Diversity of Microbial Metal Sulfide Biomineralization

Biochemical mechanism underlying the synthesis of PbS nanoparticle and its in-situ photo effect on Shinella zoogloeoides PQ7

Metal sulfide nanoparticles (NPs) with semiconductor potentials are valuable bioremediation end-products that attract great research interests. However, biochemical mechanisms underlying their biosynthesis and photo-effects remain elusive. In this study, we found that biofilm lifestyle remarkably improved lead resistance and PbS-NP biosynthesis in Shinella zoogloeoides PQ7. Surprisingly, biosynthesis of PbS-NP required more than cysteine and H2S production. Transcriptomic and metabolomic analysis indicated that PQ7 responded to lead stress by changing metabolic activities in ABC transporters, oxidative phosphorylation, EPS production, quorum sensing, protein de novo synthesis, flagella assembly and antioxidative reactions, etc. The elevated EPS production and quorum sensing gene expression echoed the favorable roles of biofilm formation in lead resistance. Biosynthesis of PbS-NP required proper oxygen supply, and was impeded by adding kanamycin or using yeast extract as the sole nutrient supply. Investigations on NAD/NADH, ATP, ROS and GSH productions indicated that biosynthesis of PbS-NP was corelated with cellular respiration, energy metabolism, and redox status. Finally, we proved that PbS-NP had the dose-dependent in-situ photo effect on PQ7's growth and ROS production. This is the first report that pinpoints the role of cellular respiration in PbS-NP biosynthesis, which is essential for further mechanism study and the development of bioremediation techniques.

Powering the Future by Iron Sulfide Type Material (FexSy) Based Electrochemical Materials for Water Splitting and Energy Storage Applications: A Review

Water electrolysis is among the recent alternatives for generating clean fuels (hydrogen). It is an efficient way to produce pure hydrogen at a rapid pace with no unwanted by-products. Effective and cheap water-splitting electrocatalysts with enhanced activity, specificity, and stability are currently widely studied. In this regard, noble metal-free transition metal-based catalysts are of high interest. Iron sulfide (FeS) is one of the essential electrocatalysts for water splitting because of its unique structural and electrochemical features. This article discusses the significance of FeS and its nanocomposites as efficient electrocatalysts for oxygen evolution reaction (OER), hydrogen evolution reaction (HER), oxygen reduction reaction (ORR), and overall water splitting. FeS and its nanocomposites have been studied also for energy storage in the form of electrode materials in supercapacitors and lithium- (LIBs) and sodium-ion batteries (SIBs). The structural and electrochemical characteristics of FeS and its nanocomposites, as well as the synthesis processes, are discussed in this work. This discussion correlates these features with the requirements for electrocatalysts in overall water splitting and its associated reactions. As a result, this study provides a road map for researchers seeking economically viable, environmentally friendly, and efficient electrochemical materials in the fields of green energy production and storage.

Biomineralization of Sulfate-Reducing Bacteria In Situ-Induced Preparation of Nano Fe2O3-Fe(Ni)S/C as High-Efficiency Oxygen Evolution Electrocatalyst

Transition metal-based catalysts possess high catalytic activity for oxygen evolution reaction (OER). However, the preparation of high-performance OER electrocatalysts using simple strategies with a low cost still faces a major challenge. Herein, this work presents an innovative, in situ-induced preparation of the Fe2O3, FeS, and NiS nanoparticles, supported on carbon blacks (CBs) (denoted as Fe2O3-Fe(Ni)S/C) as a high-efficiency oxygen evolution electrocatalyst by employing biomineralization. Biomineralization, a simple synthesis strategy, demonstrates a huge advantage in controlling the size of the Fe2O3 and Fe(Ni)S nanoparticles, as well as achieving uniform nanoparticle distribution on carbon blacks. It is found that the electrocatalyst Fe2O3-Fe(Ni)S/C-200 shows a good OER electrocatalytic activity with a small loading capacity, and it has a small overpotential and Tafel slope in 1 m KOH solution with values of 264 mV and 42 mV dec-1, respectively, at a current density of 10 mA cm-2. Additionally, it presents good electrochemical stability for over 24 h. The remarkable and robust electrocatalytic performance of Fe2O3-Fe(Ni)S/C-200 is attributed to the synergistic effect of Fe2O3, FeS, and doped-Ni species as well as its distinct 3D spherical structure. This approach indicates the promising applications of biomineralization for the bio-preparation of functional materials and energy conversion.

Reconstitution of a biofilm adhesin system from a sulfate-reducing bacterium in Pseudomonas fluorescens

Biofilms of sulfate-reducing bacterium (SRB) like Desulfovibrio vulgaris Hildenborough (DvH) can facilitate metal corrosion in various industrial and environmental settings leading to substantial economic losses. Although the mechanisms of biofilm formation by DvH are not yet well understood, recent studies indicate the large adhesin, DvhA, is a key determinant of biofilm formation. The dvhA gene neighborhood resembles the biofilm-regulating Lap system of Pseudomonas fluorescens but is curiously missing the c-di-GMP-binding regulator LapD. Instead, DvH encodes an evolutionarily unrelated c-di-GMP-binding protein (DVU1020) that we hypothesized is functionally analogous to LapD. To study this unusual Lap system and overcome experimental limitations with the slow-growing anaerobe DvH, we reconstituted its predicted SRB Lap system in a P. fluorescens strain lacking its native Lap regulatory components (ΔlapGΔlapD). Our data support the model that DvhA is a cell surface-associated LapA-like adhesin with a N-terminal "retention module" and that DvhA is released from the cell surface upon cleavage by the LapG-like protease DvhG. Further, we demonstrate DVU1020 (named here DvhD) represents a distinct class of c-di-GMP-binding, biofilm-regulating proteins that regulates DvhG activity in response to intracellular levels of this second messenger. This study provides insight into the key players responsible for biofilm formation by DvH, thereby expanding our understanding of Lap-like systems.

Biomineralization through a Symmetry-Controlled Oligomeric Peptide

Biomineralization peptides are versatile tools for generating nanostructures since they can make specific interactions with various inorganic metals, which can lead to the formation of intricate nanostructures. Previously, we examined the influence that multivalency has on inorganic structures formed by p53 tetramer-based biomineralization peptides and noted a connection between the geometry of the peptide and its ability to regulate nanostructure formation. To investigate the role of multivalency in nanostructure formation by biomineralization peptides more thoroughly, silver biomineralization peptides were engineered by linking them to additional self-assembling molecules based on coiled-coil peptides and multistranded DNA oligomers. Under mild reducing conditions at room temperature, these engineered biomineralization peptides self-assembled and formed silver nanostructures. The trimeric forms of the biomineralization peptides were the most efficient in forming a hexagonal disk nanostructure, with both the coiled-coil peptide and DNA-based multimeric forms. Together, the results suggest that the spatial arrangement of biomineralization peptides plays a more important role in regulating nanostructure formation than their valency.

Research progress and hotspots on microbial remediation of heavy metal-contaminated soil: a systematic review and future perspectives

Microbial remediation technology has received much attention as a green, ecological, and inexpensive technology, and there is great potential for the application of microbial remediation technology for heavy metals (HMs) contaminated soil alone and in conjunction with other technologies in environmental remediation. To gain an in-depth understanding of the latest research progress, research hotspots, and development trends on microbial remediation of HMs-contaminated soil, and to objectively reflect the scientific contributions and impacts of relevant countries/regions, institutions, and individuals of this field, in this manuscript, ISI Web of Knowledge's Web of Science™ core collection database, data visualization, and analysis software Bibliometrix, VOSviewer, and HistCite Pro were used to collect and analyze the relevant literature from 2000 to 2022, and 1409 publications were subjected to scientometric analyses. It involved 327 journals, 5150 authors, 75 countries/regions, and 2740 keywords. The current progress and hotspots on microbial remediation of HMs-contaminated soil since the twenty-first century were analyzed in terms of the top 10 most productive countries (regions), high-yielding authors, source journals, important research institutions, and hotspots of research directions. Over the past 22 years, China, India, and the USA have been the countries with the most articles. The institution and author with the most publications are the Chinese Acad Sci and Zhu YG, respectively. Journal of Hazardous Materials is the most productive journal. The keywords showed 6 co-occurrence clusters. These findings revealed the research hotspots, knowledge gaps, and future exploration trends related to microbial remediation of HMs-contaminated soil.

The copper resistance mechanism in a newly isolated Pseudoxanthomonas spadix ZSY-33

Resolving the heavy metal resistance mechanisms of microbes is crucial for understanding the bioremediation of the ecological environment. In this study, a multiple heavy metal resistance bacterium, Pseudoxanthomonas spadix ZSY-33 was isolated and characterized. The copper resistance mechanism was revealed by analysis of the physiological traits, copper distribution, and genomic and transcriptomic data of strain ZSY-33 cultured with different concentrations of copper. The growth inhibition assay in basic medium showed that the growth of strain ZSY-33 was inhibited in the presence of 0.5 mM copper. The production of extracellular polymeric substances increased at a lower concentration of copper and decreased at a higher concentration of copper. Integrative analysis of genomic and transcriptomic, the copper resistance mechanism in strain ZSY-33 was elucidated. At a lower concentration of copper, the Cus and Cop systems were responsible for the homeostasis of intracellular copper. As the concentration of copper increased, multiple metabolism pathways, including the metabolism of sulfur, amino acids, and pro-energy were cooperated with the Cus and Cop systems to deal with copper stress. These results indicated a flexible copper resistance mechanism in strain ZSY-33, which may acquire from the long-term interaction with the living environment.

Reconstitution of a Biofilm Adhesin System from a Sulfate-Reducing Bacterium in Pseudomonas fluorescens

Biofilms of the sulfate reducing bacterium (SRB) Desulfovibrio vulgaris Hildenborough (DvH) can facilitate metal corrosion in various industrial and environmental settings leading to substantial economic losses; however, the mechanisms of biofilm formation by DvH are not yet well-understood. Evidence suggests that a large adhesin, DvhA, may be contributing to biofilm formation in DvH. The dvhA gene and its neighbors encode proteins that resemble the Lap system, which regulates biofilm formation by Pseudomonas fluorescens, including a LapG-like protease DvhG and effector protein DvhD, which has key differences from the previously described LapD. By expressing the Lap-like adhesion components of DvH in P. fluorescens, our data support the model that the N-terminal fragment of the large adhesin DvhA serves as an adhesin "retention module" and is the target of the DvhG/DvhD regulatory module, thereby controlling cell-surface location of the adhesin. By heterologously expressing the DvhG/DvhD-like proteins in a P. fluorescens background lacking native regulation (ΔlapGΔlapD) we also show that cell surface regulation of the adhesin is dependent upon the intracellular levels of c-di-GMP. This study provides insight into the key players responsible for biofilm formation by DvH, thereby expanding our understanding of Lap-like systems.

Untapped Potential of Deep Eutectic Solvents for the Synthesis of Bioinspired Inorganic-Organic Materials

Since the discovery of deep eutectic solvents (DESs) in 2003, significant progress has been made in the field, specifically advancing aspects of their preparation and physicochemical characterization. Their low-cost and unique tailored properties are reasons for their growing importance as a sustainable medium for the resource-efficient processing and synthesis of advanced materials. In this paper, the significance of these designer solvents and their beneficial features, in particular with respect to biomimetic materials chemistry, is discussed. Finally, this article explores the unrealized potential and advantageous aspects of DESs, focusing on the development of biomineralization-inspired hybrid materials. It is anticipated that this article can stimulate new concepts and advances providing a reference for breaking down the multidisciplinary borders in the field of bioinspired materials chemistry, especially at the nexus of computation and experiment, and to develop a rigorous materials-by-design paradigm.

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 biosignatures in ancient deep-sea hydrothermal sulfides

Deep-sea hydrothermal systems provide ideal conditions for prebiotic reactions and ancient metabolic pathways and, therefore, might have played a pivotal role in the emergence of life. To understand this role better, it is paramount to examine fundamental interactions between hydrothermal processes, non-living matter, and microbial life in deep time. However, the distribution and diversity of microbial communities in ancient deep-sea hydrothermal systems are still poorly constrained, so evolutionary, and ecological relationships remain unclear. One important reason is an insufficient understanding of the formation of diagnostic microbial biosignatures in such settings and their preservation through geological time. This contribution centers around microbial biosignatures in Precambrian deep-sea hydrothermal sulfide deposits. Intending to provide a valuable resource for scientists from across the natural sciences whose research is concerned with the origins of life, we first introduce different types of biosignatures that can be preserved over geological timescales (rock fabrics and textures, microfossils, mineral precipitates, carbonaceous matter, trace metal, and isotope geochemical signatures). We then review selected reports of biosignatures from Precambrian deep-sea hydrothermal sulfide deposits and discuss their geobiological significance. Our survey highlights that Precambrian hydrothermal sulfide deposits potentially encode valuable information on environmental conditions, the presence and nature of microbial life, and the complex interactions between fluids, micro-organisms, and minerals. It further emphasizes that the geobiological interpretation of these records is challenging and requires the concerted application of analytical and experimental methods from various fields, including geology, mineralogy, geochemistry, and microbiology. Well-orchestrated multidisciplinary studies allow us to understand the formation and preservation of microbial biosignatures in deep-sea hydrothermal sulfide systems and thus help unravel the fundamental geobiology of ancient settings. This, in turn, is critical for reconstructing life's emergence and early evolution on Earth and the search for life elsewhere in the universe.

Effects of Initial pH and Carbonate Rock Dosage on Bio-Oxidation and Secondary Iron Mineral Synthesis

The effect of pH is a key factor in biomineralization mediated by Acidithiobacillus ferrooxidans to promote the transformation of Fe into secondary iron minerals. This study aimed to investigate the effects of initial pH and carbonate rock dosage on bio-oxidation and secondary iron mineral synthesis. Variations in pH and the concentrations of Ca²⁺, Fe²⁺, and total Fe (TFe) in the growth medium of A. ferrooxidans were examined in the laboratory to determine how they affect the bio-oxidation process and secondary iron mineral synthesis. The results showed that in systems with an initial pH of 1.8, 2.3, and 2.8, the optimum dosages of carbonate rock were 30, 10, and 10 g, respectively, which significantly improved the removal rate of TFe and the amount of sediments. At an initial pH of 1.8 and a carbonate rock dosage of 30 g, the final removal rate of TFe reached 67.37%, which was 28.03% higher than that of the system without the addition of carbonate rock, and 36.9 g·L^-1 of sediments were generated, which was higher than that of the system without the addition of carbonate rock (6.6 g·L^-1). Meanwhile, the number of sediments generated by adding carbonate rock were significantly higher than those without the addition of carbonate rock. The secondary minerals were characterized by a progressive transition from low crystalline assemblages composed of calcium sulfate and subordinated jarosite, to well crystal-line assemblages composed of jarosite, calcium sulfate, and goethite. These results have important implications for comprehensively understanding the dosage of carbonate rock in mineral formation under different pH conditions. The findings help reveal the growth of secondary minerals during the treatment of AMD using carbonate rocks under low-pH conditions, which offers valuable information for combining the carbonate rocks with secondary minerals to treat AMD.

Recent advances in metal sulfide nanoparticle-added bionanocomposite films for food packaging applications

Metal sulfide nanoparticles have recently attracted much attention due to their unique physical and functional properties. Metal sulfide nanoparticles used as optoelectronic and biomedical materials in the past decades are promising for making functional nanocomposite films due to their low toxicity and strong antibacterial activity. Recently, copper sulfide and zinc sulfide nanomaterials have been used to produce food packaging films for active packaging. Metal sulfide nanoparticles added as nanofillers are attracting attention in packaging applications due to their excellent potential to improve mechanical, barrier properties, and antibacterial activity. This review covers the fabrication process and important applications of metal sulfide nanoparticles. The development of metal sulfides reinforcing mainly copper sulfide and zinc sulfide nanomaterials as multifunctional nanofillers in bio-based films for active packaging applications has been comprehensively reviewed. As the recognition of metal sulfide nanoparticles as a functional filler increases, the development and application potential of active packaging films using them is expected to increase.

Periplasmic Bacterial Biomineralization of Copper Sulfide Nanoparticles

Metal sulfides are a common group of extracellular bacterial biominerals. However, only a few cases of intracellular biomineralization are reported in this group, mostly limited to greigite (Fe3 S4 ) in magnetotactic bacteria. Here, a previously unknown periplasmic biomineralization of copper sulfide produced by the magnetotactic bacterium Desulfamplus magnetovallimortis strain BW-1, a species known to mineralize greigite (Fe3 S4 ) and magnetite (Fe3 O4 ) in the cytoplasm is reported. BW-1 produces hundreds of spherical nanoparticles, composed of 1-2 nm substructures of a poorly crystalline hexagonal copper sulfide structure that remains in a thermodynamically unstable state. The particles appear to be surrounded by an organic matrix as found from staining and electron microscopy inspection. Differential proteomics suggests that periplasmic proteins, such as a DegP-like protein and a heavy metal-binding protein, could be involved in this biomineralization process. The unexpected periplasmic formation of copper sulfide nanoparticles in BW-1 reveals previously unknown possibilities for intracellular biomineralization that involves intriguing biological control and holds promise for biological metal recovery in times of copper shortage.

Glycerol amendment enhances biosulfidogenesis in acid mine drainage-affected areas: An incubation column experiment

Microbial sulfate (SO₄²⁻) reduction in Acid Mine Drainage (AMD) environments can ameliorate the acidity and extreme metal concentrations by consumption of protons via the reduction of SO₄²⁻ to hydrogen sulfide (H₂S) and the concomitant precipitation of metals as metal sulfides. The activity of sulfate-reducing bacteria can be stimulated by the amendment of suitable organic carbon sources in these generally oligotrophic environments. Here, we used incubation columns (IC) as model systems to investigate the effect of glycerol amendment on the microbial community composition and its effect on the geochemistry of sediment and waters in AMD environments. The ICs were built with natural water and sediments from four distinct AMD-affected sites with different nutrient regimes: the oligotrophic Filón Centro and Guadiana acidic pit lakes, the Tintillo river (Huelva, Spain) and the eutrophic Brunita pit lake (Murcia, Spain). Physicochemical parameters were monitored during 18 months, and the microbial community composition was determined at the end of incubation through 16S rRNA gene amplicon sequencing. SEM-EDX analysis of sediments and suspended particulate matter was performed to investigate the microbially-induced mineral (neo)formation. Glycerol amendment strongly triggered biosulfidogenesis in all ICs, with pH increase and metal sulfide formation, but the effect was much more pronounced in the ICs from oligotrophic systems. Analysis of the microbial community composition at the end of the incubations showed that the SRB Desulfosporosinus was among the dominant taxa observed in all sulfidogenic columns, whereas the SRB Desulfurispora, Desulfovibrio and Acididesulfobacillus appeared to be more site-specific. Formation of Fe³⁺ and Al³⁺ (oxy)hydroxysulfates was observed during the initial phase of incubation together with increasing pH while formation of metal sulfides (predominantly, Zn, Fe and Cu sulfides) was observed after 1–5 months of incubation. Chemical analysis of the aqueous phase at the end of incubation showed almost complete removal of dissolved metals (Cu, Zn, Cd) in the amended ICs, while Fe and SO₄²⁻ increased towards the water-sediment interface, likely as a result of the reductive dissolution of Fe(III) minerals enhanced by Fe-reducing bacteria. The combined geochemical and microbiological analyses further establish the link between biosulfidogenesis and natural attenuation through metal sulfide formation and proton consumption.