Additionally, it discusses the challenges, recent trends, and prospects associated with these applications.

The mechanism of microbial sulfate reduction in high concentration sulfate wastewater enhanced by maifanite

Excessive sulfate levels in water bodies pose a dual threat to the ecological environment and human health. The microbial removal of sulfate encounters challenges, particularly in environments with high sulfate concentrations, where the gradual accumulation of sulfide hampers microbial activity. This study focuses on elucidating the mechanisms underlying the enhancement of microbial sulfate reduction in high-concentration sulfate wastewater through a comparative analysis of maifanite and zeolite biostimulants. The investigation reveals that zeolite primarily facilitates microbial growth by providing attachment sites, while maifanite augments sulfate-reducing bacteria (SRB) activity through the release of active substances such as Mo, Ca, and Cu. The addition of maifanite proves instrumental in enhancing microbial activity, manifesting as increased microbial load and protein production, augmented extracellular polymer generation, accelerated electron transfer, and facilitated microbial growth and biofilm formation. Noteworthy is the observation that the combined application of maifanite and zeolite exhibited a synergistic effect, resulting in a 167 % and 68 % increase in sulfate reduction rate compared to the utilization of maifanite (0.12 d-1) or zeolite (0.19 d-1) in isolation. Within this synergistic context, the relative abundance of Desulfobacteraceae reaches a peak of 15.4 %. The outcomes of this study corroborate the distinct promotion mechanisms of maifanite and zeolite in microbial sulfate reduction, offering novel insights into the application of maifanite in the context of high-concentration sulfate removal.

Microorganisms uptake zero-valent sulfur via membrane lipid dissolution of octasulfur and intracellular solubilization as persulfide

Zero-valent sulfur, commonly utilized as a fertilizer or fungicide, is prevalent in various environmental contexts. Its most stable and predominant form, octasulfur (S8), plays a crucial role in microbial sulfur metabolism, either through oxidation or reduction. However, the mechanism underlying its cellular uptake remains elusive. We presented evidence that zero-valent sulfur was adsorbed to the cell surface and then dissolved into the membrane lipid layer as lipid-soluble S8 molecules, which reacted with cellular low-molecular thiols to form persulfide, e.g., glutathione persulfide (GSSH), in the cytoplasm. The process brought extracellular zero-valent sulfur into the cells. When persulfide dioxygenase is present in the cells, GSSH will be oxidized. Otherwise, GSSH will react with another glutathione (GSH) to produce glutathione disulfide (GSSG) and hydrogen sulfide (H2S). The mechanism is different from simple diffusion, as insoluble S8 becomes soluble GSSH after crossing the cytoplasmic membrane. The uptake process is limited by physical contact of insoluble zero-valent sulfur with microbial cells and the regeneration of cellular thiols. Our findings elucidate the cellular uptake mechanism of zero-valent sulfur, which provides critical information for its application in agricultural practices and the bioremediation of sulfur contaminants and heavy metals.

Nutrient structure dynamics and microbial communities at the water-sediment interface in an extremely acidic lake in northern Patagonia

Lake Caviahue (37° 50 'S and 71° 06' W; Patagonia, Argentina) is an extreme case of a glacial, naturally acidic, aquatic environment (pH ~ 3). Knowledge of the bacterial communities in the water column of this lake, is incipient, with a basal quantification of the bacterioplankton abundance distribution in the North and South Basins of Lake Caviahue, and the described the presence of sulfur and iron oxidizing bacteria in the lake sediments. The role that bacterioplankton plays in nutrient utilization and recycling in this environment, especially in the phosphorus cycle, has not been studied. In this work, we explore this aspect in further depth by assessing the diversity of pelagic, littoral and sediment bacteria, using state of the art molecular methods and identifying the differences and commonalties in the composition of the cognate communities. Also, we investigate the interactions between the sediments of Lake Caviahue and the microbial communities present in both sediments, pore water and the water column, to comprehend the ecological relationships driving nutrient structure and fluxes, with a special focus on carbon, nitrogen, and phosphorus. Two major environmental patterns were observed: (a) one distinguishing the surface water samples due to temperature, Fe2+, and electrical conductivity, and (b) another distinguishing winter and summer samples due to the high pH and increasing concentrations of N-NH4+, DOC and SO42-, from autumn and spring samples with high soluble reactive phosphorus (SRP) and iron concentrations. The largest bacterial abundance was found in autumn, alongside higher levels of dissolved phosphorus, iron forms, and increased conductivity. The highest values of bacterial biomass were found in the bottom strata of the lake, which is also where the greatest diversity in microbial communities was found. The experiments using continuous flow column microcosms showed that microbial growth over time, in both the test and control columns, was accompanied by a decrease in the concentration of dissolved nutrients (SRP and N-NH4+), providing proof that sediment microorganisms are active and contribute significantly to nutrient utilization/mobilization.

Acetic acid stress response of the acidophilic sulfate reducer Acididesulfobacillus acetoxydans

Acid mine drainage (AMD) waters are a severe environmental threat, due to their high metal content and low pH (pH <3). Current technologies treating AMD utilize neutrophilic sulfate-reducing microorganisms (SRMs), but acidophilic SRM could offer advantages. As AMDs are low in organics these processes require electron donor addition, which is often incompletely oxidized into organic acids (e.g., acetic acid). At low pH, acetic acid is undissociated and toxic to microorganisms. We investigated the stress response of the acetotrophic Acididesulfobacillus acetoxydans to acetic acid. A. acetoxydans was cultivated in bioreactors at pH 5.0 (optimum). For stress experiments, triplicate reactors were spiked until 7.5 mM of acetic acid and compared with (non-spiked) triplicate reactors for physiological, transcriptomic, and membrane lipid changes. After acetic acid spiking, the optical density initially dropped, followed by an adaptation phase during which growth resumed at a lower growth rate. Transcriptome analysis revealed a downregulation of genes involved in glutamate and aspartate synthesis following spiking. Membrane lipid analysis revealed a decrease in iso and anteiso fatty acid relative abundance; and an increase of acetyl-CoA as a fatty acid precursor. These adaptations allow A. acetoxydans to detoxify acetic acid, creating milder conditions for other microorganisms in AMD environments.

Bio-recovery of CuS nanoparticles from the treatment of acid mine drainage with potential photocatalytic and antibacterial applications

In the present work, CuS nanoparticles were biorecovered from a real acid mine drainage (AMD) and its photocatalytic and antibacterial activities were studied. CuS were formed by delivering biogenic H2S produced by a continuous sulfidogenic bioreactor to an off-line vessel containing the AMD. The main physico-chemical properties of CuS nanoparticles were analyzed by UV-vis spectroscopy, TEM, FE-SEM, XRD and XPS. Moreover, its photocatalytic activity on the photodegradation of organic dyes in water and its antibacterial activity against several bacterial strains were studied and compared with CuS nanoparticles synthetized from a CuSO4 aqueous solution based on the same synthesis method. CuS nanoparticles from the real AMD showed similar physico-chemical properties and photocatalytic and antibacterial activities in comparison to CuS nanoparticles formed with the copper solutions. These results open the way to recover valorous CuS nanoparticles from AMD with potential industrial applications using a metal bioremediation process based on sulfidogenic bioreactors.

Comparative Methods for Quantification of Sulfate-Reducing Bacteria in Environmental and Engineered Sludge Samples

This study aimed to compare microscopic counting, culture, and quantitative or real-time PCR (qPCR) to quantify sulfate-reducing bacteria in environmental and engineered sludge samples. Four sets of primers that amplified the dsrA and apsA gene encoding the two key enzymes of the sulfate-reduction pathway were initially tested. qPCR standard curves were constructed using genomic DNA from an SRB suspension and dilutions of an enriched sulfate-reducing sludge. According to specificity and reproducibility, the DSR1F/RH3-dsr-R primer set ensured a good quantification based on dsrA gene amplification; however, it exhibited inconsistencies at low and high levels of SRB concentrations in environmental and sulfate-reducing sludge samples. Ultimately, we conducted a qPCR method normalized to dsrA gene copies, using a synthetic double-stranded DNA fragment as a calibrator. This method fulfilled all validation criteria and proved to be specific, accurate, and precise. The enumeration of metabolically active SRB populations through culture methods differed from dsrA gene copies but showed a plausible positive correlation. Conversely, microscopic counting had limitations due to distinguishing densely clustered organisms, impacting precision. Hence, this study proves that a qPCR-based method optimized with dsrA gene copies as a calibrator is a sensitive molecular tool for the absolute enumeration of SRB populations in engineered and environmental sludge samples.

Contaminant containment for sustainable remediation of persistent contaminants in soil and groundwater

Contaminant containment measures are often necessary to prevent or minimize offsite movement of contaminated materials for disposal or other purposes when they can be buried or left in place due to extensive subsurface contamination. These measures can include physical, chemical, and biological technologies such as impermeable and permeable barriers, stabilization and solidification, and phytostabilization. Contaminant containment is advantageous because it can stop contaminant plumes from migrating further and allow for pollutant reduction at sites where the source is inaccessible or cannot be removed. Moreover, unlike other options, contaminant containment measures do not require the excavation of contaminated substrates. However, contaminant containment measures require regular inspections to monitor for contaminant mobilization and migration. This review critically evaluates the sources of persistent contaminants, the different approaches to contaminant remediation, and the various physical-chemical-biological processes of contaminant containment. Additionally, the review provides case studies of contaminant containment operations under real or simulated field conditions. In summary, contaminant containment measures are essential for preventing further contamination and reducing risks to public health and the environment. While periodic monitoring is necessary, the benefits of contaminant containment make it a valuable remediation option when other methods are not feasible.

Novel Microorganisms Contribute to Biosulfidogenesis in the Deep Layer of an Acidic Pit Lake

Cueva de la Mora is a permanently stratified acidic pit lake with extremely high concentrations of heavy metals at depth. In order to evaluate the potential for in situ sulfide production, we characterized the microbial community in the deep layer using metagenomics and metatranscriptomics. We retrieved 18 high quality metagenome-assembled genomes (MAGs) representing the most abundant populations. None of the MAGs were closely related to either cultured or non-cultured organisms from the Genome Taxonomy or NCBI databases (none with average nucleotide identity >95%). Despite oxygen concentrations that are consistently below detection in the deep layer, some archaeal and bacterial MAGs mapped transcripts of genes for sulfide oxidation coupled with oxygen reduction. Among these microaerophilic sulfide oxidizers, mixotrophic Thermoplasmatales archaea were the most numerous and represented 24% of the total community. Populations associated with the highest predicted in situ activity for sulfate reduction were affiliated with Actinobacteria, Chloroflexi, and Nitrospirae phyla, and together represented about 9% of the total community. These MAGs, in addition to a less abundant Proteobacteria MAG in the genus Desulfomonile, contained transcripts of genes in the Wood-Ljungdahl pathway. All MAGs had significant genetic potential for organic carbon oxidation. Our results indicate that novel acidophiles are contributing to biosulfidogenesis in the deep layer of Cueva de la Mora, and that in situ sulfide production is limited by organic carbon availability and sulfur oxidation.

Hydrous ferric oxides (HFO's) precipitated from contaminated waters at several abandoned Sb deposits - Interdisciplinary assessment

The presented paper represents a comprehensive analysis of ochre sediments precipitated from Fe rich drainage waters contaminated by arsenic and antimony. Ochre samples from three abandoned Sb deposits were collected in three different seasons and were characterized from the mineralogical, geochemical, and microbiological point of view. They were formed mainly by poorly crystallized 2-line ferrihydrite, with the content of arsenic in samples ranging from 7 g·kg^-1 to 130 g·kg^-1 and content of antimony ranging from 0.25 g·kg^-1 up to 12 g·kg^-1. Next-generation sequencing approach with 16S RNA, 18S RNA and ITS markers was used to characterize bacterial, fungal, algal, metazoal and protozoal communities occurring in the HFOs. In the 16S RNA, the analysis dominated bacteria (96.2%) were mainly Proteobacteria (68.8%) and Bacteroidetes (10.2%) and to less extent also Acidobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Nitrosprae and Chloroflexi. Alpha and beta diversity analysis revealed that the bacterial communities of individual sites do not differ significantly, and only subtle seasonal changes were observed. In this As and Sb rich, circumneutral microenvironment, rich in iron, sulfates and carbonates, methylotrophic bacteria (Methylobacter, Methylotenera), metal/reducing bacteria (Geobacter, Rhodoferax), metal-oxidizing and denitrifying bacteria (Gallionella, Azospira, Sphingopyxis, Leptothrix and Dechloromonas), sulfur-oxidizing bacteria (Sulfuricurvum, Desulphobulbaceae) and nitrifying bacteria (Nitrospira, Nitrosospira) accounted for the most dominant ecological groups and their impact over Fe, As, Sb, sulfur and nitrogen geocycles is discussed. This study provides evidence of diverse microbial communities that exist in drainage waters and are highly important in the process of mobilization or immobilization of the potentially toxic elements.

Biosulfidogenesis Mediates Natural Attenuation in Acidic Mine Pit Lakes

Acidic pit lakes are abandoned open pit mines filled with acid mine drainage (AMD)-highly acidic, metalliferous waters that pose a severe threat to the environment and are rarely properly remediated. Here, we investigated two meromictic, oligotrophic acidic mine pit lakes in the Iberian Pyrite Belt (IPB), Filón Centro (Tharsis) (FC) and La Zarza (LZ). We observed a natural attenuation of acidity and toxic metal concentrations towards the lake bottom, which was more pronounced in FC. The detection of Cu and Zn sulfides in the monimolimnion of FC suggests precipitation of dissolved metals as metal sulfides, pointing to biogenic sulfide formation. This was supported by microbial diversity analysis via 16S rRNA gene amplicon sequencing of samples from the water column, which showed the presence of sulfidogenic microbial taxa in FC and LZ. In the monimolimnion of FC, sequences affiliated with the putative sulfate-reducing genus Desulfomonile were dominant (58%), whereas in the more acidic and metal-enriched LZ, elemental sulfur-reducing Acidianus and Thermoplasma spp., and disproportionating Desulfocapsa spp. were more abundant. Furthermore, the detection of reads classified as methanogens and Desulfosporosinus spp., although at low relative abundance, represents one of the lowest pH values (2.9 in LZ) at which these taxa have been reported, to our knowledge. Analysis of potential biomarker lipids provided evidence that high levels of phosphocholine lipids with mixed acyl/ether glycerol core structures were associated with Desulfomonile, while ceramide lipids were characteristic of Microbacter in these environments. We propose that FC and LZ function as natural bioremediation reactors where metal sulfide precipitation is mediated by biosulfidogenesis starting from elemental sulfur reduction and disproportionation at an early stage (LZ), followed by sulfate reduction at a later stage (FC).