Characterization of pyomelanin secreted by Shewanella sp. and their application in metal recovery

Melanin is a biopolymer with versatile structural and functional properties and diverse applications in recovering toxic chemicals from water and wastewater, biomedical imaging, and as theragnostic agent. We report the structural characterization and biosynthetic pathway of an extracellular pyomelanin secreted by a sponge-associated bacterium, Shewanella sp. (Shewanella-melanin), and their potential application in metal recovery from liquid. Pyomelanin particles of > 50 µm size were found in the culture medium within 48 h of growth, which were formed through the self-polymerization of benzoquinone molecule produced through homogentisic acid pathway. The aspC and hppD genes involved in the biosynthetic pathway of pyomelanin were detected in the whole genome sequence of Shewanella sp. The FT-IR spectra of Shewanella-melanin, at ~ 3300-3420 cm^-1 corresponding to the stretching vibration of -NH and -OH, was in good agreement with that of Sepia melanin, while its elemental composition (C/N/H/S of 29.2:8.23:6.41:1.58) was unique. Shewanella-melanin showed ~ 300 and ~ 950 times increased chelation of manganese and iron from a liquid medium supplemented with 2 mM of MnSO₄ and FeSO₄, respectively, compared to a control. The FT-IR spectrum showed the binding of metal ions to the carboxylic acid, hydroxyl, and amine groups of Shewanella-melanin. The Shewanella-melanin, with its excellent metal biosorption, could be a potential candidate for removing toxic compounds from water, in turn contributing to the fulfillment of sustainable development goal (SDG) 6.

Extracellular pollutant degradation feedback regulates intracellular electron transfer process of exoelectrogens: Strategy and mechanism

Exoelectrogens possess extraordinary degradation ability to various pollutants through extracellular electron transfer (EET). Compared with extracellular electron release process, intracellular electron transfer network is not yet fully recognized. Especially, controversy remains regarding the role of CymA, an essential electron-transfer hub of Shewanella oneidensis MR-1, in EET process. In this study, we thoroughly surveyed the intracellular transfer strategies during EET through dye decolorization. Loss of CymA severely impaired the reduction ability of S. oneidensis MR-1 to methyl orange (MO), but hardly affected the decolorization of aniline blue (AB). Complement of cymA fully restored the MO decolorization ability of ΔcymA mutant. The contribution of CymA to extracellular decolorization was subjected to MO concentrations. The defect in the decolorization ability of ΔcymA mutant was not evident at low MO concentration, but severe at high MO concentration. Further investigation revealed that EET rate determined the significance of CymA in the extracellular bioremediation by S. oneidensis MR-1. Coupled with MO concentrations increasing from 15 to 120 mg/L, the initial electron transfer rates of S. oneidensis MR-1 increased accordingly from 2.69 × 10⁴ to 11.21 × 10⁴ electrons CFU^-1 s^-1, which led to a gradual increase of the dependency_CymA. Thus, we first revealed that extracellular degradation performance could feedback regulate the intracellular electron transfer process of S. oneidensis MR-1. This work is helpful to fully understand the complex EET process of exoelectrogens and facilitates the application of exoelectrogens in bioremediation of environmental pollutants.

Flux-Balance Analysis and Mobile CRISPRi-Guided Deletion of a Conditionally Essential Gene in Shewanella oneidensis MR-1

Carbon-neutral production of valuable bioproducts is critical to sustainable development but remains limited by the slow engineering of photosynthetic organisms. Improving existing synthetic biology tools to engineer model organisms to fix carbon dioxide is one route to overcoming the limitations of photosynthetic organisms. In this work, we describe a pipeline that enabled the deletion of a conditionally essential gene from the Shewanella oneidensis MR-1 genome. S. oneidensis is a simple bacterial host that could be used for electricity-driven conversion of carbon dioxide in the future with further genetic engineering. We used Flux Balance Analysis (FBA) to model carbon and energy flows in central metabolism and assess the effects of single and double gene deletions. We modeled the growth of deletion strains under several alternative conditions to identify substrates that restore viability to an otherwise lethal gene knockout. These predictions were tested in vivo using a Mobile-CRISPRi gene knockdown system. The information learned from FBA and knockdown experiments informed our strategy for gene deletion, allowing us to successfully delete an "expected essential" gene, gpmA. FBA predicted, knockdown experiments supported, and deletion confirmed that the "essential" gene gpmA is not needed for survival, dependent on the medium used. Removal of gpmA is a first step toward driving electrode-powered CO2 fixation via RuBisCO. This work demonstrates the potential for broadening the scope of genetic engineering in S. oneidensis as a synthetic biology chassis. By combining computational analysis with a CRISPRi knockdown system in this way, one can systematically assess the impact of conditionally essential genes and use this knowledge to generate mutations previously thought unachievable.

Versatile mechanisms and enhanced strategies of pollutants removal mediated by Shewanella oneidensis: A review

The removal of environmental pollutants is important for a sustainable ecosystem and human health. Shewanella oneidensis (S. oneidensis) has diverse electron transfer pathways and can use a variety of contaminants as electron acceptors or electron donors. This paper reviews S. oneidensis's function in removing environmental pollutants, including heavy metals, inorganic non-metallic ions (INMIs), and toxic organic pollutants. S. oneidensis can mineralize o-xylene (OX), phenanthrene (PHE), and pyridine (Py) as electron donors, and also reduce azo dyes, nitro aromatic compounds (NACs), heavy metals, and iodate by extracellular electron transfer (EET). For azo dyes, NACs, Cr(VI), nitrite, nitrate, thiosulfate, and sulfite that can cross the membrane, S. oneidensis transfers electrons to intracellular reductases to catalyze their reduction. However, most organic pollutants cannot be directly degraded by S. oneidensis, but S. oneidensis can remove these pollutants by self-synthesizing catalysts or photocatalysts, constructing bio-photocatalytic systems, driving Fenton reactions, forming microbial consortia, and genetic engineering. However, the industrial-scale application of S. oneidensis is insufficient. Future research on the metabolism of S. oneidensis and interfacial reactions with other materials needs to be deepened, and large-scale reactors should be developed that can be used for practical engineering applications.

Performance and mechanisms exploration of nano zinc oxide (nZnO) on anaerobic decolorization by Shewanella oneidensis MR-1

Although the ecological safety of nanomaterials is of widespread concern, their current ambient concentrations are not yet sufficient to cause serious toxic effects. Thus, the nontoxic bioimpact of nanomaterials in wastewater treatment has attracted increasing attention. In this study, the effect of nano zinc oxide (nZnO), one of the most widely used nanomaterials, on the anaerobic biodegradation of methyl orange (MO) by Shewanella oneidensis MR-1 was comprehensively investigated. High-dosage nZnO (>0.5 mg/L) caused severe toxic stress on S. oneidensis MR-1, resulting in the decrease in decolorization efficiency. However, nZnO at ambient concentrations could act as nanostimulants and promote the anaerobic removal of MO by S. oneidensis MR-1, which should be attributed to the improvement of decolorization efficiency rather than cell proliferation. The dissolved Zn²⁺ was found to contribute to the bioeffect of nZnO on MO decolorization. Further investigation revealed that low-dosage nZnO could promote the cell viability, membrane permeability, anaerobic metabolism, as well as related gene expression, indicating that nZnO facilitated rather than inhibited the anaerobic wastewater treatment under ambient conditions. Thus, this work provides a new insight into the bioeffect of nZnO in actual environment and facilitates the practical application of nanomaterials as nanostimulants in biological process.

Enhancement of hexavalent chromium reduction by Shewanella oneidensis MR-1 in presence of copper nanoparticles via stimulating bacterial extracellular electron transfer and environmental adaptability

The bioreduction of hexavalent chromium (Cr(VI)) depends highly on bacterial activity, while the release of copper nanoparticles (Cu NPs) poses threats to microorganisms in the environment. This work demonstrated that Cr(VI) reduction efficiency of Shewanella oneidensis MR-1 was remarkably enhanced by 83.7% under 20 mg/L Cu NPs exposure. Cu NPs improved the electron migration capacity of Shewanella oneidensis MR-1 by enhancing bioelectrochemical performance and flavin mononucleotide secretion. Moreover, key genes related to extracellular electron transfer pathways, including direct electron transfer through outer-membrane proteins, flavin-mediated electron transfer, and conductive flagella, were generally upregulated under Cu NPs exposure. In addition, environmental adaptability of Shewanella oneidensis MR-1 was enhanced under Cu NPs exposure by improving environmental information processing and energy and reducing power production, promoting Cr(VI) reduction by Shewanella oneidensis MR-1. This work indicated that Cu NPs could enhance Cr(VI) reduction by Shewanella oneidensis MR-1 through regulating extracellular electron transfer and environmental adaptability.

Culture-dependent and culture-independent methods reveal microbe-clay mineral interactions by dissimilatory iron-reducing bacteria in an integral oilfield

Fe(III) may be reasonably considered as one of the most important electron acceptors in petroleum reservoir ecosystems. The microbial mineralization of clay minerals, especially montmorillonite, is also of great significance to the exploration of petroleum and gas reservoirs. The bioreduction mechanisms of iron-poor minerals in petroleum reservoirs have been poorly investigated. This study investigated the bioreduction of montmorillonite by dissimilatory iron-reducing bacteria (DIRB) in petroleum reservoirs based on culture-independent and culture-dependent methods. Microbial diversity analysis revealed that Halolactibacillus, Bacillus, Alkaliphilus, Shewanella, Clostridium, and Pseudomonas were the key genera involved in the bioreduction of Fe(III). Through the traditional culture-dependent method, most of the key genera were isolated from the samples collected from petroleum reservoirs. Traditional culture-dependent methods can be used to reveal the metabolic characteristics of microorganisms (such as iron-reduction efficiency) to further elucidate the roles of different species (B. subtilis and B. alkalitelluris) in the environment. Moreover, many species with high iron-reduction efficiencies and relatively low abundances in the samples, such as Tessaracoccus and Flaviflexus, were isolated from petroleum reservoirs for the first time. The combination of culture-dependent and culture-independent methods can be used to further the understanding of the microbial communities and the metabolic characteristics of DIRB in petroleum reservoirs. Structural alterations that occurred during the interactions of microorganisms and montmorillonite were revealed through scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and X-ray powder diffraction (XRD). The physical and chemical analysis results demonstrated that microorganisms from petroleum reservoirs can dissolve iron-poor montmorillonite and promote the release of interlayer water. The secondary minerals illite and clinoptilolite were observed in bioreduced smectite. The formation of secondary minerals was closely related to the dissolution degrees of minerals based on iron reduction.

Investigating the interaction between Shewanella oneidensis and phenazine 1-carboxylic acid in the microbial electrochemical processes

Many exoelectrogens utilize small redox mediators for extracellular electron transfer (EET). Notable examples include Shewanella species, which synthesize flavins, and Pseudomonas species, which produce phenazines. In natural and engineered environments, redox-active metabolites from different organisms coexist. The interaction between Shewanella oneidensis and phenazine 1-carboxylic acid (PCA, a representative phenazine compound) was investigated to demonstrate exoelectrogens utilizing metabolites secreted by other organisms as redox mediators. After 24 h in a reactor with and without added PCA (1 μM), the anodic current generated by Shewanella was 235 ± 11 and 51.7 ± 2.8 μA, respectively. Shewanella produced oxidative current approximately three times as high with medium containing PCA as with medium containing the same concentration of riboflavin. PCA also stimulated inward EET in Shewanella. The strong effect of PCA on EET was attributed to its enrichment at the biofilm/electrode interface. The PCA voltammetric peak heights with a Shewanella bioanode were 25-30 times higher than under abiotic conditions. The electrochemical properties of PCA were also altered by the transition from two-electron to single-electron electrochemistry, which suggests PCA was bound between the electrode and cell surface redox proteins. This behavior would benefit electroactive bacteria, which usually dwell in open systems where mediators are present in low concentrations. Like flavins, PCA can be immobilized under both bioanode and biocathode conditions but not under metabolically inactive conditions. Shewanella rapidly transfers electrons to PCA via its Mtr pathway. Compared with wild-type Shewanella, the PCA reduction ability was decreased in gene knockout mutants lacking Mtr pathway cytochromes, especially in the mutants with severely undermined electrode-reduction capacities. These strains also lost the ability to immobilize PCA, even under current-generating conditions.

Arsenic biotransformation in industrial wastewater treatment residue: Effect of co-existing Shewanella sp. ANA-3 and MR-1

Shewanella sp. ANA-3 with the respiratory arsenate reductase (ArrAB) and MR-1 with ferric reduction ability always coexist in the presence of high arsenic (As)-containing waste residue. However, their synergistic impacts on As transformation and mobility remain unclear. To identify which bacterium, ANA-3 or MR-1, dominates As mobility in the coexisting environment, we explored the As biotransformation in the industrial waste residue in the presence of Shewanella sp. ANA-3 and MR-1. The incubation results show that As(III) was the main soluble species, and strain ANA-3 dominated As mobilization. The impact of ANA-3 was weakened by MR-1, probably due to the survival competition between these two bacteria. The results of micro X-ray fluorescence and X-ray photoelectron spectroscopy analyses further reveal the pathway for ANA-3 to enhance As mobility. Strain ANA-3 almost reduced 100% surface-bound Fe(III), and consequently led to As(V) release. The dissolved As(V) was then reduced to As(III) by ANA-3. The results of this study help to understand the fate of arsenic in the subsurface and highlight the importance of the safe disposal of high As-containing industrial waste.

Interplay between arsenic and selenium biomineralization in Shewanella sp. O23S

Bacteria play crucial roles in the biogeochemical cycle of arsenic (As) and selenium (Se) as these elements are metabolized via detoxification, energy generation (anaerobic respiration) and biosynthesis (e.g. selenocysteine) strategies. To date, arsenic and selenium biomineralization in bacteria were studied separately. In this study, the anaerobic metabolism of As and Se in Shewanella sp. O23S was investigated separately and mixed, with an emphasis put on the biomineralization products of this process. Multiple analytical techniques including ICP-MS, TEM-EDS, XRD, Micro-Raman, spectrophotometry and surface charge (zeta potential) were employed. Shewanella sp. O23S is capable of reducing selenate (SeO₄^2-) and selenite (SeO₃^2-) to red Se(-S)⁰, and arsenate (AsO₄^3-) to arsenite (AsO₃^3-). The release of H₂S from cysteine led to the precipitation of AsS minerals: nanorod AsS and granular As₂S₃. When As and Se oxyanions were mixed, both As-S and Se(-S)⁰ biominerals were synthesized. All biominerals were extracellular, amorphous and presented a negative surface charge (-24 to -38 mV). Kinetic analysis indicated the following reduction yields: SeO₃^2- (90%), AsO₄^3- (60%), and SeO₄^2- (<10%). The mix of SeO₃^2- with AsO₄^3- led to a decrease in As removal to 30%, while Se reduction yield was unaffected (88%). Interestingly, SeO₄^2- incubated with AsO₄^3- boosted the Se removal (71%). The exclusive extracellular formation of As and Se biominerals might indicate an extracellular respiratory process characteristic of various Shewanella species and strains. This is the first study documenting a complex interplay between As and Se oxyanions: selenite decreased arsenate reduction, whereas arsenate stimulated selenate reduction. Further investigation needs to clarify whether Shewanella sp. O23S employs multi-substrate respiratory enzymes or separate, high affinity enzymes for As and Se oxyanion respiration.

Imaginary admittance and charge transfer resistance correlate to the physiological status of Shewanella oneidensis cultures in real time

Monitoring microbial activity is essential for industrial and environmental applications to proceed efficiently. To minimize time and labor-intensive monitoring, a new paradigm is required for in-situ, real time analysis. Since bioconversion of organics is accomplished by microorganisms through the oxidation of feedstocks linked to the reduction of electron acceptors, microorganisms can be viewed as electrochemical catalysts. In this respect, cell membranes have an electrical potential, which is analogous to a conventional capacitor and linked dynamically to cellular activity. Here we demonstrate the use of electrochemical impedance spectrometry (EIS) and cyclic voltammetry (CV) for monitoring microbial metabolic activity in real time, in-situ. The effect of organic electron donors as a function of concentration to the physiological status of strains of Shewanella oneidensis was determined. In this study, the pyomelanin overproducer (S. oneidensis ΔhmgA) and the pyomelanin deficient mutant (S. oneidensis ΔmelA) were chosen due to different surface electrochemical characteristics along with differences in oxygen utilization efficiency. CV, relative admittance, phase shift and permittivity changed with growth status and correlated with electron flow from organic carbon sources and terminal electron acceptor availability. This work offers a novel and inexpensive approach to real time monitoring with the advantage of abundant data.

Unveiling the chemotactic response and mechanism of Shewanella oneidensis MR-1 to nitrobenzene

Bioreduction by electroactive bacteria (EAB) is considered as a potential and cost-effective approach for the removal of nitroaromatic compounds (NACs). However, little is known about how the widespread EAB sense and respond to slightly soluble NACs in aquatic environments. Here, the chemotactic behaviors of Shewanella oneidensis MR-1, a model EAB, toward several NACs were examined and their underlying molecular mechanism was elucidated. S. oneidensis MR-1 was found to exhibit a strong chemotactic response to nitrobenzene (NB), but not to other selected NACs under aerobic conditions. To sense NB, this bacterium requires both the histidine kinase (CheA-3)-involved chemotactic signal transduction pathway and an inner-membrane c-type cytochrome CymA. Such a chemotactic response is mediated by an energy taxis mechanism. Additionally, external riboflavin was shown to greatly enhance the Shewanella taxis toward NB, implying a feasible way to increase the bioavailability of NACs. The present study deepens our understanding of the role of microbial chemotaxis in the removal of NACs and provides more options for the bioremediation of NAC-contaminated sites.

Mutual interaction between the secreted flavins and immobilized quinone in anaerobic removal of high-polarity aromatic compounds containing nitrogen by Shewanella sp. RQs-106

The immobilized anthraquinone-2-sulfonate (iAQS) could significantly promote anaerobic biotransformation of the contaminants. During this process, the role of flavins secreted by bacteria remains unclear. In the present study, mutual interaction between extracellular flavins and AQS-modified polyurethane foam (AQS-PUF) during the reduction of azo dye Acid Red 18 and 3-nitrobenzenesulfonate (3-NBS) was investigated. Results showed that the amount of extracellular flavins secreted by Shewanella sp. RQs-106 was positively correlated with the concentration of iAQS ranging from 10 to 100 μM. The presence of iAQS resulted in the increased concentration of extracellular and intracellular flavins, implying that iAQS could induce the synthesis and secretion of flavins. The deletion of gene bfe encoding the flavin adenine dinucleotide exporter resulted in approximately 63.8% decrease in the amount of extracellular flavins. Further analysis showed that the decreased amount of extracellular flavins could contribute to around 50.8% reduction of iAQS. Moreover, around 23.2% and 34.0% decreases were observed in AQS-PUF-mediated removal rates of AR 18 and 3-NBS by mutant lacking bfe gene, respectively, compared with that by wild type strain RQs-106. These results indicated that the secreted flavins played an important role in the bio-reduction of AQS-PUF, resulting in their contribution to AQS-PUF-mediated removals of high-polarity aromatic compounds containing nitrogen.

Accumulation and Pulse Electron Paramagnetic Resonance Spectroscopic Investigation of the 4-Oxidobenzyl Radical Generated in the Radical S-Adenosyl-l-methionine Enzyme HydG

The radical S-adenosyl-l-methionine (SAM) enzyme HydG cleaves tyrosine to generate CO and CN- ligands of the [FeFe] hydrogenase H-cluster, accompanied by the formation of a 4-oxidobenzyl radical (4-OB•), which is the precursor to the HydG p-cresol byproduct. Native HydG only generates a small amount of 4-OB•, limiting detailed electron paramagnetic resonance (EPR) spectral characterization beyond our initial EPR lineshape study employing various tyrosine isotopologues. Here, we show that the concentration of trapped 4-OB• is significantly increased in reactions using HydG variants, in which the "dangler Fe" to which CO and CN- bind is missing or substituted by a redox-inert Zn2+ ion. This allows for the detailed characterization of 4-OB• using high-field EPR and electron nuclear double resonance spectroscopy to extract its g-values and 1H/13C hyperfine couplings. These results are compared to density functional theory-predicted values of several 4-OB• models with different sizes and protonation states, with a best fit to the deprotonated radical anion configuration of 4-OB•. Overall, our results depict a clearer electronic structure of the transient 4-OB• radical and provide new insights into the radical SAM chemistry of HydG.

Enhanced Microbial Ferrihydrite Reduction by Pyrogenic Carbon: Impact of Graphitic Structures

Electron-shuttling agents such as pyrogenic carbon (PC) can mediate long-distance electron transfer and play numerous key roles in aquatic and soil biogeochemical processes. The electron-shuttling capacity of PC relies on both the surface oxygen-containing functional groups and bulk graphitic structures. Although the impacts of oxygen-containing functional groups on the electron-shuttling performance of PC are well studied, there remains insufficient understanding on the function of graphitic structures. Here, we studied the functions of PC in mediating microbial (Shewanella oneidensis MR-1) reduction of ferrihydrite, a classic and geochemically important soil redox process. The results show that PC enhanced microbial ferrihydrite reduction by 20-115% and the reduction rates increased with PC pyrolysis temperature increasing from 500 to 900 °C. For PC prepared at low temperature (500-600 °C), the electron-shuttling capacity of PC is mainly attributed to its oxygen-containing functional groups, as indicated by a 50-60% decline in the ferrihydrite reduction rate when PC was reduced under a H₂ atmosphere to remove surface oxygen-containing functional groups. In stark contrast, for PC prepared at higher temperature (700-900 °C), the formation of PC graphitic structures was enhanced, as suggested by the higher electrical conductivity; accordingly, the graphitic structure exhibits greater importance in shuttling electrons, as demonstrated by a minor decline (10-18%) in the ferrihydrite reduction rate after H₂ treatment of PC. This study provides new insights into the nonlinear and combined role of graphitic structures and oxygen-containing functional groups of PC in mediating electron transfer, where the pyrolysis temperature of PC acts as a key factor in determining the electron-shuttling pathways.

Malonyl-acyl carrier protein decarboxylase activity promotes fatty acid and cell envelope biosynthesis in Proteobacteria

Bacterial fatty acid synthesis in Escherichia coli is initiated by the condensation of an acetyl-CoA with a malonyl-acyl carrier protein (ACP) by the β-ketoacyl-ACP synthase III enzyme, FabH. E. coli ΔfabH knockout strains are viable because of the yiiD gene that allows FabH-independent fatty acid synthesis initiation. However, the molecular function of the yiiD gene product is not known. Here, we show the yiiD gene product is a malonyl-ACP decarboxylase (MadA). MadA has two independently folded domains: an amino-terminal N-acetyl transferase (GNAT) domain (MadAN) and a carboxy-terminal hot dog dimerization domain (MadAC) that encodes the malonyl-ACP decarboxylase function. Members of the proteobacterial Mad protein family are either two domain MadA (GNAT-hot dog) or standalone MadB (hot dog) decarboxylases. Using structure-guided, site-directed mutagenesis of MadB from Shewanella oneidensis, we identified Asn45 on a conserved catalytic loop as critical for decarboxylase activity. We also found that MadA, MadAC, or MadB expression all restored normal cell size and growth rates to an E. coli ΔfabH strain, whereas the expression of MadAN did not. Finally, we verified that GlmU, a bifunctional glucosamine-1-phosphate N-acetyl transferase/N-acetyl-glucosamine-1-phosphate uridylyltransferase that synthesizes the key intermediate UDP-GlcNAc, is an ACP binding protein. Acetyl-ACP is the preferred glucosamine-1-phosphate N-acetyl transferase/N-acetyl-glucosamine-1-phosphate uridylyltransferase substrate, in addition to being the substrate for the elongation-condensing enzymes FabB and FabF. Thus, we conclude that the Mad family of malonyl-ACP decarboxylases supplies acetyl-ACP to support the initiation of fatty acid, lipopolysaccharide, peptidoglycan, and enterobacterial common antigen biosynthesis in Proteobacteria.

Iron can be microbially extracted from Lunar and Martian regolith simulants and 3D printed into tough structural materials

In-situ resource utilization (ISRU) is increasingly acknowledged as an essential requirement for the construction of sustainable extra-terrestrial colonies. Even with decreasing launch costs, the ultimate goal of establishing colonies must be the usage of resources found at the destination of interest. Typical approaches towards ISRU are often constrained by the mass and energy requirements of transporting processing machineries, such as rovers and massive reactors, and the vast amount of consumables needed. Application of self-reproducing bacteria for the extraction of resources is a promising approach to reduce these pitfalls. In this work, the bacterium Shewanella oneidensis was used to reduce three different types of Lunar and Martian regolith simulants, allowing for the magnetic extraction of iron-rich materials. The combination of bacterial treatment and magnetic extraction resulted in a 5.8-times higher quantity of iron and 43.6% higher iron concentration compared to solely magnetic extraction. The materials were 3D printed into cylinders and the mechanical properties were tested, resulting in a 400% improvement in compressive strength in the bacterially treated samples. This work demonstrates a proof of concept for the on-demand production of construction and replacement parts in space exploration.

FKBP22 from the psychrophilic bacterium Shewanella sp. SIB1 selectively binds to the reduced state of insulin to prevent its aggregation

FKBP22 of a psychrophilic bacterium, Shewanella sp. SIB1 (SIB1 FKBP22), is a member of peptidyl-prolyl cis-trans isomerase (PPIase) and consists of N- and C-domains responsible for chaperone-like and PPIase catalytic activities, respectively. The chaperone-like activity of SIB1 FKBP22 was previously evidenced by its ability to prevent dithiothreitol (DTT)-induced insulin aggregation. Nevertheless, the mechanism by which this protein inhibits the aggregation remains unclear. To address this, the binding affinity of SIB1 FKBP22 to the native or reduced states of insulin was examined using surface plasmon resonance (SPR). The native and reduced states refer to insulin in the absence or DTT presence, respectively. The SPR sensorgram showed that SIB1 FKBP22 binds specifically to the reduced state of insulin, with a KD value of 37.31 ± 3.20 μM. This binding was facilitated by the N-domain, as indicated by the comparable KD values of the N-domain and SIB1 FKBP22. Meanwhile, the reduced state of insulin was found to have no affinity towards the C-domain. The KD value of SIB1 FKBP22 was slightly decreased by NaCl but was not severely affected by FK506, a specific FKBP inhibitor. Similarly, the prevention of DTT-induced aggregation by SIB1 FKBP22 was also modulated by the N-domain and was not affected by FK506. Further, the reduced and native states of insulin had no effect on the catalytic efficiency (kcat/KM) of SIB1 FKBP22 towards a peptide substrate. Nevertheless, the reduced state of insulin slightly reduced the catalytic efficiency towards refolding RNase T1, at up to 1.5-fold lower than in the absence of insulin. These results suggested that the binding event was mainly facilitated by hydrophobic interaction and was independent from its PPIase activity. Altogether, a possible mechanism by which SIB1 FKBP22 prevents DTT-induced insulin aggregation was proposed.

Outer membrane compositions enhance the rate of extracellular electron transport via cell-surface MtrC protein in Shewanella oneidensis MR-1

While cell membrane composition is critical for the function of membrane proteins, membrane modification has not been used to control the rate of extracellular electron transfer (EET) via the outer membrane protein complexes. Here, the rate of electron flow via the cell-surface redox protein, MtrC, was highly enhanced upon change in the outer membrane composition in Shewanella oneidensis MR-1. The MR-1 strain was pre-cultured at 4 °C and 30 °C to initiate differentiation of membrane composition. The whole-cell difference electrochemical assay of wild-type and mutant strains lacking MtrC suggested that the rate of EET via MtrC increased approximately 18 times at 4 °C than 30 °C. Circular dichroism spectroscopy showed that the molar exciton coupling coefficient for inter-heme interaction in MtrC increased in MR-1 at 4 °C than 30 °C. Results suggest that membrane modification may be a novel strategy for improving the efficiency of EET-based technologies.

A second riboswitch class for the enzyme cofactor NAD. RNA (NEW YORK, N.Y.) 2021;27:99-105. [PMID: 33087526 PMCID: PMC7749635 DOI: 10.1261/rna.077891.120]

A bacterial noncoding RNA motif almost exclusively associated with pnuC genes was uncovered using comparative sequence analysis. Some PnuC proteins are known to transport nicotinamide riboside (NR), which is a component of the ubiquitous and abundant enzyme cofactor nicotinamide adenine dinucleotide (NAD⁺). Thus, we speculated that the newly found "pnuC motif" RNAs might function as aptamers for a novel class of NAD⁺-sensing riboswitches. RNA constructs that encompass the conserved nucleotides and secondary structure features that define the motif indeed selectively bind NAD⁺, nicotinamide mononucleotide (NMN), and NR. Mutations that disrupt strictly conserved nucleotides of the aptamer also disrupt ligand binding. These bioinformatic and biochemical findings indicate that pnuC motif RNAs are likely members of a second riboswitch class that regulates gene expression in response to NAD⁺ binding.

Genetic Identification of Antimonate Respiratory Reductase in Shewanella sp. ANA-3

Microbial antimonate [Sb(V)] respiratory reduction is an important process regulating Sb redox transformation in the environment. However, little is known about the microbial respiratory reductase for Sb(V). Herein, we report Sb(V)-respiring reduction by Shewanella sp. ANA-3 through an arsenate respiratory reductase encoded by arrAB. Incubation experiments showed that Shewanella sp. ANA-3 mediated Sb(V)-respiring reduction, which was dependent on the cell concentration. Both protein analysis and reverse transcriptase-polymerase chain reaction results revealed that arrAB was highly expressed in Sb(V)-respiring reduction. In vivo evidence with mutants indicated that neither ANA-3-ΔarrA nor ANA-3-ΔarrB was capable of reducing Sb(V) as efficiently as the wild type, whereas complementation by the wild-type sequences of arrA and arrB rescued the mutants' ability. Our in vitro results showed that ArrAB purified by His-Tag was able to mediate Sb(V) reduction, though with much suppressed catalytic kinetics compared with As(V) reduction. The cell-concentration-dependent reduction of Sb(V) was regulated by quorum sensing via the luxS gene. This study opens a new chapter in the mechanistic understanding of microbial Sb(V) respiratory reduction.

Elevated intracellular cyclic-di-GMP level in Shewanella oneidensis increases expression of c-type cytochromes

Electrochemically active biofilms are capable of exchanging electrons with solid electron acceptors and have many energy and environmental applications such as bioelectricity generation and environmental remediation. The performance of electrochemically active biofilms is usually dependent on c-type cytochromes, while biofilm development is controlled by a signal cascade mediated by the intracellular secondary messenger bis-(3'-5') cyclic dimeric guanosine monophosphate (c-di-GMP). However, it is unclear whether there are any links between the c-di-GMP regulatory system and the expression of c-type cytochromes. In this study, we constructed a S. oneidensis MR-1 strain with a higher cytoplasmic c-di-GMP level by constitutively expressing a c-di-GMP synthase and it exhibited expected c-di-GMP-influenced traits, such as lowered motility and increased biofilm formation. Compared to MR-1 wild-type strain, the high c-di-GMP strain had a higher Fe(III) reduction rate (21.58 vs 11.88 pM of Fe(III)/h cell) and greater expression of genes that code for the proteins involved in the Mtr pathway, including CymA, MtrA, MtrB, MtrC and OmcA. Furthermore, single-cell Raman microspectroscopy (SCRM) revealed a great increase of c-type cytochromes in the high c-di-GMP strain as compared to MR-1 wild-type strain. Our results reveal for the first time that the c-di-GMP regulation system indirectly or directly positively regulates the expression of cytochromes involved in the extracellular electron transport (EET) in S. oneidensis, which would help to understand the regulatory mechanism of c-di-GMP on electricity production in bacteria.

Biosynthesis of Silver Nanoparticles Using Culture Supernatant of Shewanella sp. ARY1 and Their Antibacterial Activity

PURPOSE

In this study, silver nanoparticles (AgNPs) were biosynthesized using culture supernatant of strain Shewanella sp. ARY1, characterized and their antibacterial activity was investigated against Gram-negative bacteria Escherichia coli and Klebsiella pneumoniae.

METHODS

The strain Shewanella sp. ARY1 was isolated from river Yamuna, Delhi and used for biosynthesis of AgNPs via extracellular approach. Biosynthesized AgNPs were characterized by UV-Visible (UV-Vis) spectrophotometer, fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), energy dispersive X-ray (EDX), transmission electron microscopy (TEM) and scanning electron microscopy (SEM). Antibacterial activity of AgNPs was determined by well diffusion, broth microdilution and streaking plate assay to determine the zone of inhibition (ZOI), minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC), respectively. The effect of AgNPs on treated bacteria was investigated by electron microscopy analysis. Further, the biocompatibility of AgNPs was tested against mice erythrocytes (RBC) by hemolytic assay.

RESULTS

The UV-Vis spectral analysis revealed absorption maxima at 450 nm which confirmed the formation of AgNPs. The FTIR analysis suggested the involvement of various supernatant biomolecules, as reducing and capping agents in the synthesis of AgNPs. The XRD and EDX analysis confirmed the crystalline and metallic nature of AgNPs, respectively. The TEM and SEM analysis showed nanoparticles were spherical with an average size of 38 nm. The biosynthesized AgNPs inhibited the growth and formed a clear zone of inhibition (ZOI) against tested Gram-negative strains. The MIC and MBC were determined as 8-16 µg/mL and 32 µg/mL, respectively. Further, electron microscopy analysis of treated cells showed that AgNPs can damage the outer membrane, release of cytoplasmic contents, and alter the normal morphology of Gram-negative bacteria, leading to cell death. The hemolytic assay indicated that the biosynthesized AgNPs were biocompatible at low dose concentrations.

CONCLUSION

This study demonstrates an eco-friendly process for extracellular synthesis of AgNPs using Shewanella sp. ARY1 and these AgNPs exhibited excellent antibacterial activity, which may be used to combat Gram-negative pathogens.

Selective Promotion of Adhesion of Shewanella oneidensis on Mannose-Decorated Glycopolymer Surfaces

Using glycopolymer surfaces, we have stimulated Shewanella oneidensis bacterial colonization and induced where the bacteria attach on a molecular pattern. When adherent bacteria were rinsed with methyl α-d-mannopyranoside, the glycopolymer-functionalized surfaces retained more cells than self-assembled monolayers terminated by a single mannose unit. These results suggest that the three-dimensional multivalency of the glycopolymers both promotes and retains bacterial attachment. When the methyl α-d-mannopyranoside competitor was codeposited with the cell culture, however, the mannose-based polymer was not significantly different from bare gold surfaces. The necessity for equilibration between methyl α-d-mannopyranoside and the cell culture to remove the enhancement suggests that the retention of cells on glycopolymer surfaces is kinetically controlled and is not a thermodynamic result of the cluster glycoside effect. The MshA lectin appears to facilitate the improved adhesion observed. Our findings that the surfaces studied here can induce stable initial attachment and influence the ratio of bacterial strains on the surface may be applied to harness useful microbial communities.

Biotic dissolution of autunite under anaerobic conditions: effect of bicarbonates and Shewanella oneidensis MR1 microbial activity

Uranium is a contaminant of major concern across the US Department of Energy complex that served a leading role in nuclear weapon fabrication for half a century. In an effort to decrease the concentration of soluble uranium, tripolyphosphate injections were identified as a feasible remediation strategy for sequestering uranium in situ in contaminated groundwater at the Hanford Site. The introduction of sodium tripolyphosphate into uranium-bearing porous media results in the formation of uranyl phosphate minerals (autunite) of general formula {X_1-2[(UO₂)(PO₄)]_2-1·nH₂O}, where X is a monovalent or divalent cation. The stability of the uranyl phosphate minerals is a critical factor that determines the long-term effectiveness of this remediation strategy that can be affected by biogeochemical factors such as the presence of bicarbonates and bacterial activity. The objective of this research was to investigate the effect of bicarbonate ions present in the aqueous phase on Ca-autunite dissolution under anaerobic conditions, as well as the role of metal-reducing facultative bacterium Shewanella oneidensis MR1. The concentration of total uranium determined in the aqueous phase was in direct correlation to the concentration of bicarbonate present in the solution, and the release of Ca, U and P into the aqueous phase was non-stoichiometric. Experiments revealed the absence of an extensive biofilm on autunite surface, while thermodynamic modeling predicted the presence of secondary minerals, which were identified through microscopy. In conclusion, the dissolution of autunite under the conditions studied is susceptible to bicarbonate concentration, as well as microbial presence.