Rapid pyritization in the presence of a sulfur/sulfate-reducing bacterial consortium

Sulfidation of Cd-Sch during the microbial sulfate reduction: Nanoscale redistribution of Cd

Schwertmannite (Sch) is found in environments abundant in iron and sulfate. Microorganisms that utilize iron or sulfate can induce the phase transition of Schwertmannite, consequently leading to the redistribution of coexisting pollutants. However, the impact of the molar ratio of sulfate to iron (S/Fe) on the microbial-mediated transformation of Schwertmannite and its implications for the fate of cadmium (Cd) have not been elucidated. In this study, we examined how S/Fe influenced mineral transformation and the fate of Cd during microbial reduction of Cd-loaded Schwertmannite by Desulfovibrio vulgaris. Our findings revealed that an increase in the S/Fe ratio facilitated sulfate-reducing bacteria (SRB) in mitigating the toxicity of Cd, thereby expediting the generation of sulfide (S(-II)) and subsequently triggering mineral phase transformation. As the S/Fe ratio increased, the predominant minerals in the system transitioned from prismatic-cluster vivianite to rose-shaped mackinawite. The Cd phase and distribution underwent corresponding alterations. Cd primarily existed in its oxidizable state, with its distribution being directly linked not only to FeS content but also showing a robust correlation with phosphorus. The coexistence of vivianite and FeS minerals proved to be more favorable for Cd immobilization. These findings have significant implications for understanding the biogeochemistry of iron (oxyhydr)oxides and Cd fate in anaerobic environments.

Sulfate availability drives the reductive transformation of schwertmannite by co-cultured iron- and sulfate-reducing bacteria

Schwertmannite (Sch) is a highly bioavailable iron-hydroxysulfate mineral commonly found in acid mine drainage contaminated environment rich in sulfate (SO42-). Microbial-mediated Sch transformation has been well-studied, however, the understanding of how SO42- availability affects the microbial-mediated Sch transformation and the secondary minerals influence microbes is relatively limited. This study examined the effect of SO42- availability on the iron-reducing bacteria (FeRB) and SO42--reducing bacteria (SRB) consortium-mediated Sch transformation and the resulting secondary minerals in turn on bacteria. Increased SO42- accelerated the onset of microbial SO42- reduction, which significantly accelerated Sch reduction transformation. The extent of intermediate products such as lepidocrocite (22.1 % ~ 76.3 %, all treatments) and goethite (15.3 %, 10 mM SO42-, 5 d) formed by Sch transformation depended on SO42- concentrations. Vivianite, siderite and iron‑sulfur minerals (e.g., FeS and FeS2) were the dominant secondary minerals, in which the relative content of vivianite and siderite decreased while iron‑sulfur minerals increased with increasing SO42- concentration. Correspondingly, the abundance of FeRB and SRB was negatively and positively correlated with SO42- concentration, respectively; 1 mM SO42- promoted the cymA and omcA expression of FeRB, but 10 mM SO42- lowerd the cymA and omcA expression compared to the 1 mM SO42-; the dsr expression of SRB related linearly to the SO42- concentration. These secondary minerals accumulated on the cell surface to form cell encrustations, which limited the growth and gene expression of FeRB and SRB, and even inhibited the activity of SRB in the 10 mM SO42- treatment group. The 10 mM SO42- treatment group with low-intensity ultrasound effectively restored the SRB activity for reducing SO42- by disintegrating the cell-mineral aggregation, further indicating that cell encrustations limited the microbial metabolism. The results highlight the critical role that SO42- availability can play in controlling microbial transformation of mineral, and the influence of secondary minerals on microbial metabolism.

The aggregated biofilm dominated by Delftia tsuruhatensis enhances the removal efficiency of 2,4-dichlorophenol in a bioelectrochemical system

Bioelectrochemical system is a prospective strategy in organic-contaminated groundwater treatment, while few studies clearly distinguish the mechanisms of adsorption or biodegradation in this process, especially when dense biofilm is formed. This study employed a single chamber microbial electrolysis cell (MEC) with two three-dimensional electrodes for removing a typical organic contaminant, 2,4-dichlorophenol (DCP) from groundwater, which inoculated with anaerobic bacteria derived from sewage treatment plant. Compared with the single biodegradation system without electrodes, the three-dimensional electrodes with a high surface enabled an increase of alpha diversity of the microbial community (increased by 52.6% in Shannon index), and provided adaptive ecological niche for more bacteria. The application of weak voltage (0.6 V) furtherly optimized the microbial community structure, and promoted the aggregation of microorganisms with the formation of dense biofilm. Desorption experiment proved that the contaminants were removed from the groundwater mainly via adsorption by the biofilm rather than biodegradation, and compared with the reactor without electricity, the bioelectrochemical system increased the adsorption capacity from 50.0% to 74.5%. The aggregated bacteria on the surface of electrodes were mainly dominated by Delftia tsuruhatensis (85.0%), which could secrete extracellular polymers and has a high adsorption capacity (0.30 mg/g electrode material) for the contaminants. We found that a bioelectrochemical system with a three-dimensional electrode could stimulate the formation of dense biofilm and remove the organic contaminants as well as their possible more toxic degradation intermediates via adsorption. This study provides important guidance for applying bioelectrochemical system in groundwater or wastewater treatment.

Sulphate-reducing bacteria-mediated pyrite formation in the Dachang Tongkeng tin polymetallic deposit, Guangxi, China

Mediation by sulphate-reducing bacteria (SRB) is responsible for pyrite (FeS₂) formation. The origin of the Dachang tin polymetallic ore field is related to the mineralisation of submarine hydrothermal vent sediments. Here, we investigated SRB in these ores via morphological, chemical, and isotopic analyses. Polarised and scanning electron microscopy indicated that trace SRB fossils in the metal sulphide ore were present in the form of tubular, beaded, and coccoidal bodies comprising FeS₂ and were enclosed within a pyrrhotite (FeS) matrix in the vicinity of micro-hydrothermal vents. The carbon (C), nitrogen (N), and oxygen (O) contents in the FeS₂ synthesised by SRB were high, and a clear biological Raman signal was detected. No such signals were discerned in the peripheral FeS. This co-occurrence of FeS, FeS₂, and the remains of bacteria (probably chemoautotrophic bacteria) was interpreted as the coprecipitation process of SRB-mediated FeS₂ formation, which has, to the best of our knowledge, not been reported before. Our study also illustrates that combined energy-dispersive X-ray spectroscopy, Raman spectroscopy, and isotopic analysis can be used as a novel methodology to document microbial-mediated processes of mineral deposition in submarine hydrothermal vent ecology on geological time scales.

Production of carbon-containing pyrite spherules induced by hyperthermophilic Thermococcales: a biosignature?

Thermococcales, a major order of hyperthermophilic archaea inhabiting iron- and sulfur-rich anaerobic parts of hydrothermal deep-sea vents, are known to induce the formation of iron phosphates, greigite (Fe3S4) and abundant quantities of pyrite (FeS2), including pyrite spherules. In the present study, we report the characterization of the sulfide and phosphate minerals produced in the presence of Thermococcales using X-ray diffraction, synchrotron-based X ray absorption spectroscopy and scanning and transmission electron microscopies. Mixed valence Fe(II)-Fe(III) phosphates are interpreted as resulting from the activity of Thermococcales controlling phosphorus-iron-sulfur dynamics. The pyrite spherules (absent in abiotic control) consist of an assemblage of ultra-small nanocrystals of a few ten nanometers in size, showing coherently diffracting domain sizes of few nanometers. The production of these spherules occurs via a sulfur redox swing from S0 to S-2 and then to S-1, involving a comproportionation of (-II) and (0) oxidation states of sulfur, as supported by S-XANES data. Importantly, these pyrite spherules sequester biogenic organic compounds in small but detectable quantities, possibly making them good biosignatures to be searched for in extreme environments.

Microbial pathways in the coupling of iron, sulfur, and phosphorus cycles at the sediment-water interface of a river system: An in situ study involving the DGT technique

It is imperative to solve the problem of endogenous phosphorus (P) release from sediments in the governance of natural water bodies. Deciphering P migration and transformation patterns that are coupled to iron (Fe) and sulfur (S) cycling at the sediment-water interface (SWI) is the key to understanding the mechanisms underlying endogenous P release. In the present study, we deployed diffusive gradients in thin films (DGT) probes in situ at the SWI in Fuyang River, Hebei Province, China. When the probes were retrieved, the surrounding sediments were synchronously sampled. We analyzed the longitudinal spatiotemporal distribution of Fe, S, and P at the SWI. We also explored how functional bacterial community diversity was associated with the coupling reactions of Fe, S, and P as well as endogenous P release from sediments at the functional gene level. The results showed that labile Fe, S, and P occurred at low concentrations in sediments 0-2 cm below the SWI, while they were enriched in sediments at depths of 4-8 cm. The longitudinal distribution of different labile elements exhibited greater differences between October and February than regional differences, with higher concentrations at downstream locations than upstream locations. In February, Fe/Al-bound P and sulfide (S^2-) concentrations increased in sediments compared with those in October owing to an increase in the relative abundances of dominant genera among P-mineralizing bacteria and sulfate-reducing bacteria. As a result, Fe in Fe-bound P precipitated as FeS₂, which induced P remobilization and release into the overlying water. The spatiotemporal distribution patterns of functional genes related to P (phoD and ppk) and S (aprA) transformation were consistent with those of labile P and S, which strongly suggests that microorganisms played a role in driving and regulating the coupled cycling of P and S at the SWI.

Soft X-ray Fluorescence and Near-Edge Absorption Microscopy for Investigating Metabolic Features in Biological Systems: A Review

Scanning transmission X-ray microscopy (STXM) provides the imaging of biological specimens allowing the parallel collection of localized spectroscopic information by X-ray fluorescence (XRF) and/or X-ray Absorption Near Edge Spectroscopy (XANES). The complex metabolic mechanisms which can take place in biological systems can be explored by these techniques by tracing even small quantities of the chemical elements involved in the metabolic pathways. Here, we present a review of the most recent publications in the synchrotrons' scenario where soft X-ray spectro-microscopy has been employed in life science as well as in environmental research.

The blackening process of black-odor water: Substance types determination and crucial roles analysis

Black-odor water is a serious environmental issue in many developing counties. Iron sulfides and chromophoric dissolved organic matter are considered possible blackening substances. However, the specific type of blackening iron sulfides and the contributions of blackening substances are unclear. This study performed a laboratory simulation experiment to identify the blackening iron sulfides and quantify the contribution of blackening substances. The environmental conditions for forming blackening substances and their blackening process were also determined. We demonstrated that the black iron sulfide was mackinawite. Humic acid is another substance that absorbs light. The equivalent contributions of mackinawite and humic acid were 18.94 m^-1/mg Fe²⁺ and 1.11 m^-1/mg DOC, respectively. A pH of more than 6 is a precondition for producing mackinawite. The production of black substances is the foundation of the blackening process, but the suspension of black substances is essential in causing water blackening. Fulvic acid stabilizes the suspension by changing the surface charge of blackening substances. Moreover, blackening substances can also be suspended with microbial flocs. Determining blackening substances and their role during the blackening process would allow for developing precise and targeted control technologies, improving urban water over the long term.

Active Sulfate-Reducing Bacterial Community in the Camel Gut

The diversity and activity of sulfate-reducing bacteria (SRB) in the camel gut remains largely unexplored. An abundant SRB community has been previously revealed in the feces of Bactrian camels (Camelus bactrianus). This study aims to combine the 16S rRNA gene profiling, sulfate reduction rate (SRR) measurement with a radioactive tracer, and targeted cultivation to shed light on SRB activity in the camel gut. Fresh feces of 55 domestic Bactrian camels grazing freely on semi-arid mountain pastures in the Kosh-Agach district of the Russian Altai area were analyzed. Feces were sampled in early winter at an ambient temperature of -15 °C, which prevented possible contamination. SRR values measured with a radioactive tracer in feces were relatively high and ranged from 0.018 to 0.168 nmol S cm^-3 day^-1. The 16S rRNA gene profiles revealed the presence of Gram-negative Desulfovibrionaceae and spore-forming Desulfotomaculaceae. Targeted isolation allowed us to obtain four pure culture isolates belonging to Desulfovibrio and Desulforamulus. An active SRB community may affect the iron and copper availability in the camel intestine due to metal ions precipitation in the form of sparingly soluble sulfides. The copper-iron sulfide, chalcopyrite (CuFeS₂), was detected by X-ray diffraction in 36 out of 55 analyzed camel feces. In semi-arid areas, gypsum, like other evaporite sulfates, can be used as a solid-phase electron acceptor for sulfate reduction in the camel gastrointestinal tract.

Raman spectroscopic peculiarities of Icelandic poorly crystalline minerals and their implications for Mars exploration

In this work, we have analyzed natural samples collected at three hydrothermal areas of Iceland by Raman spectroscopy. The studied high-latitude regions are considered environmentally and mineralogically appropriate Martian analogues since they are rich in weathered basalts that have been altered by hydrothermalism to mineral phases such as silica, clay minerals, sulfates, oxides, and sulfur. The main objective of this work was to assess the relation of the spectroscopic signatures of alteration to hydrothermal processes and biomediation, considering previous studies focused on the detection of lipid biomarkers in the same samples. The recorded Raman spectra, taken with optical parameters similar to the ExoMars 2022 Raman spectrometer, showed structural modifications in all secondary minerals in the form of peak shifts (in the case of sulfur and clay minerals), changes in the relative ratio intensity (in anatase) and/or shape broadening (in sulfates and hematite). These results reveal the suitability of Raman spectroscopy to examine areas rich in water-altered minerals, where a mixture of crystalline and amorphous phases can co-exist. The detection of silica is singularly interesting since, on the one hand, it can imply the past existence of hydrothermal hot springs rich in nutrient and redox gradients and, on the other hand, provides excellent matrix for biosignature preservation. The data can be helpful as an astrobiological database for the forthcoming missions to Mars, where potential upwelling groundwater systems could have altered the mineral phases in a similar way to that observed in this work.

Sulfur Cycling as a Viable Metabolism under Simulated Noachian/Hesperian Chemistries

Water present on the surface of early Mars (>3.0 Ga) may have been habitable. Characterising analogue environments and investigating the aspects of their microbiome best suited for growth under simulated martian chemical conditions is key to understanding potential habitability. Experiments were conducted to investigate the viability of microbes from a Mars analogue environment, Colour Peak Springs (Axel Heiberg Island, Canadian High Arctic), under simulated martian chemistries. The fluid was designed to emulate waters thought to be typical of the late Noachian, in combination with regolith simulant material based on two distinct martian geologies. These experiments were performed with a microbial community from Colour Peak Springs sediment. The impact on the microbes was assessed by cell counting and 16S rRNA gene amplicon sequencing. Changes in fluid chemistries were tested using ICP-OES. Both chemistries were shown to be habitable, with growth in both chemistries. Microbial communities exhibited distinct growth dynamics and taxonomic composition, comprised of sulfur-cycling bacteria, represented by either sulfate-reducing or sulfur-oxidising bacteria, and additional heterotrophic halophiles. Our data support the identification of Colour Peak Springs as an analogue for former martian environments, with a specific subsection of the biota able to survive under more accurate proxies for martian chemistries.

Precipitation of greigite and pyrite induced by Thermococcales: an advantage to live in Fe- and S-rich environments?

Thermococcales, a major order of archaea inhabiting the iron- and sulfur-rich anaerobic parts of hydrothermal deep-sea vents, have been shown to rapidly produce abundant quantities of pyrite FeS₂ in iron-sulfur-rich fluids at 85°C, suggesting that they may contribute to the formation of 'low temperature' FeS₂ in their ecosystem. We show that this process operates in Thermococcus kodakarensis only when zero-valent sulfur is directly available as intracellular sulfur vesicles. Whether in the presence or absence of zero-valent sulfur, significant amounts of Fe₃ S₄ greigite nanocrystals are formed extracellularly. We also show that mineralization of iron sulfides induces massive cell mortality but that concomitantly with the formation of greigite and/or pyrite, a new generation of cells can grow. This phenomenon is observed for Fe concentrations of 5 mM but not higher suggesting that above a threshold in the iron pulse all cells are lysed. We hypothesize that iron sulfides precipitation on former cell materials might induce the release of nutrients in the mineralization medium further used by a fraction of surviving non-mineralized cells allowing production of new alive cells. This suggests that biologically induced mineralization of iron-sulfides could be part of a survival strategy employed by Thermococcales to cope with mineralizing high-temperature hydrothermal environments.

Diversity of Microbial Metal Sulfide Biomineralization

Since the emergence of life on Earth, microorganisms have contributed to biogeochemical cycles. Sulfate-reducing bacteria are an example of widespread microorganisms that participate in the metal and sulfur cycles by biomineralization of biogenic metal sulfides. In this work, we review the microbial biomineralization of metal sulfide particles and summarize distinctive features from exemplary cases. We highlight that metal sulfide biomineralization is highly metal- and organism-specific. The properties of metal sulfide biominerals depend on the degree of cellular control and on environmental factors, such as pH, temperature, and concentration of metals. Moreover, biogenic macromolecules, including peptides and proteins, help cells control their extracellular and intracellular environments that regulate biomineralization. Accordingly, metal sulfide biominerals exhibit unique features when compared to abiotic minerals or biominerals produced by dead cell debris.

Long-Term Arsenic Sequestration in Biogenic Pyrite from Contaminated Groundwater: Insights from Field and Laboratory Studies

Pumping groundwater from arsenic (As)-contaminated aquifers exposes millions of people, especially those in developing countries, to high doses of the toxic contaminant. Previous studies have investigated cost-effective techniques to remove groundwater arsenic by stimulating sulfate-reducing bacteria (SRB) to form biogenic arsenian pyrite. This study intends to improve upon these past methods to demonstrate the effectiveness of SRB arsenic remediation at an industrial site in Florida. This study developed a ferrous sulfate and molasses mixture to sequester groundwater arsenic in arsenian pyrite over nine months. The optimal dosage of the remediating mixture consisted of 5 kg of ferrous sulfate, ~27 kg (60 lbs) of molasses, and ~1 kg (2 lbs) of fertilizer per 3785.4 L (1000 gallons) of water. The remediating mixture was injected into 11 wells hydrologically upgradient of the arsenic plume in an attempt to obtain full-scale remediation. Groundwater samples and precipitated biominerals were collected from June 2018 to March 2019. X-ray diffraction (XRD), X-ray fluorescence (XRF), electron microprobe (EMP), and scanning electron microscope (SEM) analyses determined that As has been sequestered mainly in the form of arsenian pyrite, which rapidly precipitated as euhedral crystals and spherical aggregates (framboids) 1–30 μm in diameter within two weeks of the injection. The analyses confirmed that the remediating mixture and injection scheme reduced As concentrations to near or below the site’s clean-up standard of 0.05 mg/L over the nine months. Moreover, the arsenian pyrite contained 0.03–0.89 weight percentage (wt%) of sequestered arsenic, with >80% of groundwater arsenic removed by SRB biomineralization. Considering these promising findings, the study is close to optimizing an affordable procedure for sequestrating dissolved As in industry settings.

Trace element fixation in sediments rich in organic matter from a saline lake in tropical latitude with hydrothermal inputs (Sochagota Lake, Colombia): The role of bacterial communities

We studied the relationships between the trace element concentration in sediments from a saline lake at a tropical latitude (Sochagota Lake, Colombia) containing hydrothermal and anthropic inputs with the organic matter content, the mineral assemblage composition and the activity of the bacterial communities of the sediments. Organic matter-poor sediments (TOC < 0.7%) with quartz and kaolinite near the southern entrance of the lake were enriched in Zr (up to 603 mg/kg) and some major detrital elements (Na, Ti, Al and Si). Fine-sized clay-rich sediments deposited in the deep zones of the lake (central and northern segments) were characterized by substantial organic matter (up to 11.10%) and the crystallization of S-bearing minerals, clay mineral mixed layers and illite. These sediments were enriched in S, Fe, Zn, Mo, Rb, Co, K, Cr, Sb, Ni, As, Ba, Cu, Mn, Pb, P, Mg, and Sr. The presence of Fe sulfide nanoparticles enriched in heavy metals encrusting microbial cells and a dominant sulfate-reducing bacteria (SRB) community (Desulfatiglans, Desulfobacterales and Sva0485) suggested that the precipitation of the hydrothermal S and the accumulation of trace elements in the sediments was regulated by SRB activity. The crystallization of S°, barite and calcite and the good correlations between Ba, Sr and Ca indicated that previously precipitated sulfide can be oxidized by the activity of a relevant sulfur-oxidizing bacterial community (Thioalkalimicrobium, Sulfurovum, Arcobacter and Sulfurimonas), possibly facilitating the release of the metals.

Transformation of redox-sensitive to redox-stable iron-bound phosphorus in anoxic lake sediments under laboratory conditions

Phosphorus (P) can be retained in mineral association with ferrous iron (Fe) as vivianite, Fe(II)₃(PO₄)₂ ∙ 8 H₂O, in lake sediments. The mineral is formed and remains stable under anoxic non-sulphidogenic conditions and, therefore, acts as a long-term P sink. In laboratory experiments under anoxic conditions, we investigated whether P adsorbed to amorphous Fe(III)-hydroxide functioned as a precursor phase of vivianite when added to different sediments as a treatment. The untreated sediments served as controls and were naturally Fe-rich (559 µmol/g DW) and Fe-poor (219 µmol/g DW), respectively. The solid P binding forms analysed by sequential extraction and X-ray diffraction were related to coinciding pore water analyses and the bacterial community compositions of the sediments by bacterial 16S rRNA gene amplicon sequencing. In the treatments, within a period of 40 d, 70 % of the redox-sensitive Fe(III)-P was transformed into redox-stable P, which contained vivianite. The mineral was supersaturated in the pore water, but the presence of Fe(III)-P functioning as a precursor was sufficient for measurable vivianite formation. The composition of the microbial community did not differ significantly (PERMANOVA, p = 0.09) between treatment and control of the naturally Fe-rich sediment. In the naturally Fe-poor sediment, the microbial community changed significantly (PERMANOVA, p = 0.001) in response to the addition of Fe(III)-P to the sediment. The freshly formed redox-stable P was not retransferred to a redox-sensitive compound by aeration for 24 h until 90 % O₂ saturation was reached in the sediment slurry. We conclude that 1) Fe(III)-hydroxide bound P, resulting from oxic conditions at the sediment-water interface, is immobilised during anoxic conditions and stable even after re-oxygenation; 2) the process is feasible within the time scales of anoxic lake stratification periods; and 3) in relatively Fe-poor lakes, Fe dosing can provide excess Fe to form the precursor.