Nickel uptake and utilization by microorganisms

2-hydroxy-1- Naphthaldehyde Based Colorimetric Probe for the Simultaneous Detection of Bivalent Copper and Nickel with High Sensitivity and Selectivity

A neoteric colorimetric probe based on 2-hydroxy-1-naphthaldehyde (PMB3) was designed and synthesized for the real-time as well as on-site naked-eye detection of Cu2+/Ni2+ ions. Various physicochemical methods were employed to characterize the probe, and its colorimetric response to different metal ions was meticulously investigated. The probe, PMB3, exhibited a sensitive colorimetric response to Cu2+/Ni2+ ions among other competing metal ions, culminating in a prominent colour change from colourless to yellow. The stoichiometry of the ligand metal complexes was ascertained to be in a 1:1 ratio using Job's plot analysis, which was further corroborated by ESI-MS data. With detection limits of 4.56 µM for Cu2+ and 2.68 µM for Ni2+, the method was effectively extended to real sample analysis, ensuring propitious results that closely aligned with the actual values.

Comparative genomic analysis of nickel homeostasis in cable bacteria

BACKGROUND

Cable bacteria are filamentous members of the Desulfobulbaceae family that are capable of performing centimetre‑scale electron transport in marine and freshwater sediments. This long‑distance electron transport is mediated by a network of parallel conductive fibres embedded in the cell envelope. This fibre network efficiently transports electrical currents along the entire length of the centimetre‑long filament. Recent analyses show that these fibres consist of metalloproteins that harbour a novel nickel‑containing cofactor, which indicates that cable bacteria have evolved a unique form of biological electron transport. This nickel‑dependent conduction mechanism suggests that cable bacteria are strongly dependent on nickel as a biosynthetic resource. Here, we performed a comprehensive comparative genomic analysis of the genes linked to nickel homeostasis. We compared the genome‑encoded adaptation to nickel of cable bacteria to related members of the Desulfobulbaceae family and other members of the Desulfobulbales order.

RESULTS

Presently, four closed genomes are available for the monophyletic cable bacteria clade that consists of the genera Candidatus Electrothrix and Candidatus Electronema. To increase the phylogenomic coverage, we additionally generated two closed genomes of cable bacteria: Candidatus Electrothrix gigas strain HY10‑6 and Candidatus Electrothrix antwerpensis strain GW3‑4, which are the first closed genomes of their respective species. Nickel homeostasis genes were identified in a database of 38 cable bacteria genomes (including 6 closed genomes). Gene prevalence was compared to 19 genomes of related strains, residing within the Desulfobulbales order but outside of the cable bacteria clade, revealing several genome‑encoded adaptations to nickel homeostasis in cable bacteria. Phylogenetic analysis indicates that nickel importers, nickel‑binding enzymes and nickel chaperones of cable bacteria are affiliated to organisms outside the Desulfobulbaceae family, with several proteins showing affiliation to organisms outside of the Desulfobacterota phylum. Conspicuously, cable bacteria encode a unique periplasmic nickel export protein RcnA, which possesses a putative cytoplasmic histidine‑rich loop that has been largely expanded compared to RcnA homologs in other organisms.

CONCLUSION

Cable bacteria genomes show a clear genetic adaptation for nickel utilization when compared to closely related genera. This fully aligns with the nickel‑dependent conduction mechanism that is uniquely found in cable bacteria.

Targeting bacterial nickel transport with aspergillomarasmine A suppresses virulence-associated Ni-dependent enzymes

Microbial Ni2+ homeostasis underpins the virulence of several clinical pathogens. Ni2+ is an essential cofactor in urease and [NiFe]-hydrogenases involved in colonization and persistence. Many microbes produce metallophores to sequester metals necessary for their metabolism and starve competing neighboring organisms. The fungal metallophore aspergillomarasmine A (AMA) shows narrow specificity for Zn2+, Ni2+, and Co2+. Here, we show that this specificity allows AMA to block the uptake of Ni2+ and attenuate bacterial Ni-dependent enzymes, offering a potential strategy for reducing virulence. Bacterial exposure to AMA perturbs H2 metabolism, ureolysis, struvite crystallization, and biofilm formation and shows efficacy in a Galleria mellonella animal infection model. The inhibition of Ni-dependent enzymes was aided by Zn2+, which complexes with AMA and competes with the native nickelophore for the uptake of Ni2+. Biochemical analyses demonstrated high-affinity binding of AMA-metal complexes to NikA, the periplasmic substrate-binding protein of the Ni2+ uptake system. Structural examination of NikA in complex with Ni-AMA revealed that the coordination geometry of Ni-AMA mimics the native ligand, Ni-(L-His)2, providing a structural basis for binding AMA-metal complexes. Structure-activity relationship studies of AMA identified regions of the molecule that improve NikA affinity and offer potential routes for further developing this compound as an anti-virulence agent.

Bacterial adhesion and corrosion behavior of different pure metals induced by sulfate reducing bacteria

The corrosion behaviors of four pure metals (Fe, Ni, Mo and Cr) in the presence of sulfate reducing bacteria (SRB) were investigated in enriched artificial seawater (EASW) after 14-day incubation. Metal Fe and metal Ni experienced weight losses of 1.96 mg cm-2 and 1.26 mg cm-2, respectively. In contrast, metal Mo and metal Cr exhibited minimal weight losses, with values of only 0.05 mg cm-2 and 0.03 mg cm-2, respectively. In comparison to Mo (2.2 × 106 cells cm-2) or Cr (1.4 × 106 cells cm-2) surface, the sessile cell counts on Fe (4.0 × 107 cells cm-2) or Ni (3.1 × 107 cells cm-2) surface was higher.

Effects of heavy metals on bacterial growth parameters in degradation of phenol by an Antarctic bacterial consortium

Antarctica has often been perceived as a pristine continent until the recent few decades as pollutants have been observed accruing in the Antarctic environment. Irresponsible human activities such as accidental oil spills, waste incineration and sewage disposal are among the primary anthropogenic sources of heavy metal contaminants in Antarctica. Natural sources including animal excrement, volcanism and geological weathering also contribute to the increase of heavy metals in the ecosystem. A microbial growth model is presented for the growth of a bacterial cell consortium used in the biodegradation of phenol in media containing different metal ions, namely arsenic (As), cadmium (Cd), aluminium (Al), nickel (Ni), silver (Ag), lead (Pb) and cobalt (Co). Bacterial growth was inhibited by these ions in the rank order of Al < As < Co < Pb < Ni < Cd < Ag. Greatest bacterial growth occurred in 1 ppm Al achieving an OD600 of 0.985 and lowest in 1 ppm Ag with an OD600 of 0.090. At a concentration of 1.0 ppm, Ag had a considerable effect on the bacterial consortium, inhibiting the degradation of phenol, whereas this concentration of the other metal ions tested had no effect on degradation. The biokinetic growth model developed supports the suitability of the bacterial consortium for use in phenol degradation.

Metal selectivity and translocation mechanism characterization in proteoliposomes of the transmembrane NiCoT transporter NixA from Helicobacter pylori

Essential trace metals play key roles in the survival, replication, and virulence of bacterial pathogens. Helicobacter pylori (H. pylori), the main bacterial cause of gastric ulcers, requires Ni(ii) to colonize and persist in the acidic environment inside the stomach, exploiting the nickel-containing enzyme urease to catalyze the hydrolysis of urea to ammonia and bicarbonate and create a pH-buffered microenvironment. Urease utilizes Ni(ii) as a catalytic cofactor for its activity. In ureolytic bacteria, unique transmembrane (TM) transporters evolved to guarantee the selective uptake and efflux of Ni(ii) across cellular membranes to meet the cellular requirements. NixA is an essential Ni(ii) transporter expressed by H. pylori when the extracellular environment experiences a drop in pH. This Class I nickel-cobalt transporter of the NiCoT family catalyzes the uptake of Ni(ii) across the inner membrane from the periplasm. In this study, we characterized NixA using a platform whereby, for the first time on a NiCoT transporter, recombinantly expressed and purified NixA and key mutants in the translocation pathway have been reconstituted in artificial lipid bilayer vesicles (proteoliposomes). Fluorescent sensors responsive to Ni(ii) transport (Fluozin-3-Zn(ii)), luminal pH changes (pyranine), and membrane potential (oxonol VI) were encapsulated in the proteoliposomes lumen to monitor, in real-time, NixA transport properties and translocation mechanism. Kinetic transport analysis revealed that NixA is highly selective for Ni(ii) with no substrate promiscuity towards Co(ii), the other putative metal substrate of the NiCoT family, nor Zn(ii). NixA-mediated Ni(ii) transport exhibited a Michaelis-Menten-type saturable substrate concentration dependence, with an experimental KM, Ni(ii) = 31.0 ± 1.2 μM. Ni(ii) transport by NixA was demonstrated to be electrogenic, and metal translocation did not require a proton motive force, resulting in the generation of a positive-inside transmembrane potential in the proteoliposome lumen. Mutation analysis characterized key transmembrane residues for substrate recognition, binding, and/or transport, suggesting the presence of a three-step transmembrane translocation conduit. Taken together, these investigations reveal that NixA is a Ni(ii)-selective Class I NiCoT electrogenic uniporter. The work also provides an in vitro approach to characterize the transport properties of metal transporters responsible for Ni(ii) acquisition and extrusion in prokaryotes.

Fluorescent and chromogenic organic probes to detect group 10 metal ions: design strategies and sensing applications

Group 10 metals including Ni, Pd and Pt have been extensively applied in various essential aspects of human social life, material science, industrial manufactures, medicines and biology. The ionic forms of these metals are involved in several biologically important processes due to their strong binding capability towards different biomolecules. However, the mishandling or overuse of such metals has been linked to serious contamination of our ecological system, more specifically in soil and water bodies with acute consequences. Therefore, the detection of group 10 metal ions in biological as well as environmental samples is of huge significance from the human health point of view. Related to this, considerable efforts are underway to develop adequately efficient and facile methods to achieve their selective detection. Optical sensing of metal ions has gained increasing attention of researchers, particularly in the environmental and biological settings. Innovatively designed optical probes (fluorescent or colorimetric) are usually comprised of three basic components: an explicitly tailored receptor unit, a signalling unit and a clearly defined reporter unit. This review deals with the recent progress in the design and fabrication of fluorescent or colorimetric organic sensors for the detection of group 10 metal ions (Ni(II), Pd(II) and Pt(II)), with attention to the general aspects for design of such sensors.

The Role of Adhesion in Helicobacter pylori Persistent Colonization

Helicobacter pylori (H. pylori) has coevolved with its human host for more than 100 000 years. It can safely colonize around the epithelium of gastric glands via their specific microstructures and proteins. Unless patients receive eradication treatment, H. pylori infection is always lifelong. However, few studies have discussed the reasons. This review will focus on the adhesion of H. pylori from the oral cavity to gastric mucosa and summarize the possible binding and translocation characteristics. Adhesion is the first step for persistent colonization after the directional motility, and factors related to adhesion are necessary. Outer membrane proteins, such as the blood group antigen binding adhesin (BabA) and the sialic acid binding adhesin (SabA), play pivotal roles in binding to human mucins and cellular surfaces. And this may offer different perspectives on eradication.

Adaptive Mechanisms of Shewanella xiamenensis DCB 2-1 Metallophilicity

The dose-dependent effects of single metals (Zn, Ni, and Cu) and their combinations at steady time-actions on the cell viability of the bacteria Shewanella xiamenensis DCB 2-1, isolated from a radionuclide-contaminated area, have been estimated. The accumulation of metals by Shewanella xiamenensis DCB 2-1 in single and multi-metal systems was assessed using the inductively coupled plasma atomic emission spectroscopy. To estimate the response of the bacteria's antioxidant defense system, doses of 20 and 50 mg/L of single studied metals and 20 mg/L of each metal in their combinations (non-toxic doses, determined by the colony-forming viability assay) were used. Emphasis was given to catalase and superoxide dismutase since they form the primary line of defense against heavy metal action and their regulatory circuit of activity is crucial. The effect of metal ions on total thiol content, an indicator of cellular redox homeostasis, in bacterial cells was evaluated. Genome sequencing of Shewanella xiamenensis DCB 2-1 reveals genes responsible for heavy metal tolerance and detoxification, thereby improving understanding of the potential of the bacterial strain for bioremediation.

Enhanced Bacterial Growth by Polyelemental Glycerolate Particles

While polyelemental alloys are shown to be promising for healthcare applications, their effectiveness in promoting bacterial growth remains unexplored. In the present work, we evaluated the interaction of polyelemental glycerolate particles (PGPs) with Escherichia coli (E. coli) bacteria. PGPs were synthesized using the solvothermal route, and nanoscale random distribution of metal cations in the glycerol matrix of PGPs was confirmed. We observed 7-fold growth of E. coli bacteria upon 4 h of interaction with quinary glycerolate (NiZnMnMgSr-Gly) particles in comparison to control E. coli bacteria. Nanoscale microscopic studies on bacteria interactions with PGPs showed the release of metal cations in the bacterium cytoplasm from PGPs. The electron microscopy imaging and chemical mapping indicated bacterial biofilm formation on PGPs without causing significant cell membrane damage. The data showed that the presence of glycerol in PGPs is effective in controlling the release of metal cations, thus preventing bacterial toxicity. The presence of multiple metal cations is expected to provide synergistic effects of nutrients needed for bacterial growth. The present work provides key microscopic insights of mechanisms by which PGPs enhance biofilm growth. This study opens the door for future applications of PGPs in areas where bacterial growth is essential including healthcare, clean energy, and the food industry.

Application of microbial-induced carbonate precipitation (MICP) techniques to remove heavy metal in the natural environment: A critical review

The occurrence of imbalanced heavy metals concentration due to anthropogenic hindrances in the aquatic and terrestrial environment has become a potential risk to life after circulating through different food chains. The microbial-induced carbonate precipitation (MICP) method has gradually received great attention from global researchers but the underlying mechanism of heavy metal mineralization is not well-understood and challenging, limiting the applications in wastewater engineering. This paper reviews the metabolic pathways, mechanisms, operational factors, and mathematical/modeling approaches in the MICP process. Subsequently, the recent advancement in MICP for the remediation of heavy metal pollution is being discussed. In the follow-up, the key challenges and prospective associated with technical bottlenecks of MICP method are elaborated. The prospective study reveals that MICP technology could be efficiently used to remediate heavy metal contaminants from the natural environment in a cost-effective way and has the potential to improve soil properties while remediating heavy metal contaminated soil.

Increasing lysine level improved methanol assimilation toward butyric acid production in Butyribacterium methylotrophicum

BACKGROUND

Methanol, a promising non-food fermentation substrate, has gained increasing interest as an alternative feedstock to sugars for the bio-based production of value-added chemicals. Butyribacterium methylotrophicum, one of methylotrophic-acetogenic bacterium, is a promising host to assimilate methanol coupled with CO₂ fixation for the production of organic acids, such as butyric acid. Although the methanol utilization pathway has been identified in B. methylotrophicum, little knowledge was currently known about its regulatory targets, limiting the rational engineering to improve methanol utilization.

RESULTS

In this study, we found that methanol assimilation of B. methylotrophicum could be significantly improved when using corn steep liquor (CSL) as the co-substrate. The further investigation revealed that high level of lysine was responsible for enhanced methanol utilization. Through the transcriptome analysis, we proposed a potential mechanism by which lysine confers improved methylotrophy via modulating NikABCDE and FhuBCD transporters, both of which are involved in the uptake of cofactors essential for enzymes of methanol assimilation. The improved methylotrophy was also confirmed by overexpressing NikABCDE or FhuBCD operon. Finally, the de novo synthetic pathway of lysine was further engineered and the methanol utilization and butyric acid production of B. methylotrophicum were improved by 63.2% and 79.7%, respectively. After an optimization of cultivation medium, 3.69 g/L of butyric acid was finally achieved from methanol with a yield of 76.3%, the highest level reported to date.

CONCLUSION

This study revealed a novel mechanism to regulate methanol assimilation by lysine in B. methylotrophicum and engineered it to improve methanol bioconversion to butyric acid, culminating in the synthesis of the highest butyric acid titer reported so far in B. methylotrophicum. What's more, our work represents a further advancement in the engineering of methylotrophic-acetogenic bacterium to improve C1-compound utilization.

Effect of metals on mesophilic anaerobic digestion of strawberry extrudate in batch mode

According to recent studies, the anaerobic digestion of strawberry extrudate is a promising option with potential in the berry industry biorefinery. However, the lack and/or unbalance of concentrations of metals in some agro-industrial residues could hamper methane production during the anaerobic digestion of these kinds of wastes. In this study, a fractional factorial design was applied to screen the supplementation requirements regarding six metals (Co, Ni, Fe, Cu, Mn, and Zn) for methane production from strawberry extrudate (SE). The logistic model was used to fit the experimental data of methane production-time. It allowed identifying two different stages in the anaerobic process and obtaining the kinetic parameters for each step. Maximum methane production obtained in the first (B_max) kinetic stage, the methane production in the second stage (P), and the maximum methane production rates (R_max) concluded a statistically significant effect for Ni and Zn. The second set of experiments was carried out with Ni and Zn through a central composite design to study the concentration effect in the anaerobic digestion process of the strawberry extrudate. The parameters P and R_max demonstrated a positive interaction between Ni and Zn. Although, B_max did not prove a statistically significant effect between Ni and Zn.

How Theoretical Evaluations Can Generate Guidelines for Designing/Engineering Metalloproteins with Desired Metal Affinity and Selectivity

Almost half of all known proteins contain metal co-factors. Crucial for the flawless performance of a metalloprotein is the selection with high fidelity of the cognate metal cation from the surrounding biological fluids. Therefore, elucidating the factors controlling the metal binding and selectivity in metalloproteins is of particular significance. The knowledge thus acquired not only contributes to better understanding of the intimate mechanism of these events but, also, significantly enriches the researcher's toolbox that could be used in designing/engineering novel metalloprotein structures with pre-programmed properties. A powerful tool in aid of deciphering the physical principles behind the processes of metal recognition and selectivity is theoretical modeling of metal-containing biological structures. This review summarizes recent findings in the field with an emphasis on elucidating the major factors governing these processes. The results from theoretical evaluations are discussed. It is the hope that the physical principles evaluated can serve as guidelines in designing/engineering of novel metalloproteins of interest to both science and industry.

Assessing the effects of nickel on, e.g., Medicago sativa L. nodules using multidisciplinary approach

Industrial wastes and fertilizers can introduce excessive levels of nickel (Ni) into the environment, potentially causing threats to plants, animals, as well as human beings. However, the number of studies on the effects of Ni toxicity on nodules is fairly limited. To address this issue, the effects of increasing Ni concentration on alfalfa nodules were assessed at chemical, biochemical, and transcriptomic levels. For this purpose, plants were grown in soils supplied with Ni (control, 0 mg/kg; C1, 50 mg/kg; C2, 150 mg/kg; C3, 250 mg/kg; and C4, 500 mg/kg) for 90 days. Ni loads in leaves, roots, and nodules were monitored after the exposure period. A set of biochemical biomarkers of oxidative stress was determined in nodules including antioxidants and metal homeostasis as well as lipid peroxidation. Gene expression levels of the main targets involved in oxidative stress and metal homeostasis were assessed. Our data indicated a high concentration of Ni in leaves, roots, and nodules where values reached 25.64 ± 3.04 mg/kg, 83.23 ± 5.16 mg/kg, and 125.71 ± 4.53 mg/kg in dry weight, respectively. Moreover, a significant increase in nodule biomass was observed in plants exposed to C4 in comparison to control treatment and percentage increased by 63%. Then, lipid peroxidation increased with a rate of 95% in nodules exposed to C4. Enzymatic activities were enhanced remarkably, suggesting the occurrence of oxidative stress, with increased superoxide dismutase (SOD), glutathione reductase (GR), and ascorbate peroxidase (APX). Our results showed also a significant upregulation of SOD, GR and APX genes in nodules. Nodule homoglutathione (HGSH) levels increased with the different Ni concentrations, with a remarkable decrease of glutathione S-transferase (GST) activity and glutathione (GSH) content for the highest Ni concentration with 43% and 52% reduction, respectively. The phytochelatin (PC) and metallothionein (MT) concentrations increased in nodules, which implied the triggering of a cellular protection mechanism for coping with Ni toxicity. The results suggested that Ni promotes a drastic oxidative stress in alfalfa nodules, yet the expression of MT and PC to reduce Ni toxicity could be used as Ni stress bioindicators. Our findings provide new insights into the central role of alfalfa nodules in limiting the harmful effects of soil pollution. Therefore, nodules co-expressing antioxidant enzymes may have high phytoremediation potential.

Nickel (ii) effects on Anammox reaction: reactor performance, dehydrogenase, sludge morphology and microbial community changes

Nickel (ii) (Ni²⁺) is considered as one of the necessary trace elements in the process of Anammox culture, but it may have toxic effects at high concentration. This study explored the long-term influence of Ni²⁺ on the denitrification efficiency of Anammox bioreactors. The results showed that when the concentration of Ni²⁺ was 0.5 mg/L, the bioreactor had the highest denitrification efficiency, while the removal efficiency of ammonia nitrogen and nitrite nitrogen gradually decreased at concentrations higher than 2 mg/L, and the removal rates of ammonia nitrogen and nitrite nitrogen were 26% and 39.81% at the end of the experiment, respectively. The NRR was decreased from 7.47 kg N/m³ d to 3.28 kg N/m³ d during the whole process. The highest concentration of microbial dehydrogenase was attained in about 40 days; in the meantime, its ability to consume organic matter was also maximized. The sludge morphology was changed from granular cluster to loose flocculant with a small number of spherical and filamentous bacteria and bacilli distributed on the surface. At the end of the experiment, both species richness and community diversity were reduced, and the proportion of the dominant bacteria Candidatus Kuenenia was also decreased from 59.89% to 36.72%.

A NiCoT family metal transporter of Mycobacterium tuberculosis (Rv2856/NicT) behaves as a drug efflux pump that facilitates cross-resistance to antibiotics

Metals often act as a facilitator in the proliferation and persistence of antibiotic resistance. Efflux pumps play key roles in the co-selection of metal and antibiotic resistance. Here, we report the ability of a putative nickel/cobalt transporter (NiCoT family), Rv2856 or NicT of Mycobacterium tuberculosis (Mtb), to transport metal and antibiotics and identified some key amino acid residues that are important for its function. Ectopic expression of NicT in Escherichia coli CS109 resulted in the increase of intracellular nickel uptake. Additionally, enhanced tolerance towards several antibiotics (norfloxacin, sparfloxacin, ofloxacin, gentamicin, nalidixic acid and isoniazid) was observed with NicT overexpression in E. coli and Mycobacterium smegmatis. A comparatively lower intracellular accumulation of norfloxacin upon NicT overexpression than that of the cells without NicT indicated the involvement of NicT in an active efflux process. Although expression of NicT did not alter the sensitivity towards kanamycin, doxycycline, tetracycline, apramycin, neomycin and ethambutol, the presence of a sub-inhibitory dose of Ni²⁺ resulted in the manifestation of low-level tolerance towards these drugs. Further, substitution of four residues (H77I, D82I, H83L and D227I) in the conserved regions of NicT by isoleucine and leucine resulted in reduced to nearly complete loss of the transport function for both metals and antimicrobials. Therefore, the study suggests that nickel transporter Rv2856/NicT may actively export different drugs and the presence of nickel might drive the cross-resistance to some of the antibiotics.

Antioxidant, Protoscolicidal, Hemocompatibility, and Antibacterial Activity of Nickel Oxide Nanoparticles Synthesized by Ziziphus spina-christi

Over the past several years, the greener fabrication of metal oxide nanoparticles has attracted significant attention due to their simplicity, eco-friendliness, availability, and nontoxicity. This paper focused on the fabrication of nickel oxide nanoparticles (NiO-NPs) using the leaf extract of Ziziphus spina-christi L. and evaluating its potential biological activities. The characterization of synthesized NiO-NPs was confirmed using ultraviolet–visible spectroscopy, field emission-scanning electron microscope, energy-dispersive X-ray spectroscopy, and X-ray diffraction. Furthermore, protoscolicidal, antibacterial, and antioxidant activities and hemocompatibility of NiO-NPs were investigated. The findings revealed that the NiO-NPs were crystalline on nanoscale between 50- and 90-nm particle sizes. The NiO-NPs showed high scolicidal activity against Echinococcus granulosus. The viability of the treated protoscoleces exponentially decreased with an increase in the concentration of NiO-NPs. The NiO-NPs exhibited effective antibacterial activity against Escherichia coli and Staphylococcus aureus. NiO-NPs also possess a H2O2 scavenging activity in a dose-dependent manner. This study revealed that the Z. spina-christi L. leaf extract is an effective reducing and capping agent for the production of NiO-NPs; it showed critical biological properties. Moreover, NiO-NPs have a potent antioxidant activity and low toxicity on the erythrocytes and appear hemocompatible.

Metalation calculators for E. coli strain JM109 (DE3): Aerobic, anaerobic and hydrogen peroxide exposed cells cultured in LB media

Three web-based calculators, and three analogous spreadsheets, have been generated that predict in vivo metal occupancies of proteins based on known metal affinities. The calculations exploit estimates of the availabilities of the labile buffered pools of different metals inside a cell. Here, metal availabilities have been estimated for a strain of E. coli that is commonly used in molecular biology and biochemistry research, for example in the production of recombinant proteins. Metal availabilities have been examined for cells grown in LB medium aerobically, anaerobically and in response to H2O2 by monitoring the abundance of a selected set of metal-responsive transcripts by qPCR. The selected genes are regulated by DNA-binding metal sensors that have been thermodynamically characterised in related bacterial cells enabling gene expression to be read-out as a function of intracellular metal availabilities expressed as free energies for forming metal complexes. The calculators compare these values with the free energies for forming complexes with the protein of interest, derived from metal affinities, to estimate how effectively the protein can compete with exchangeable binding sites in the intracellular milieu. The calculators then inter-compete the different metals, limiting total occupancy of the site to a maximum stoichiometry of 1, to output percentage occupancies with each metal. In addition to making these new and conditional calculators available, an original purpose of this article was to provide a tutorial which discusses constraints of this approach and presents ways in which such calculators might be exploited in basic and applied research, and in next-generation manufacturing.

Metal Homeostasis in Pathogenic Streptococci

Streptococcus spp. are an important genus of Gram-positive bacteria, many of which are opportunistic pathogens that are capable of causing invasive disease in a wide range of populations. Metals, especially transition metal ions, are an essential nutrient for all organisms. Therefore, to survive across dynamic host environments, Streptococci have evolved complex systems to withstand metal stress and maintain metal homeostasis, especially during colonization and infection. There are many different types of transport systems that are used by bacteria to import or export metals that can be highly specific or promiscuous. Focusing on the most well studied transition metals of zinc, manganese, iron, nickel, and copper, this review aims to summarize the current knowledge of metal homeostasis in pathogenic Streptococci, and their role in virulence.

Benthic diatoms and macroinvertebrates status with relevant to sediment quality of islands shores in the Nile River, Egypt

Sediments are utilized as a marker for events that endure long enough to manifest their environmental impacts and determine the contamination levels. The purpose of the present study was to highlight the current sediment quality of four Nile islands shores by utilizing a variety of physical, chemical, and biological aspects and indices. In addition, the status of benthic diatoms and macroinvertebrates, as well as their responses to sediment variables were investigated. The metals followed a decreasing concentration order: Al > Fe > Mn > Zn > Ni ≈ Cr > Cu > Co > Pb > Cd. The outcomes of metal pollution indices revealed some localized contaminated sites, by mostly Ni and Cd. In addition, a moderate toxic risk from metals was observed for El-Keratten shores, while the sediments of El-Warraq, El-Zamalek, and El-Manial islands shores were at low toxic risk. A total of 112 diatom species belonging to 24 genera were identified in the total sample set, where most of the diatoms encountered were cosmopolitan. Metals had a remarkable impact on the composition, distribution, and dominance of diatom assemblages, but had little effect on diatom diversity, while there was a noticeable effect of grain size on diatom distribution and diversity. Thirty-four species of benthic invertebrates were identified in the collected samples from the islands shores. The dominant taxa and groups of benthic invertebrates at different islands were affected by various sediment parameters, where the levels and types of such variables differed from one species to another.

Graphical abstract

Assessment of Metal Accumulation by Arthrospira platensis and Its Adaptation to Iterative Action of Nickel Mono- and Polymetallic Synthetic Effluents

Cyanobacteria-mediated wastewater remediation is an economical, efficient, and eco-friendly technology. The present work deals with the bioaccumulation performance of Arthrospira platensis (Spirulina) grown for four cycles in a medium containing nickel mono- and polymetallic synthetic effluents. The metal uptake by spirulina biomass was evaluated using neutron activation analysis. The effects of effluents on biomass production, protein, and phycobiliprotein content were assessed. Metal accumulation in the biomass depended on the effluent composition and metal ion concentrations. Nickel accumulation in the biomass was directly proportional to its concentration in effluents, and maximum uptake (1310 mg/kg) was attained in the Ni/Cr/Fe system. In the same system, biomass accumulated 110 times more chromium and 4.7 times more iron than control. The highest accumulation of copper (2870 mg/kg) was achieved in the Ni/Cu/Zn/Mo system and zinc (1860 mg/kg)—in the Ni/Cu/Zn/Sr system. In biomass grown in the media loaded with nickel and also chromium, iron, copper, strontium, zinc, and molybdenum, a decrease in productivity (on average by 10%) during the first cycle of cultivation and moderate reduction of protein content (by 15–27%) was observed. The presence of metals in the cultivation media inhibited phycobiliprotein synthesis, especially of phycocyanin, and promoted the synthesis of allophycocyanin. The maximum reduction of phycocyanin content was 77%, and the increase of allophycocyanin content—by 45%. Arthrospira platensis may be deemed as bioremediation of nickel-polluted wastewaters of complex composition.

Sustainable approaches for nickel removal from wastewater using bacterial biomass and nanocomposite adsorbents: A review

In this article, the nickel (Ni²⁺) ions removal from the wastewater is reviewed. Adsorption is widely used to remove Ni²⁺ ions from waters and wastewaters. The usage of biomass is becoming more common for Ni²⁺ ions removal, while the commercial activated carbon from different agriculture wastes is preferred as an adsorbent for Ni²⁺ ion removal. The present review aimed to organise the available information regarding sustainable approaches for Ni²⁺ ions removal from water and wastewaters. These include adsorption by nanoparticles, bacterial biomass, and activated carbon from agriculture wastes, since they are the most common used for the Ni²⁺ ions removal. The bacterial and agricultural waste adsorbents exhibited high efficiency with a renewable source of biomass for Ni²⁺ ion removal. The biosorption capacity of the Ni²⁺ ions by the bacterial biomass range from 5.7 to 556 mg/g, while ranging from 5.8 to 150 mg/g by the activated carbon from different organic materials. The biosorption capacity of the nanocomposite adsorbents might reach to 400 mg/g. It appeared that the elimination of nickel ions need a selective biomass adsorbent such as the tolerant bacterial cells biomass which acts as a store for Ni²⁺ ion accumulations as a results for the active and passive transportation of the Ni²⁺ ions through the bacterial cell membrane.

Helicobacter pylori: an up-to-date overview on the virulence and pathogenesis mechanisms

Helicobacter pylori is an organism associated with ulcer disease and gastric cancer. The latter is one of the most prevalent malignancies and currently the fourth major cause of cancer-related deaths globally. The pathogen infects about 50% of the world population, and currently, no treatment ensures its total elimination. There has been an increase in our understanding of the pathophysiology and pathogenesis mechanisms of H. pylori over the years. H. pylori can induce several genetic alterations, express numerous virulence factors, and trigger diverse adaptive mechanisms during its adherence and colonization. For successful colonization and infection establishment, several effector proteins/toxins are released by the organism. Evidence is also available reporting spiral to coccoid transition as a unique tactic H. pylori uses to survive in the host's gastrointestinal tract (GIT). Thus, the virulence and pathogenicity of H. pylori are under the control of complex interplay between the virulence factors, host, and environmental factors. Expounding the role of the various virulence factors in H. pylori pathogenesis and clinical outcomes is crucial for vaccine development and in providing and developing a more effective therapeutic intervention. Here we critically reflect on H. pylori infection and delineate what is currently known about the virulence and pathogenesis mechanisms of H. pylori.

Bio- and phytoremediation: plants and microbes to the rescue of heavy metal polluted soils

Bio- and phytoremediation, being encouraging terms implying the use of biological systems for cleansing purposes, have risen a worthy venture toward environmental restoration in discouraging scenarios, such as the augmentation of indestructible heavy metals. Hyperaccumulating plants and heavy metal resistant microbes own mechanisms embedded in their metabolism, proteins, and genes that confer them with “super characteristics” allowing them to assimilate heavy metals in order to amend polluted soils, and when combined in a symbiotic system, these super features could complement each other and be enhanced to overpower the exposure to toxic environments. Though xenobiotic pollution has been an object of concern for decades and physicochemical procedures are commonly carried out to offset this purpose, a “live” remediation is rather chosen and looked upon for promising results. A variety of benefits have been registered from symbiotic relationships, including plants teaming up with microbes to cope down with non-biodegradable elements such as heavy metals; but a carefully maneuvered interaction might signify a greater insight toward the application of bioremediation systems. These manipulations could consist of genetic engineering and/or additional supplementation of molecules and microbes. In the present study, a contemporary connection between plants and microbes involving their controlled management is summarized in a visionary display.

Ni (II) detection by 2-amino-5-substituted-1,3,4-oxadiazole as a chemosensor using photo-physical method: Antifungal, antioxidant, DNA binding, and molecular docking studies

An oxadiazole derivative 2 was prepared by condensation reaction through cyclization of semicarbazone in the presence of bromine and the structural confirmation was supported by ¹ H and ¹³ C NMR, FT-IR spectroscopy, and LC-MS spectrometry. Its sensing ability was examined towards Ni²⁺ ion with binding constant 1.04 x 10⁵ over the other suitable metal cations (Ca²⁺ , Co²⁺ , Cr³⁺ , Ag⁺ , Pb²⁺ , Fe³⁺ , Mg²⁺ , and K⁺ ) by UV-visible and fluorescence spectroscopic studies and the minimum concentration of Ni²⁺ ion with LOD was found to be 9.4μM. Job's plot method gives the binding stoichiometry ratio of Ni²⁺ ion vs oxadiazole derivative 2 to be 2:1. Furthermore, the intercalative binding mode of oxadiazole derivative 2 with Calf Thymus DNA was supported by UV-Vis, fluorescence, viscosity, cyclic voltammetry, time-resolved fluorescence, and circular dichroism measurements. The molecular docking result gives the binding score for oxadiazole derivative 2 to be -6.5 kcal/mol, which further confirms the intercalative interaction. In addition, the anti-fungal activity of oxadiazole derivative 2 was also screened against fungal strains (C. albicans, C. glabrata, and C. tropicalis) by broth dilution and disc diffusion method. In the antioxidant studies, the oxadiazole derivative 2 showed potential scavenging activity against DPPH and H₂ O₂ free radicals.

Immunological Perspective: Helicobacter pylori Infection and Gastritis

Helicobacter pylori is a spiral-shaped gram-negative bacterium. Its infection is mainly transmitted via oral-oral and fecal-oral routes usually during early childhood. It can achieve persistent colonization by manipulating the host immune responses, which also causes mucosal damage and inflammation. H. pylori gastritis is an infectious disease and results in chronic gastritis of different severity in near all patients with infection. It may develop from acute/chronic inflammation, chronic atrophic gastritis, intestinal metaplasia, dysplasia, and intraepithelial neoplasia, eventually to gastric cancer. This review attempts to cover recent studies which provide important insights into how H. pylori causes chronic inflammation and what the characteristic is, which will immunologically explain H. pylori gastritis.

Medicinal chemistry and biomedical applications of bismuth-based compounds and nanoparticles

Bismuth as a relatively non-toxic and inexpensive metal with exceptional properties has numerous biomedical applications. Bismuth-based compounds are used extensively as medicines for the treatment of gastrointestinal disorders including dyspepsia, gastric ulcers and H. pylori infections. Recently, its medicinal application was further extended to potential treatments of viral infection, multidrug resistant microbial infections, cancer and also imaging, drug delivery and biosensing. In this review we have highlighted the unique chemistry and biological chemistry of bismuth-209 as a prelude to sections covering the unique antibacterial activity of bismuth including a description of research undertaken to date to elucidate key molecular mechanisms of action against H. pylori, the development of novel compounds to treat infection from microbes beyond H. pylori and the significant role bismuth compounds can play as resistance breakers. Furthermore we have provided an account of the potential therapeutic application of bismuth-213 in targeted alpha therapy as well as a summary of the biomedical applications of bismuth-based nanoparticles and composites. Ultimately this review aims to provide the state of the art, highlight the untapped biomedical potential of bismuth and encourage original contributions to this exciting and important field.

Transcriptomic analysis of Streptococcus agalactiae periprosthetic joint infection

Although Streptococcus agalactiae periprosthetic joint infection (PJI) is not as prevalent as staphylococcal PJI, invasive S. agalactiae infection is not uncommon. Here, RNA-seq was used to perform transcriptomic analysis of S. agalactiae PJI using fluid derived from sonication of explanted arthroplasties of subjects with S. agalactiae PJI, with results compared to those of S. agalactiae strain NEM316 grown in vitro. A total of 227 genes with outlier expression were found (164 upregulated and 63 downregulated) between PJI sonicate fluid and in vitro conditions. Functional enrichment analysis showed genes involved in mobilome and inorganic ion transport and metabolism to be most enriched. Genes involved in nickel, copper, and zinc transport, were upregulated. Among known virulence factors, cyl operon genes, encoding β-hemolysin/cytolysin, were consistently highly expressed in PJI versus in vitro. The data presented provide insight into S. agalactiae PJI pathogenesis and may be a resource for identification of novel PJI therapeutics or vaccines against invasive S. agalactiae infections.

Effect of Nickel as Stress Factor on Phenol Biodegradation by Stenotrophomonas maltophilia KB2

This study focuses on the phenol biodegradation kinetics by Stenotrophomonas maltophilia KB2 in a nickel-contaminated medium. Initial tests proved that a nickel concentration of 33.3 mg·L⁻¹ caused a cessation of bacterial growth. The experiments were conducted in a batch bioreactor in several series: without nickel, at constant nickel concentration and at varying metal concentrations (1.67–13.33 g·m⁻³). For a constant Ni²⁺ concentration (1.67 or 3.33 g·m⁻³), a comparable bacterial growth rate was obtained regardless of the initial phenol concentration (50–300 g·m⁻³). The dependence µ = f (S₀) at constant Ni²⁺ concentration was very well described by the Monod equations. The created varying nickel concentrations experimental database was used to estimate the parameters of selected mathematical models, and the analysis included different methods of determining metal inhibition constant K_IM. Each model showed a very good fit with the experimental data (R² values were higher than 0.9). The best agreement (R² = 0.995) was achieved using a modified Andrews equation, which considers the metal influence and substrate inhibition. Therefore, kinetic equation parameters were estimated: µ_max = 1.584 h⁻¹, K_S = 185.367 g·m⁻³, K_IS = 106.137 g·m⁻³, K_IM = 1.249 g·m⁻³ and n = 1.0706.

The Microbiology of Metal Mine Waste: Bioremediation Applications and Implications for Planetary Health

Mine wastes pollute the environment with metals and metalloids in toxic concentrations, causing problems for humans and wildlife. Microorganisms colonize and inhabit mine wastes, and can influence the environmental mobility of metals through metabolic activity, biogeochemical cycling and detoxification mechanisms. In this article we review the microbiology of the metals and metalloids most commonly associated with mine wastes: arsenic, cadmium, chromium, copper, lead, mercury, nickel and zinc. We discuss the molecular mechanisms by which bacteria, archaea, and fungi interact with contaminant metals and the consequences for metal fate in the environment, focusing on long-term field studies of metal-impacted mine wastes where possible. Metal contamination can decrease the efficiency of soil functioning and essential element cycling due to the need for microbes to expend energy to maintain and repair cells. However, microbial communities are able to tolerate and adapt to metal contamination, particularly when the contaminant metals are essential elements that are subject to homeostasis or have a close biochemical analog. Stimulating the development of microbially reducing conditions, for example in constructed wetlands, is beneficial for remediating many metals associated with mine wastes. It has been shown to be effective at low pH, circumneutral and high pH conditions in the laboratory and at pilot field-scale. Further demonstration of this technology at full field-scale is required, as is more research to optimize bioremediation and to investigate combined remediation strategies. Microbial activity has the potential to mitigate the impacts of metal mine wastes, and therefore lessen the impact of this pollution on planetary health.

Nickel stress-tolerance in plant-bacterial associations

Nickel (Ni) is an essential element for plant growth and is a constituent of several metalloenzymes, such as urease, Ni-Fe hydrogenase, Ni-superoxide dismutase. However, in high concentrations, Ni is toxic and hazardous to plants, humans and animals. High levels of Ni inhibit plant germination, reduce chlorophyll content, and cause osmotic imbalance and oxidative stress. Sustainable plant-bacterial native associations are formed under Ni-stress, such as Ni hyperaccumulator plants and rhizobacteria showed tolerance to high levels of Ni. Both partners (plants and bacteria) are capable to reduce the Ni toxicity and developed different mechanisms and strategies which they manifest in plant-bacterial associations. In addition to physical barriers, such as plants cell walls, thick cuticles and trichomes, which reduce the elevated levels of Ni entrance, plants are mitigating the Ni toxicity using their own antioxidant defense mechanisms including enzymes and other antioxidants. Bacteria in its turn effectively protect plants from Ni stress and can be used in phytoremediation. PGPR (plant growth promotion rhizobacteria) possess various mechanisms of biological protection of plants at both whole population and single cell levels. In this review, we highlighted the current understanding of the bacterial induced protective mechanisms in plant-bacterial associations under Ni stress.

Naphthyridine derived colorimetric and fluorescent turn off sensors for Ni2+ in aqueous media

Highly selective and sensitive 2,7-naphthyridine based colorimetric and fluorescence "Turn Off" chemosensors (L1-L4) for detection of Ni2+ in aqueous media are reported. The receptors (L1-L4) showed a distinct color change from yellow to red by addition of Ni2+ with spectral changes in bands at 535-550 nm. The changes are reversible and pH independent. The detection limits for Ni2+ by (L1-L4) are in the range of 0.2-0.5 µM by UV-Visible data and 0.040-0.47 µM by fluorescence data, which is lower than the permissible value of Ni2+ (1.2 µM) in drinking water defined by EPA. The binding stoichiometries of L1-L4 for Ni2+ were found to be 2:1 through Job's plot and ESI-MS analysis. Moreover the receptors can be used to quantify Ni2+ in real water samples. Formation of test strips by the dip-stick method increases the practical applicability of the Ni2+ test for "in-the-field" measurements. DFT calculations and AIM analyses supported the experimentally determined 2:1 stoichiometries of complexation. TD-DFT calculations were performed which showed slightly decreased FMO energy gaps due to ligand-metal charge transfer (LMCT).

Deriving Nickel (Ni(II)) and Chromium (Cr(III)) Based Environmentally Safe Olivine Guidelines for Coastal Enhanced Silicate Weathering

Enhanced silicate weathering (ESW) by spreading finely ground silicate rock along the coastal zone to remove atmospheric carbon dioxide (CO₂) is a proposed climate change mitigation technique. The abundant and fast-dissolving mineral olivine has received the most attention for this application. However, olivine contains nickel (Ni) and chromium (Cr), which may pose a risk to marine biota during a gigaton-scale ESW application. Herein we derive a first guideline for coastal olivine dispersal based on existing marine environmental quality standards (EQS) for Ni and Cr. Results show that benthic biota are at the highest risk when olivine and its associated trace metals are mixed in the surface sediment. Specifically, depending on local sedimentary Ni concentrations, 0.059-1.4 kg of olivine m^-2 of seabed could be supplied without posing risks for benthic biota. Accordingly, globally coastal ESW could safely sequester only 0.51-37 Gt of CO₂ in the 21st century. On the basis of current EQS, we conclude that adverse environmental impacts from Ni and Cr release could reduce the applicability of olivine in coastal ESW. Our findings call for more in-depth studies on the potential toxicity of olivine toward benthic marine biota, especially in regard to bioavailability and metal mixture toxicity.

Functions of elements in soil microorganisms

The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.

Sustainable approaches for removal of cephalexin antibiotic from non-clinical environments: A critical review

In this article, the removal of cephalexin (CFX) antibiotic from non-clinical environment is reviewed. Adsorption and photocatalytic degradation techniques are widely used to remove CFX from waters and wastewaters, the combination of these methods is becoming more common for CFX removal. The treatment methods of CFX has not been reviewed before, the present article aim is to organize the scattered available information regarding sustainable approaches for CFX removal from non-clinical environment. These include adsorption by nanoparticles, bacterial biomass, biodegradation by bacterial enzymes and the photocatalysis using different catalysts and Photo-Fenton photocatalysis. The metal-organic frameworks (MOFs) appeared to have high potential for CFX degradation. It is evident from the recently papers reviewed that the effective methods could be used in place of commercial activated carbon. The widespread uses of photocatalytic degradation for CFX remediation are strongly recommended due to their engineering applicability, technical feasibility, and high effectiveness. The adsorption capacity of the CFX is ranging from 7 mg CFX g^-1 of activated carbon nanoparticles to 1667 mg CFX g^-1 of Nano-zero-valent iron from Nettle. In contrast, the photo-degradation was 45% using Photo-Fenton while has increased to 100% using heterogeneous photoelectro-Fenton (HPEF) with UVA light using chalcopyrite catalyst.

Nickel in terrestrial biota: Comprehensive review on contamination, toxicity, tolerance and its remediation approaches

Nickel (Ni) has been a subject of interest for environmental, physiological, biological scientists due to its dual effect (toxicity and essentiality) in terrestrial biota. In general, the safer limit of Ni is 1.5 μg g^-1 in plants and 75-150 μg g^-1 in soil. Litreature review indicates that Ni concentrations have been estimated up to 26 g kg^-1 in terrestrial, and 0.2 mg L^-1 in aquatic resources. In case of vegetables and fruits, mean Ni content has been reported in the range of 0.08-0.26 and 0.03-0.16 mg kg^-1. Considering, Ni toxicity and its potential health hazards, there is an urgent need to find out the suitable remedial approaches. Plant vascular (>80%) and cortical (<20%) tissues are the major sequestration site (cation exchange) of absorbed Ni. Deciphering molecular mechanisms in transgenic plants have immense potential for enhancing Ni phytoremediation and microbial remediation efficiency. Further, it has been suggested that integrated bioremediation approaches have a potential futuristic path for Ni decontamination in natural resources. This systematic review provides insight on Ni effects on terrestrial biota including human and further explores its transportation, bioaccumulation through food chain contamination, human health hazards, and possible Ni remediation approaches.

Microbial Community Composition Correlates with Metal Sorption in an Ombrotrophic Boreal Bog: Implications for Radionuclide Retention

Microbial communities throughout the 6.5 m depth profile of a boreal ombrotrophic bog were characterized using amplicon sequencing of archaeal, fungal, and bacterial marker genes. Microbial populations and their relationship to oxic and anoxic batch sorption of radionuclides (using radioactive tracers of I, Se, Cs, Ni, and Ag) and the prevailing metal concentrations in the natural bog was investigated. The majority of the detected archaea belonged to the Crenarchaeota, Halobacterota, and Thermoplasmatota, whereas the fungal communities consisted of Ascomycota, Basidiomycota, and unclassified fungi. The bacterial communities consisted mostly of Acidobacteriota, Proteobacteria, and Chloroflexi. The occurrence of several microbial genera were found to statistically significantly correlate with metal concentrations as well as with Se, Cs, I, and Ag batch sorption data. We suggest that the metal concentrations of peat, gyttja, and clay layers affect the composition of the microbial populations in these nutrient-low conditions and that particularly parts of the bacterial and archaeal communities tolerate high concentrations of potentially toxic metals and may concurrently contribute to the total retention of metals and radionuclides in this ombrotrophic environment. In addition, the varying metal concentrations together with chemical, mineralogical, and physical factors may contribute to the shape of the total archaeal and bacterial populations and most probably shifts the populations for more metal resistant genera.

Halogen content relative to the chemical and biochemical composition of fifteen marine macro and micro algae: nutritional value, energy supply, antioxidant potency, and health risk assessment

Marine algae have made a strong contribution to global food security in the future. This study is the first report describing the concentration, pathways, and interactions of halogens in 15 species of marine algae collected from the Eastern Harbor in Alexandria, Egypt, relative to 22 key variables. The relationship between halogen content and chemical and biochemical parameters was studied through multivariate analysis. Among all the tested algae, the iodine content was the lowest (2.53-3.00 μg/g). The range of fluoride and chloride in macroalgae (1.12-1.70 and 0.10-0.46 mg/g) was smaller than that of microalgae (0.10-0.46 and 1.48-3.17 mg/g). The bromide content in macroalgae (0.36-5.45 mg/g) was higher than that in microalgae (0.40-0.76 mg/g). The halogen content in macroalgae was arranged in the order of Br > F > Cl > I. In addition, the biochemical parameters such as carbohydrates, proteins, lipids, and certain heavy metals (Fe, Zn, Cu, Mn, Pb, Ni, Co, Cd, and Cr) were determined. Calories, energy, total antioxidant activity (TAC), K/Na, and ion quotient amounts were estimated. The results showed that the green seaweed species had the highest TAC content. In most of the studied algal species, the calculated ion quotient referred to their likelihood of overcoming high blood pressure. The estimated daily intake (EDI) of algae showed no adverse effects on human health. Most of the research variables are below the acceptable WHO/FAO level. Generally, the calorie content of the selected algae is less than 2 kcal, which makes the algae considered an alternative source of healthy food to reduce obesity.Graphical abstract.

Functional Changes of the Community of Microbes With Ni-Dependent Enzyme Genes Accompany Adaptation of the Ruminal Microbiome to Urea-Supplemented Diets

Urea is an inexpensive non-protein nitrogen source commonly supplemented to the diets of ruminants. It is cleaved to ammonia by bacterial ureases, which require Ni as a catalyst for ureolysis. The key event in the changes of the ruminal microbiome after urea supplementation remains unknown. We have therefore investigated changes in the ruminal microbiome and its community with Ni-dependent enzyme genes following urea supplementation and analyzed the associations of rumen environmental factors, including fermentation variables and Ni concentrations, with the compositional and functional changes of these communities. We found that urea supplementation increased urease activity and the concentrations of ammonia and Ni, and tended to increase concentrations of short chain fatty acids and acetate, whereas it decreased rumen pH and the L-/D-lactate ratio. With standards for genome completeness >60% and strain heterogeneity <10%, 20 bacterial species containing five Ni-dependent enzyme genes were detected in the metagenome sequences. For the five Ni-dependent enzyme genes, urea supplementation increased the relative abundances of genes of urease and acetyl-CoA synthase, whereas it decreased the relative abundances of genes of glyoxalase I, [NiFe]-hydrogenase, and lactate racemase. For the 20 microbes with Ni-dependent enzyme genes, urea supplementation increased the relative abundances of five bacteria exhibiting high capacities for the utilization of hemicellulose and pectin for butyrate and fatty acid biosynthesis. For the ruminal microbiome, urea supplementation increased the metagenomic capacities for hemicellulose and pectin degradation, butyrate generation, fatty acid biosynthesis, and carbon fixation, whereas it decreased the metagenomic capacities for starch degradation, propionate generation, and sulfur and nitrogen metabolism. Constrained correspondence analysis identified rumen ammonia and Ni concentrations as likely driving factors in the reshaping of the ruminal microbiome and, together with pH, of the community of microbes with Ni-dependent enzyme genes. Thus, the functional change of the latter community is probably an important event in the adaptation of the ruminal microbiome to urea-supplemented diets. This result provides a new perspective for the understanding of the effects of urea supplementation on rumen fermentation.

Bioinformatics of Metalloproteins and Metalloproteomes

Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, function, and evolution in nature. This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life. We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases. Furthermore, we discuss the latest research progress in comparative genomics of several important metals in both prokaryotes and eukaryotes, which demonstrates divergent and dynamic evolutionary patterns of different metalloprotein families and metalloproteomes. Overall, bioinformatic studies of metalloproteins provide a foundation for systematic understanding of trace metal utilization in all three domains of life.

Efficient Photoelectron Capture by Ni Decoration in Methanosarcina barkeri-CdS Biohybrids for Enhanced Photocatalytic CO2-to-CH4 Conversion

Semi-artificial photosynthesis (biohybrid) provides an intriguing opportunity for efficient CO₂-to-CH₄ conversion. However, creating a desirable semiconductor in biohybrids remains a great challenge. Here, by doping Ni into CdS nanoparticles, we have successfully developed the Methanosarcina barkeri-Ni:CdS biohybrids. The CH₄ yield by the M. barkeri-Ni_(0.75%):CdS biohybrids was approximately 250% higher than that by the M. barkeri-CdS biohybrids. The suitable Ni dopants serve as an effective electron sink, which accelerates the photoelectron transfer in biohybrids. In addition, Ni doping changes the metabolic status of M. barkeri and results in a higher expression of a series of proteins for electron transfer, energy conversion, and CO₂ fixation. These increased proteins can promote the photoelectron capture by M. barkeri and injection into cells, which trigger a higher intracellular reduction potential to drive the reduction of CO₂ to CH₄. Our discovery will offer a promising strategy for the optimization of biohybrids in the solar-to-chemical conversion.

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M. barkeri-Ni:CdS biohybrids were successfully developed for CO₂ reduction

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A highest QE of 2.08% was achieved by the M. barkeri-Ni_(0.75%):CdS biohybrids

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Ni dopants effectively suppressed the electron-hole recombination in biohybrids

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Ni doping changed the metabolic status of M. barkeri in biohybrids

Investigating the microbial-influenced corrosion of UNS S32750 stainless-steel base alloy and weld seams by biofilm-forming marine bacterium Macrococcus equipercicus

This study investigates the microbial-influenced corrosion of UNS S32750 super-duplex stainless-steel joints fabricated using different welding methods. Herein, the samples were introduced into a medium inoculated with Macrococcus equipercicus isolated from a marine environment. Confocal laser scanning microscopy and atomic force microscopy were used to characterise the topography and formation of pits in the corroded samples, respectively. Potentiodynamic polarisation studies were conducted on both the base alloy and weld seams exposed for 30 and 60 days in the experimental system inoculated with M. equipercicus and un-inoculated system. Results indicate that the thickness of the biofilm formed due to this bacterium increased and became heterogeneous with an increase in the exposure time, thereby resulting in micro-pits. Bacterial colonisation was observed in all the coupons after exposure to the inoculated medium. Although micro-pits were observed in all the coupons, the base metal and flux-cored arc weld seams showed highest sensitivity to bacterial attack.