Correlative Cryogenic Spectromicroscopy to Investigate Selenium Bioreduction Products

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

BACKGROUND

Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling.

RESULTS

Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa, dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix. Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems.

CONCLUSIONS

Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix, and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling. Video Abstract.

Time-Resolved Examination of Fungal Selenium Redox Transformations

Selenium (Se) is both a micronutrient required for most life and an element of environmental concern due to its toxicity at high concentrations, and both bioavailability and toxicity are largely influenced by the Se oxidation state. Environmentally relevant fungi have been shown to aerobically reduce Se(IV) and Se(VI), the generally more toxic and bioavailable Se forms. The goal of this study was to shed light on fungal Se(IV) reduction pathways and biotransformation products over time and fungal growth stages. Two Ascomycete fungi were grown with moderate (0.1 mM) and high (0.5 mM) Se(IV) concentrations in batch culture over 1 month. Fungal growth was measured throughout the experiments, and aqueous and biomass-associated Se was quantified and speciated using analytical geochemistry, transmission electron microscopy (TEM), and synchrotron-based X-ray absorption spectroscopy (XAS) approaches. The results show that Se transformation products were largely Se(0) nanoparticles, with a smaller proportion of volatile, methylated Se compounds and Se-containing amino acids. Interestingly, the relative proportions of these products were consistent throughout all fungal growth stages, and the products appeared stable over time even as growth and Se(IV) concentration declined. This time-series experiment showing different biotransformation products throughout the different growth phases suggests that multiple mechanisms are responsible for Se detoxification, but some of these mechanisms might be independent of Se presence and serve other cellular functions. Knowing and predicting fungal Se transformation products has important implications for environmental and biological health as well as for biotechnology applications such as bioremediation, nanobiosensors, and chemotherapeutic agents.

Selenium nanoparticles improve nickel-induced testosterone synthesis disturbance by down-regulating miR-708-5p/p38 MAPK pathway in Leydig cells

The present study was designed to investigate the role of miR-708-5p/p38 mitogen-activated protein kinase (MAPK) pathway during the mechanism of selenium nanoparticles (Nano-Se) against nickel (Ni)-induced testosterone synthesis disorder in rat Leydig cells. We conducted all procedures based on in vitro culture of rat primary Leydig cells. After treating Leydig cells with Nano-Se and NiSO₄ alone or in combination for 24 h, we determined the cell viability, reactive oxygen species (ROS) levels, testosterone production, and the protein expression of key enzymes involved in testosterone biosynthesis: steroidogenic acute regulatory (StAR) and cytochrome P450 cholesterol side chain cleavage enzyme (CYP11A1). The results indicated that Nano-Se antagonized cytotoxicity and eliminated ROS generation induced by NiSO₄ , suppressed p38 MAPK protein phosphorylation and reduced miR-708-5p expression. Importantly, we found that Nano-Se upregulated the expression of testosterone synthase and increased testosterone production in Leydig cells. Furthermore, we investigated the effects of p38 MAPK and miR-708-5p using their specific inhibitor during Nano-Se against Ni-induced testosterone synthesis disorder. The results showed that Ni-inhibited testosterone secretion was alleviated by Nano-Se co-treatment with p38 MAPK specific inhibitor SB203580 and miR-708-5p inhibitor, respectively. In conclusion, these findings suggested Nano-Se could inhibit miR-708-5p/p38 MAPK pathway, and up-regulate the key enzymes protein expression for testosterone synthesis, thereby antagonizing Ni-induced disorder of testosterone synthesis in Leydig cells.

Does inorganic carbon species alter chromium reduction mechanism in sulfur-based autotrophic biosystem?

Sulfur-based autotrophic bioremediation is recognized as an environmentally-friendly and effective method for the treatment of Cr(VI) in groundwater. However, inorganic carbon (IC), especially IC-rich solid kitchen waste, has rarely been reported as an important factor in the autotrophic process. In China, kitchen waste containing IC is generated in large quantities, and in combination with Cr(VI) autotrophic treatment technology in groundwater can achieve a win-win situation. Herein, the efficiency of Cr(VI)-bioreduction coupling solid inorganic carbon (SIC) (e.g. marble, egg shell, oyster shell, and NSAD synthetic material) and liquid inorganic carbon (LIC) was compared for the first time. After 18 d incubation, there were significant differences in Cr(VI) reduction efficiency and microbial community between SIC-bioreactors and LIC-bioreactors. Higher electron transfer activity, greater bioavailability of organics, and multiple Cr(VI) reductases were detected in SIC-biosystems, which effectively promoted Cr(VI) energy metabolism and enzyme-mediated biological reduction. High-throughput 16S rRNA gene sequencing reveled multiple cooperative mechanism in different substrate biosystems. This study not only advances the understanding of SIC coupled with Cr(VI) autotrophic bioreduction, but also provides new insights for the treatment of solid kitchen waste and groundwater bioremediation.

Microbial selenate detoxification linked to elemental sulfur oxidation: Independent and synergic pathways

Elevated selenium levels in the environment, with soluble selenate [Se(VI)] as the common chemical species, pose a severe threat to human health. Anaerobic Se(VI) bioreduction is a promising approach for selenium detoxification, and various organic/inorganic electron donors have proved effective in supporting this bioprocess. Nevertheless, autotrophic Se(VI) bioreduction driven by solid inorganic electron donors is still not fully understood. This work is the first to employ elemental sulfur [S(0)] as electron donor to support Se(VI) bioreduction. A batch trial with mixed culture demonstrated the feasibility of this bioprocess, with Se(VI) removal efficiency of 92.4 ± 0.7% at an initial Se(VI) concentration of 10 mg/L within 36 h. Continuous column tests showed that increased initial concentration, flow rate, and introduction of NO₃^--N depressed Se(VI) removal. Se(VI) was mainly bioreduced to solid elemental Se with trace selenite in the effluent, while S(0) was oxidized to SO₄^2-. Enrichment of Thiobacillus, Desulfurivibrio, and Sulfuricurvum combined with upregulation of genes serA, tatC, and soxB indicated Se(VI) bioreduction was coupled to S(0) oxidation. Thiobacillus performed S(0) oxidation and Se(VI) reduction independently. Intermediate metabolites as volatile fatty acids, hydrogen and methane from S(0) oxidation were utilized by heterotrophic Se(VI) reducers for Se(VI) detoxification, indicative of microbial synergy.

Hydrodynamics- and hydrochemistry-affected microbial selenate reduction in aquifer: Performance and mechanisms

Selenate [Se(VI)] with higher content in groundwater will be harmful for human beings. Hence, effective treatment for Se(VI) in aquifer should be conducted reasonably. Microbial reduction of Se(VI) to elemental selenium with weak movability and toxicity has attracted significant attention due to its high efficiency and no secondary contamination. However, hydrodynamic and hydrochemical influences with corresponding mechanisms during Se(VI) bioreduction are still not clear. In this study, influences of flow rate, initial Se(VI) and organic concentrations, coexisting nitrate were evaluated. Se(VI) removal efficiency and capacity reached 96.42 ± 6.82% and 41.28 ± 3.41 (g/m³·d) with flow rate of 0.56 mL/min, initial Se(VI) and chemical organic demand concentrations of 10 mg/L and 400 mg/L. Dechloromonas and Pseudomonas were presumably contributed to Se(VI) reduction, with upregulated serA and tatC genes. Solid Se⁰ was identified as the final product from Se(VI) reduction. These results will be beneficial for the further comprehending of Se(VI) remediation in aquifer.

The role of natural Fe(II)-bearing minerals in chemoautotrophic chromium (VI) bio-reduction in groundwater

To date, comparatively little is known about the role of natural Fe(II)-bearing minerals in bioremediation of chromium (VI) contaminated aquifers subject to chemoautotrophic conditions. This work employed four kinds of Fe(II)-bearing minerals (pyrite, mackinawite, wustite, and magnetite) as inorganic electron donors to support Cr(VI) bio-reduction. In batch experiments, mackinawite (FeS) performed best, with Cr(VI) removal efficiency of 98.1 ± 1.21 % in 96 h. Continuous column experiments lasting 180 d implied that groundwater chemistry and hydrodynamics influenced the Cr(VI) removal process. A breakthrough study suggested that biotic and abiotic contributions to Cr(VI) reduction were 76.0 ± 1.12 % and 24.1 ± 1.43 %, respectively. Cr(VI) was reduced to insoluble Cr(III), whereas Fe(II) and S(-II) in mackinawite were finally oxidized to Fe(III) and sulfate. Mackinawite evolved progressively into pyrrhotite. High-throughput 16S rRNA gene sequencing indicated that mackinawite-driven Cr(VI) reduction was mediated through synergistic interactions of microbial consortia; i.e. autotrophs as Acidovorax synthesized volatile fatty acids as metabolic intermediates, which were consumed by Cr(VI) reducers as Geobacter. Genes encoding enzymes for S oxidation (soxB) and Cr(VI) reduction (chrA, yieF) were upregulated. Cytochrome c participating in Fe(II) oxidation increased significantly. This work advances the development of sustainable techniques for Cr(VI) polluted groundwater remediation.

Selenium Metabolism in Hemp (Cannabis sativa L.)-Potential for Phytoremediation and Biofortification

Selenium (Se) deficiency and toxicity affect over a billion people worldwide. Plants can mitigate both problems, via Se biofortification and phytoremediation. Here we explore the potential of hemp (Cannabis sativa L.) for these phytotechnologies. Field surveys in naturally seleniferous agricultural areas in Colorado, United States, found 15-25 μg of Se/g in seed and 5-10 μg of Se/g dry weight (DW) in flowers and leaves. Thus, 4 g of this hemp seed provides the U.S. recommended daily allowance of 55-75 μg of Se. In controlled greenhouse experiments, hemp seedlings grown in Turface supplied with 40-320 μM selenate showed complete tolerance up to 160 μM and accumulated up to 1300 mg of Se/kg shoot dry weight. Mature hemp grown in Turface supplied with 5-80 μM selenate was completely tolerant up to 40 μM selenate and accumulated up to 200 mg of Se/kg DW in leaves, flowers, and seeds. Synchrotron X-ray fluorescence and X-ray absorption spectroscopies of selenate-supplied hemp showed Se to accumulate mainly in the leaf vasculature and in the seed embryos, with predominant Se speciation in C-Se-C forms (57-75% in leaf and more than 86% in seeds). Aqueous seed extracts were found by liquid chromatography mass spectrometry to contain selenomethionine and methyl-selenocysteine (1:1-3 ratio), both excellent dietary Se sources. Floral concentrations of medicinal cannabidiol (CBD) and terpenoids were not affected by Se. We conclude that hemp has good potential for Se phytoremediation while producing Se-biofortified dietary products.

Distribution and chemical form of selenium in Neptunia amplexicaulis from Central Queensland, Australia

Selenium (Se), a trace element essential for human and animal biological processes, is deficient in many agricultural soils. Some extremely rare plants can naturally accumulate extraordinarily high concentrations of Se. The native legume Neptunia amplexicaulis, endemic to a small area near Richmond and Hughenden in Central Queensland, Australia, is one of the strongest Se hyperaccumulators known on Earth, with foliar concentrations in excess of 4000 μg Se g^-1 previously recorded. Here, we report on the Se distribution at a whole plant level using laboratory micro X-ray Fluorescence Microscopy (μXRF) and scanning electron microscopy (SEM-EDS), as well as on chemical forms of Se in various tissues using liquid chromatography-mass spectrometry (LC-MS) and synchrotron X-ray absorption spectroscopy (XAS). The results show that Se occurs in the forms of methyl-selenocysteine and seleno-methionine in the foliar tissues, with up to 13 600 μg Se g^-1 total in young leaves. Selenium was found to accumulate primarily in the young leaves, flowers, pods and taproot, with lower concentrations present in the fine-roots and stem and the lowest present in the oldest leaves. Trichomes were not found to accumulate Se. We postulate that Se is (re)distributed in this plant via the phloem from older leaves to newer leaves, using the taproot as the main storage organ. High concentrations of Se in the nodes (pulvini) indicate this structure may play an important a role in Se (re)distribution. The overall pattern of Se distribution was similar in a non-Se tolerant closely related species (Neptunia gracilis), although the prevailing Se concentrations were substantially lower than in N. amplexicaulis.

Selenium tolerance, accumulation, localization and speciation in a Cardamine hyperaccumulator and a non-hyperaccumulator

Cardamine violifolia (family Brassicaceae) is the first discovered selenium hyperaccumulator from the genus Cardamine with unique properties in terms of selenium accumulation, i.e., high abundance of selenolanthionine. In our study, a fully comprehensive experiment was conducted with the comparison of a non-hyperaccumulator Cardamine species, Cardamine pratensis, covering growth characteristics, chlorophyll fluorescence, spatial selenium/sulfur distribution patterns through elemental analyses (synchrotron-based X-Ray Fluorescence and ICP-OES) and speciation data through selenium K-edge micro X-ray absorption near-edge structure analysis (μXANES) and strong cation exchange (SCX)-ICP-MS. The results revealed remarkable differences in contrast to other selenium hyperaccumulators as neither Cardamine species showed evidence of growth stimulation by selenium. Also, selenite uptake was not inhibited by phosphate for either of the Cardamine species. Sulfate inhibited selenate uptake, but the two Cardamine species did not show any difference in this respect. However, μXRF derived speciation maps and selenium/sulfur uptake characteristics provided results that are similar to other formerly reported hyperaccumulator and non-hyperaccumulator Brassicaceae species. μXANES showed organic selenium, "C-Se-C", in seedlings of both species and also in mature C. violifolia plants. In contrast, selenate-supplied mature C. pratensis contained approximately half "C-Se-C" and half selenate. SCX-ICP-MS data showed evidence of the lack of selenocystine in any of the Cardamine plant extracts. Thus, C. violifolia shows clear selenium-related physiological and biochemical differences compared to C. pratensis and other selenium hyperaccumulators.

Identification and physiological comparison of plant species that show positive or negative co-occurrence with selenium hyperaccumulators

Reynolds and coworkers investigated effects of selenium hyperaccumulator plants on local vegetation. Shown is elemental distribution in Alyssum simplex.

Selenium Accumulation, Speciation and Localization in Brazil Nuts (Bertholletia excelsa H.B.K.)

More than a billion people worldwide may be selenium (Se) deficient, and supplementation with Se-rich Brazil nuts may be a good strategy to prevent deficiency. Since different forms of Se have different nutritional value, and Se is toxic at elevated levels, careful seed characterization is important. Variation in Se concentration and correlations of this element with other nutrients were found in two batches of commercially available nuts. Selenium tissue localization and speciation were further determined. Mean Se levels were between 28 and 49 mg kg⁻¹, with up to 8-fold seed-to-seed variation (n = 13) within batches. Brazil nut Se was mainly in organic form. While present throughout the seed, Se was most concentrated in a ring 1 to 2 mm below the surface. While healthy, Brazil nuts should be consumed in moderation. Consumption of one seed (5 g) from a high-Se area meets its recommended daily allowance; the recommended serving size of 30 g may exceed the allowable daily intake (400 μg) or even its toxicity threshold (1200 μg). Based on these findings, the recommended serving size may be re-evaluated, consumers should be warned not to exceed the serving size and the seed may be sold as part of mixed nuts, to avoid excess Se intake.

Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock

Watersheds are important suppliers of freshwater for human societies. Within mountainous watersheds, microbial communities impact water chemistry and element fluxes as water from precipitation events discharge through soils and underlying weathered rock, yet there is limited information regarding the structure and function of these communities. Within the East River, CO watershed, we conducted a depth-resolved, hillslope to riparian zone transect study to identify factors that control how microorganisms are distributed and their functions. Metagenomic and geochemical analyses indicate that distance from the East River and proximity to groundwater and underlying weathered shale strongly impact microbial community structure and metabolic potential. Riparian zone microbial communities are compositionally distinct, from the phylum down to the species level, from all hillslope communities. Bacteria from phyla lacking isolated representatives consistently increase in abundance with increasing depth, but only in the riparian zone saturated sediments we found Candidate Phyla Radiation bacteria. Riparian zone microbial communities are functionally differentiated from hillslope communities based on their capacities for carbon and nitrogen fixation and sulfate reduction. Selenium reduction is prominent at depth in weathered shale and saturated riparian zone sediments and could impact water quality. We anticipate that the drivers of community composition and metabolic potential identified throughout the studied transect will predict patterns across the larger watershed hillslope system.

Analysis of uranium removal capacity of anaerobic granular sludge bacterial communities under different initial pH conditions

The bacterial community of an anaerobic granular sludge associated with uranium depletion was investigated following its exposure to uranium under different initial pH conditions (pH 4.5, 5.5, and 6.5). The highest uranium removal efficiency (98.1%) was obtained for the sample with an initial pH of 6.5, which also supported the highest bacterial community richness and diversity. Venn diagrams visualized the decrease in the number of genera present in both the inoculum and the uranium-exposed biomass as the initial pH decreased from 6.5 to 4.5. Compared with the inoculum, a significant increase in the abundances of the phyla Chloroflexi and Proteobacteria was observed following uranium exposure. At initial pH conditions of 6.5 to 4.5, the proportions of the taxa Anaerolineaceae, Chryseobacterium, Acinetobacter, Pseudomonas, and Sulfurovum increased significantly, likely contributing to the observed uranium removal. Uranium exposure induced a greater level of dynamic diversification of bacterial abundances than did the initial pH difference.

Enhancement of synchronous bio-reductions of vanadium (V) and chromium (VI) by mixed anaerobic culture

The co-occurrence of toxic vanadium (V) and chromium (VI) in groundwater receives incremental attention while knowledge on their interactions in biogeochemical processes is limited, with lack of efficient removal means. This study is the first to realize synchronous bio-reductions of V(V) and Cr(VI) with high efficiency by mixed anaerobic culture. After 72-h operation, 97.0 ± 1.0% of V(V) and 99.1 ± 0.7% of Cr(VI) were removed, respectively, with initial concentration of 1 mM for both V(V) and Cr(VI). Cr(VI) bio-reduction took priority while V(V) detoxification was inhibited. V(IV) and Cr(III) were the identified reduction products, both of which could precipitate naturally. Initial Cr(VI) and acetate concentrations as well as pH affected this process significantly. High-throughput 16S rRNA gene sequencing analysis indicated the accumulation of Anaerolineaceae, Spirochaeta and Spirochaetaceae, which could contribute to V(V) and Cr(VI) bio-reductions. The new knowledge obtained in this study will facilitate understanding the biogeochemical fate of co-existing V(V) and Cr(VI) in groundwater and development of bioremediation strategy for their induced combined pollution.

Adsorption of Selenite onto Bacillus subtilis: The Overlooked Role of Cell Envelope Sulfhydryl Sites in the Microbial Conversion of Se(IV)

Microbial activities play a central role in the global cycling of selenium. Microorganisms can reduce, methylate, and assimilate Se, controlling the transport and fate of Se in the environment. However, the mechanisms controlling these microbial activities are still poorly understood. In particular, it is unknown how the negatively charged Se(IV) and Se(VI) oxyanions that dominate the aqueous Se speciation in oxidizing environments bind to negatively charged microbial cell surfaces in order to become bioavailable. Here, we show that the adsorption of selenite onto Bacillus subtilis bacterial cells is controlled by cell envelope sulfhydryl sites. Once adsorbed onto the bacteria, selenite is reduced and forms reduced organo-Se compounds (e.g., R₁S-Se-SR₂). Because sulfhydryl sites are present within cell envelopes of a wide range of bacterial species, sulfhydryl-controlled adsorption of selenite likely represents a general mechanism adopted by bacteria to make selenite bioavailable. Therefore, sulfhydryl binding of selenite likely occurs in a wide range of oxidized Se-bearing environments, and because it is followed by microbial conversion of selenite to other Se species, the process represents a crucial step in the global cycling of Se.

Imaging the Microprocesses in Biofilm Matrices

Biofilms, which are aggregates of microorganisms and extracellular matrices, widely colonize natural water bodies, wastewater treatment systems, and body tissues, and have vital roles in water purification, biofouling, and infectious diseases. Recently, multiple imaging modalities have been developed to visualize the morphological structure and material distribution within biofilms and to probe the microprocesses in biofilm matrices, including biofilm formation, transfer and metabolism of substrates, and cell-cell communication. These technologies have improved our understanding of biofilm control and the fates of substrates in biofilms. In this review, we describe the principles of various imaging techniques and discuss the advantages and limitations of each approach to characterizing microprocesses in biofilm matrices.

Selenium (IV,VI) reduction and tolerance by fungi in an oxic environment

Microbial processes are known to mediate selenium (Se) oxidation-reduction reactions, strongly influencing Se speciation, bioavailability, and transport throughout the environment. While these processes have commonly been studied in anaerobic bacteria, the role that aerobic fungi play in Se redox reactions could be important for Se-rich soil systems, dominated by microbial activity. We quantified fungal growth, aerobic Se(IV, VI) reduction, and Se immobilization and volatilization in the presence of six, metal-tolerant Ascomycete fungi. We found that the removal of dissolved Se was dependent on the fungal species, Se form (i.e., selenite or selenate), and Se concentration. All six species grew and removed dissolved Se(IV) or Se(VI) from solution, with five species reducing both oxyanions to Se(0) biominerals, and all six species removing at least 15%-20% of the supplied Se via volatilization. Growth rates of all fungi, however, decreased with increasing Se(IV,VI) concentrations. All fungi removed 85%-93% of the dissolved Se(IV) within 10 d in the presence of 0.01 mm Se(IV), although only about 20%-30% Se(VI) was removed when grown with 0.01 mm Se(VI). Fungi-produced biominerals were typically 50- to 300-nm-diameter amorphous or paracrystalline spherical Se(0) nanoparticles. Our results demonstrate that activity of common soil fungi can influence Se form and distribution, and these organisms may therefore play a role in detoxifying Se-polluted environments.

Sponge-associated bacteria mineralize arsenic and barium on intracellular vesicles

Arsenic and barium are ubiquitous environmental toxins that accumulate in higher trophic-level organisms. Whereas metazoans have detoxifying organs to cope with toxic metals, sponges lack organs but harbour a symbiotic microbiome performing various functions. Here we examine the potential roles of microorganisms in arsenic and barium cycles in the sponge Theonella swinhoei, known to accumulate high levels of these metals. We show that a single sponge symbiotic bacterium, Entotheonella sp., constitutes the arsenic- and barium-accumulating entity within the host. These bacteria mineralize both arsenic and barium on intracellular vesicles. Our results indicate that Entotheonella sp. may act as a detoxifying organ for its host.

The marine sponge Theonella swinhoei accumulates toxic arsenic and barium. Here the authors show that these toxic elements are actually accumulated and mineralized within vesicles inside bacteria that live within the sponge tissues.