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Angius F, Cremers G, Frank J, Witkowski C, Pol A, van Alen TA, Jetten MSM, Op den Camp HJM, Berben T. Gene-centered metagenome analysis of Vulcano Island soil (Aeolian archipelago, Italy) reveals diverse microbial key players in methane, hydrogen and sulfur cycles. Antonie Van Leeuwenhoek 2024; 117:94. [PMID: 38954064 PMCID: PMC11219375 DOI: 10.1007/s10482-024-01995-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024]
Abstract
The Aeolian archipelago is known worldwide for its volcanic activity and hydrothermal emissions, of mainly carbon dioxide and hydrogen sulfide. Hydrogen, methane, and carbon monoxide are minor components of these emissions which together can feed large quantities of bacteria and archaea that do contribute to the removal of these notorious greenhouse gases. Here we analyzed the metagenome of samples taken from the Levante bay on Vulcano Island, Italy. Using a gene-centric approach, the hydrothermal vent community appeared to be dominated by Proteobacteria, and Sulfurimonas was the most abundant genus. Metabolic reconstructions highlight a prominent role of formaldehyde oxidation and the reverse TCA cycle in carbon fixation. [NiFe]-hydrogenases seemed to constitute the preferred strategy to oxidize H2, indicating that besides H2S, H2 could be an essential electron donor in this system. Moreover, the sulfur cycle analysis showed a high abundance and diversity of sulfate reduction genes underpinning the H2S production. This study covers the diversity and metabolic potential of the microbial soil community in Levante bay and adds to our understanding of the biogeochemistry of volcanic ecosystems.
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Affiliation(s)
- Federica Angius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Geert Cremers
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jeroen Frank
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Caitlyn Witkowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
- School of Earth Sciences, Wills Memorial Building, University of Bristol, Queens Road, Clifton, BS8 1RJ, UK
| | - Arjan Pol
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Theo A van Alen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Tom Berben
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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2
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Coimbra C, Branco R, da Silva PSP, Paixão JA, Martins JMF, Spadini L, Morais PV. Yttrium immobilization through biomineralization with phosphate by the resistant strain Mesorhizobium qingshengii J19. J Appl Microbiol 2024; 135:lxae156. [PMID: 38925658 DOI: 10.1093/jambio/lxae156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 06/28/2024]
Abstract
AIMS Yttrium (Y) holds significant industrial and economic importance, being listed as a critical element on the European list of critical elements, thus emphasizing the high priority for its recovery. Bacterial strategies play a crucial role in the biorecovery of metals, offering a promising and environmentally friendly approach. Therefore, gaining a comprehensive understanding of the underlying mechanisms behind bacterial resistance, as well as the processes of bioaccumulation and biotransformation, is of paramount importance. METHODS AND RESULTS A total of 207 Alphaproteobacteria strains from the University of Coimbra Bacteria Culture Collection were tested for Y-resistance. Among these, strain Mesorhizobium qingshengii J19 exhibited high resistance (up to 4 mM Y) and remarkable Y accumulation capacity, particularly in the cell membrane. Electron microscopy revealed Y-phosphate interactions, while X-ray diffraction identified Y(PO3)3·9H2O biocrystals produced by J19 cells. CONCLUSION This study elucidates Y immobilization through biomineralization within phosphate biocrystals using M. qingshengii J19 cells.
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Affiliation(s)
- Carina Coimbra
- University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, ARISE, Department of Life Sciences, 3000-456 Coimbra, Portugal
| | - Rita Branco
- University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, ARISE, Department of Life Sciences, 3000-456 Coimbra, Portugal
| | - Pedro S P da Silva
- University of Coimbra, CFisUC, Department of Physics, 3004-516 Coimbra, Portugal
| | - José A Paixão
- University of Coimbra, CFisUC, Department of Physics, 3004-516 Coimbra, Portugal
| | - Jean M F Martins
- Univ. Grenoble Alpes, CNRS, IRD, Grenoble-INP, IGE, 38000 Grenoble, France
| | - Lorenzo Spadini
- Univ. Grenoble Alpes, CNRS, IRD, Grenoble-INP, IGE, 38000 Grenoble, France
| | - Paula V Morais
- University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, ARISE, Department of Life Sciences, 3000-456 Coimbra, Portugal
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3
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Samanta D, Rauniyar S, Saxena P, Sani RK. From genome to evolution: investigating type II methylotrophs using a pangenomic analysis. mSystems 2024; 9:e0024824. [PMID: 38695578 PMCID: PMC11237726 DOI: 10.1128/msystems.00248-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/04/2024] [Indexed: 06/19/2024] Open
Abstract
A comprehensive pangenomic approach was employed to analyze the genomes of 75 type II methylotrophs spanning various genera. Our investigation revealed 256 exact core gene families shared by all 75 organisms, emphasizing their crucial role in the survival and adaptability of these organisms. Additionally, we predicted the functionality of 12 hypothetical proteins. The analysis unveiled a diverse array of genes associated with key metabolic pathways, including methane, serine, glyoxylate, and ethylmalonyl-CoA (EMC) metabolic pathways. While all selected organisms possessed essential genes for the serine pathway, Methylooceanibacter marginalis lacked serine hydroxymethyltransferase (SHMT), and Methylobacterium variabile exhibited both isozymes of SHMT, suggesting its potential to utilize a broader range of carbon sources. Notably, Methylobrevis sp. displayed a unique serine-glyoxylate transaminase isozyme not found in other organisms. Only nine organisms featured anaplerotic enzymes (isocitrate lyase and malate synthase) for the glyoxylate pathway, with the rest following the EMC pathway. Methylovirgula sp. 4MZ18 stood out by acquiring genes from both glyoxylate and EMC pathways, and Methylocapsa sp. S129 featured an A-form malate synthase, unlike the G-form found in the remaining organisms. Our findings also revealed distinct phylogenetic relationships and clustering patterns among type II methylotrophs, leading to the proposal of a separate genus for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129. This pangenomic study unveils remarkable metabolic diversity, unique gene characteristics, and distinct clustering patterns of type II methylotrophs, providing valuable insights for future carbon sequestration and biotechnological applications. IMPORTANCE Methylotrophs have played a significant role in methane-based product production for many years. However, a comprehensive investigation into the diverse genetic architectures across different genera of methylotrophs has been lacking. This study fills this knowledge gap by enhancing our understanding of core hypothetical proteins and unique enzymes involved in methane oxidation, serine, glyoxylate, and ethylmalonyl-CoA pathways. These findings provide a valuable reference for researchers working with other methylotrophic species. Furthermore, this study not only unveils distinctive gene characteristics and phylogenetic relationships but also suggests a reclassification for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129 into separate genera due to their unique attributes within their respective genus. Leveraging the synergies among various methylotrophic organisms, the scientific community can potentially optimize metabolite production, increasing the yield of desired end products and overall productivity.
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Affiliation(s)
- Dipayan Samanta
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
| | - Shailabh Rauniyar
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
| | - Priya Saxena
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
| | - Rajesh K Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
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4
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Chen Y, Su Y, Han J, Chen C, Fan H, Zhang C. Synthetic Mn 3Ce 2O 5-Cluster Mimicking the Oxygen-Evolving Center in Photosynthesis. CHEMSUSCHEM 2024:e202401031. [PMID: 38829180 DOI: 10.1002/cssc.202401031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
The photosynthetic oxygen-evolving center (OEC) is a unique Mn4CaO5-cluster that catalyses water splitting into electrons, protons, and dioxygen. Precisely structural and functional mimicking of the OEC is a long-standing challenge and pressingly needed for understanding the structure-function relationship and catalytic mechanism of O-O bond formation. Herein we report two simple and robust artificial Mn3Ce2O5-complexes that display a remarkable structural similarity to the OEC in regarding of the ten-atom core (five metal ions and five oxygen bridges) and the alkyl carboxylate peripheral ligands. This Mn3Ce2O5-cluster can catalyse the water-splitting reaction on the surface of ITO electrode. These results clearly show that cerium can structurally and functionally replace both calcium and manganese in the cluster. Mass spectroscopic measurements demonstrate that the oxide bridges in the cluster are exchangeable and can be rapidly replaced by the isotopic oxygen of H2 18O in acetonitrile solution, which supports that the oxide bridge(s) may serve as the active site for the formation of O-O bond during the water-splitting reaction. These results would contribute to our understanding of the structure-reactivity relationship of both natural and artificial clusters and shed new light on the development of efficient water-splitting catalysts in artificial photosynthesis.
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Affiliation(s)
- Yang Chen
- Beijing National Laboratory for Molecular Sciences and Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yao Su
- Beijing National Laboratory for Molecular Sciences and Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juanjuan Han
- Center for Physicochemical Analysis and Measurement, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Changhui Chen
- Beijing National Laboratory for Molecular Sciences and Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Hongjun Fan
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Chunxi Zhang
- Beijing National Laboratory for Molecular Sciences and Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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5
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Rabbani M, Taqi Rabbani M, Muthoni F, Sun Y, Vahidi E. Advancing phytomining: Harnessing plant potential for sustainable rare earth element extraction. BIORESOURCE TECHNOLOGY 2024; 401:130751. [PMID: 38685517 DOI: 10.1016/j.biortech.2024.130751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Rare earth elements (REEs) are pivotal for advanced technologies, driving a surge in global demand. Import dependency on clean energy minerals raises concerns about supply chain vulnerabilities and geopolitical risks. Conventional REEs productionis resource-intensive and environmentally harmful, necessitating a sustainable supply approach. Phytomining (agromining) utilizes plants for eco-friendly REE extraction, contributing to the circular economy and exploiting untapped metal resources in enriched soils. Critical parameters like soil pH, Casparian strip, and REE valence influence soil and plant uptake bioavailability. Hyperaccumulator species efficiently accumulate REEs, serving as energy resources. Despite a lack of a comprehensive database, phytomining exhibits lower environmental impacts due to minimal chemical usage and CO2 absorption. This review proposes phytomining as a system for REEs extraction, remediating contaminated areas, and rehabilitating abandoned mines. The phytomining of REEs offers a promising avenue for sustainable REEs extraction but requires technological advancements to realize its full potential.
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Affiliation(s)
- Mohsen Rabbani
- Department of Mining and Metallurgical Engineering, Mackay School of Earth Sciences and Engineering, University of Nevada, Reno, USA
| | | | - Frida Muthoni
- Department of Mining and Metallurgical Engineering, Mackay School of Earth Sciences and Engineering, University of Nevada, Reno, USA
| | - Ying Sun
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ehsan Vahidi
- Department of Mining and Metallurgical Engineering, Mackay School of Earth Sciences and Engineering, University of Nevada, Reno, USA.
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6
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Soleimanifar M, Rodriguez-Freire L. Cerium oxide and neodymium oxide phytoextraction by ryegrass in bioenhanced hydroponic environments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123978. [PMID: 38615839 DOI: 10.1016/j.envpol.2024.123978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/29/2024] [Accepted: 04/12/2024] [Indexed: 04/16/2024]
Abstract
Sustainable technologies for the recovery of rare earth elements (REE) from waste need to be developed to decrease the volume of ore mining extractions and its negative environmental consequences, while simultaneously restoring previously impacted lands. This is critical due to the extensive application of REE in everyday life from electronic devices to energy and medical technologies, and the dispersed distribution of REE resources in the world. REE recovery by plants has been previously studied but the feasibility of REE phytoextraction from a poorly soluble solid phase (i.e., nanoparticles) by different plant species has been rarely investigated. In this study, the effect of biostimulation and bioaugmentation on phytorecovery of REE nanoparticles (REE-NP) was investigated by exposing ryegrass seeds to REE-NP in hydroponic environments. This was studied in two sets of experiments: bioaugmentation (using CeO2 nanoparticles and Methylobacterium extorquens AM1 pure culture), and biostimulation (using CeO2 or Nd2O3 nanoparticles and endogenous microorganisms). Addition of M. extorquens AM1 in bioaugmentation experiment including 500 mg/L CeO2 nanoparticles could not promote the nanoparticles accumulation in both natural and surface-sterilized treatments. However, it enhanced the translocation of Ce from roots to shoots in sterile samples. Moreover, another REE-utilizing bacterium, Bacillus subtilis, was enriched more than M. extorquens in control samples (no M. extorquens AM1), and associated with 52% and 14% higher Ce extraction in both natural (165 μg/gdried-plant) and surface-sterilized samples (136 μg/gdried-plant), respectively; showing the superior effect of endogenous microorganisms' enrichment over bioaugmentation in this experiment. In the biostimulation experiments, up to 705 μg/gdried-plant Ce and 19,641 μg/gdried-plant Nd could be extracted when 500 mg/L REE-NP were added. Furthermore, SEM-EDS analysis of the surface and longitudinal cross-sections of roots in Nd2O3 treatments confirmed surface and intracellular accumulation of Nd2O3-NP. These results demonstrate stimulation of endogenous microbial community can lead to an enhanced REE phytoaccumulation.
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Affiliation(s)
- Maedeh Soleimanifar
- John A. Reif, Jr. Department of Civil & Environmental Engineering, New Jersey Institute of Technology, 07102, Newark, NJ, United States; Now at Civil Engineering Department, The City College of New York, The City University of New York, 10031, New York, NY, United States.
| | - Lucia Rodriguez-Freire
- John A. Reif, Jr. Department of Civil & Environmental Engineering, New Jersey Institute of Technology, 07102, Newark, NJ, United States; Now at Civil, Structural and Geospatial Engineering Department, School of Engineering, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, United Kingdom
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7
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Ye Q, Wang D, Wei N. Engineering biomaterials for the recovery of rare earth elements. Trends Biotechnol 2024; 42:575-590. [PMID: 37985335 DOI: 10.1016/j.tibtech.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023]
Abstract
The escalating global demand for rare earth elements (REEs) and the overabundance of REE-containing waste require innovative technologies for REE recovery from waste to achieve a sustainable supply of REEs while reducing the environmental burden. Biosorption mediated by peptides or proteins has emerged as a promising approach for selective REE recovery. To date, multiple peptides and proteins with high REE-binding affinity and selectivity have been discovered, and various strategies are being exploited to engineer robust and reusable biosorptive materials for selective REE recovery. This review highlights recent advances in discovering and engineering peptides and proteins for REE recovery. Future research prospects and challenges are also discussed.
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Affiliation(s)
- Quanhui Ye
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dong Wang
- School of Information Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Na Wei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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8
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Breeze CW, Nakano Y, Campbell EC, Frkic RL, Lupton DW, Jackson CJ. Mononuclear binding and catalytic activity of europium(III) and gadolinium(III) at the active site of the model metalloenzyme phosphotriesterase. Acta Crystallogr D Struct Biol 2024; 80:289-298. [PMID: 38512071 PMCID: PMC10994177 DOI: 10.1107/s2059798324002316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/10/2024] [Indexed: 03/22/2024] Open
Abstract
Lanthanide ions have ideal chemical properties for catalysis, such as hard Lewis acidity, fast ligand-exchange kinetics, high coordination-number preferences and low geometric requirements for coordination. As a result, many small-molecule lanthanide catalysts have been described in the literature. Yet, despite the ability of enzymes to catalyse highly stereoselective reactions under gentle conditions, very few lanthanoenzymes have been investigated. In this work, the mononuclear binding of europium(III) and gadolinium(III) to the active site of a mutant of the model enzyme phosphotriesterase are described using X-ray crystallography at 1.78 and 1.61 Å resolution, respectively. It is also shown that despite coordinating a single non-natural metal cation, the PTE-R18 mutant is still able to maintain esterase activity.
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Affiliation(s)
- Callum W. Breeze
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Yuji Nakano
- School of Chemistry, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Eleanor C. Campbell
- Australian Synchrotron, 800 Blackburn Road, Clayton, Melbourne, VIC 3168, Australia
| | - Rebecca L. Frkic
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - David W. Lupton
- School of Chemistry, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Colin J. Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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9
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Falandysz J, Kilanowicz A, Fernandes AR, Zhang J. Rare earth contamination of edible vegetation: Ce, La, and summed REE in fungi. Appl Microbiol Biotechnol 2024; 108:268. [PMID: 38506962 PMCID: PMC10954923 DOI: 10.1007/s00253-024-13087-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
The increasing and diversified use of rare earth elements (REE) is considered a potential source of pollution of environmental media including soils. This work documents critically overview data on the occurrence of REE in the fruiting bodies of wild and farmed species of edible and medicinal mushrooms, as this was identified as the largest published dataset of REE occurrence in foodstuff. Most of the literature reported occurrences of cerium (Ce) and lanthanum (La), but a number of studies lacked data on all lanthanides. The Ce, La, and summed REE occurrences were assessed through the criteria of environmental geochemistry, analytical chemistry, food toxicology, mushroom systematics, and ecology. Ce and La accumulate similarly in fruiting bodies and are not fractionated during uptake, maintaining the occurrence patterns of their growing substrates. Similarly, there is no credible evidence of variable REE uptake because the evaluated species data show natural, unfractionated patterns in accordance with the Oddo-Harkins' order of environmental lanthanide occurrence. Thus, lithosphere occurrence patterns of Ce and La as the first and the third most abundant lanthanides are reflected in wild and farmed mushrooms regardless of substrate and show that Ce is around twice more abundant than La. The current state of knowledge provides no evidence that mushroom consumption at these REE occurrence levels poses a health risk either by themselves or when included with other dietary exposure. Macromycetes appear to bio-exclude lanthanides because independently reported bioconcentration factors for different species and collection sites, typically range from < 1 to 0.001. This is reflected in fruiting body concentrations which are four to two orders of magnitude lower than growing substrates. KEY POINTS: •Original REE occurrence patterns in soils/substrates are reflected in mushrooms •No evidence for the fractionation of REE during uptake by fungi •Mushrooms bio-exclude REE in fruiting bodies.
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Affiliation(s)
- Jerzy Falandysz
- Faculty of Pharmacy, Department of Toxicology, Medical University of Lodz, 1 Muszyńskiego Street, 90-151, Łódź, Poland.
| | - Anna Kilanowicz
- Faculty of Pharmacy, Department of Toxicology, Medical University of Lodz, 1 Muszyńskiego Street, 90-151, Łódź, Poland
| | - Alwyn R Fernandes
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Ji Zhang
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, 2238 Beijing Road, Panlong District, Kunming, 650200, China
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10
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Jones E, Su Y, Sander C, Justman QA, Springer M, Silver PA. LanTERN: A Fluorescent Sensor That Specifically Responds to Lanthanides. ACS Synth Biol 2024; 13:958-962. [PMID: 38377571 PMCID: PMC10949232 DOI: 10.1021/acssynbio.3c00600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/10/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024]
Abstract
Lanthanides, a series of 15 f-block elements, are crucial in modern technology, and their purification by conventional chemical means comes at a significant environmental cost. Synthetic biology offers promising solutions. However, progress in developing synthetic biology approaches is bottlenecked because it is challenging to measure lanthanide binding with current biochemical tools. Here we introduce LanTERN, a lanthanide-responsive fluorescent protein. LanTERN was designed based on GCaMP, a genetically encoded calcium indicator that couples the ion binding of four EF hand motifs to increased GFP fluorescence. We engineered eight mutations across the parent construct's four EF hand motifs to switch specificity from calcium to lanthanides. The resulting protein, LanTERN, directly converts the binding of 10 measured lanthanides to 14-fold or greater increased fluorescence. LanTERN development opens new avenues for creating improved lanthanide-binding proteins and biosensing systems.
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Affiliation(s)
- Ethan
M. Jones
- Department
of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Yang Su
- Department
of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Chris Sander
- Department
of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Quincey A. Justman
- Department
of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Michael Springer
- Department
of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Pamela A. Silver
- Department
of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
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11
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Phi MT, Singer H, Zäh F, Haisch C, Schneider S, Op den Camp HJM, Daumann LJ. Assessing Lanthanide-Dependent Methanol Dehydrogenase Activity: The Assay Matters. Chembiochem 2024; 25:e202300811. [PMID: 38269599 DOI: 10.1002/cbic.202300811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/22/2023] [Indexed: 01/26/2024]
Abstract
Artificial dye-coupled assays have been widely adopted as a rapid and convenient method to assess the activity of methanol dehydrogenases (MDH). Lanthanide(Ln)-dependent XoxF-MDHs are able to incorporate different lanthanides (Lns) in their active site. Dye-coupled assays showed that the earlier Lns exhibit a higher enzyme activity than the late Lns. Despite widespread use, there are limitations: oftentimes a pH of 9 and activators are required for the assay. Moreover, Ln-MDH variants are not obtained by isolation from the cells grown with the respective Ln, but by incubation of an apo-MDH with the Ln. Herein, we report the cultivation of Ln-dependent methanotroph Methylacidiphilum fumariolicum SolV with nine different Lns, the isolation of the respective MDHs and the assessment of the enzyme activity using the dye-coupled assay. We compare these results with a protein-coupled assay using its physiological electron acceptor cytochrome cGJ (cyt cGJ ). Depending on the assay, two distinct trends are observed among the Ln series. The specific enzyme activity of La-, Ce- and Pr-MDH, as measured by the protein-coupled assay, exceeds that measured by the dye-coupled assay. This suggests that early Lns also have a positive effect on the interaction between XoxF-MDH and its cyt cGJ thereby increasing functional efficiency.
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Affiliation(s)
- Manh Tri Phi
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Helena Singer
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Felix Zäh
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Christoph Haisch
- Faculty of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Sabine Schneider
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Huub J M Op den Camp
- Department of Microbiology, Research Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Lena J Daumann
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
- Chair of Bioinorganic Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
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12
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Barrat JA, Bayon G. Practical guidelines for representing and interpreting rare earth abundances in environmental and biological studies. CHEMOSPHERE 2024; 352:141487. [PMID: 38373443 DOI: 10.1016/j.chemosphere.2024.141487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/20/2024] [Accepted: 02/15/2024] [Indexed: 02/21/2024]
Abstract
This paper summarizes the main guidelines for representing rare earth element (REE) abundance patterns, along with a review of the common mistakes or omissions that can alter REE plots and bias interpretations. It is specifically designed for ecotoxicologists and biologists, for whom the study of these elements has become an important field of research in recent years. Prior to applying REE diagrams to the study of living organisms, it is important to understand the rationale that led geochemists and cosmochemists to develop them. Used with the practical recommendations described here, these diagrams have the capacity to highlight fundamental processes taking place in the biosphere.
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Affiliation(s)
- Jean-Alix Barrat
- Univ Brest, CNRS, Ifremer, IRD, LEMAR, Institut Universitaire Européen de la Mer (IUEM), Place Nicolas Copernic, 29280, Plouzané, France; Institut Universitaire de France, Paris, France.
| | - Germain Bayon
- Univ Brest, CNRS, Ifremer, Geo-Ocean, F-29280, Plouzané, France
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13
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Voutsinos MY, West-Roberts JA, Sachdeva R, Moreau JW, Banfield JF. Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes. BMC Biol 2024; 22:41. [PMID: 38369453 PMCID: PMC10875860 DOI: 10.1186/s12915-024-01841-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/07/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Currently, the microorganisms involved in phosphate mineral dissolution and the role of lanthanides in microbial metabolism are poorly understood. RESULTS Although there have been many studies of soil microbiology, very little research has investigated microbiomes of weathered rock. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilisation and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found that gene clusters implicated in lanthanide-based metabolism of methanol (primarily xoxF3 and xoxF5) are surprisingly common in microbial communities in moderately weathered granite. Notably, xoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes and Alphaproteobacteria. The xoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied xoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilise lanthanide phosphates, it is notable that candidate metallophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems. CONCLUSIONS Phosphate mineral dissolution, putative metallophore production and lanthanide utilisation by enzymes involved in methanol oxidation linked to carbonic acid production co-occur in the zone of moderate granite weathering. In combination, these microbial processes likely accelerate the conversion of granitic rock to soil.
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Affiliation(s)
- Marcos Y Voutsinos
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Jacob A West-Roberts
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Rohan Sachdeva
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - John W Moreau
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow, UK
| | - Jillian F Banfield
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, Melbourne, VIC, Australia.
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
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14
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Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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15
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Lim J, Wehmeyer H, Heffner T, Aeppli M, Gu W, Kim PJ, Horn MA, Ho A. Resilience of aerobic methanotrophs in soils; spotlight on the methane sink under agriculture. FEMS Microbiol Ecol 2024; 100:fiae008. [PMID: 38327184 PMCID: PMC10872700 DOI: 10.1093/femsec/fiae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/09/2024] Open
Abstract
Aerobic methanotrophs are a specialized microbial group, catalyzing the oxidation of methane. Disturbance-induced loss of methanotroph diversity/abundance, thus results in the loss of this biological methane sink. Here, we synthesized and conceptualized the resilience of the methanotrophs to sporadic, recurring, and compounded disturbances in soils. The methanotrophs showed remarkable resilience to sporadic disturbances, recovering in activity and population size. However, activity was severely compromised when disturbance persisted or reoccurred at increasing frequency, and was significantly impaired following change in land use. Next, we consolidated the impact of agricultural practices after land conversion on the soil methane sink. The effects of key interventions (tillage, organic matter input, and cover cropping) where much knowledge has been gathered were considered. Pairwise comparisons of these interventions to nontreated agricultural soils indicate that the agriculture-induced impact on the methane sink depends on the cropping system, which can be associated to the physiology of the methanotrophs. The impact of agriculture is more evident in upland soils, where the methanotrophs play a more prominent role than the methanogens in modulating overall methane flux. Although resilient to sporadic disturbances, the methanotrophs are vulnerable to compounded disturbances induced by anthropogenic activities, significantly affecting the methane sink function.
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Affiliation(s)
- Jiyeon Lim
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Helena Wehmeyer
- Nestlè Research, Route du Jorat 57, CH 1000 Lausanne 26, Switzerland
| | - Tanja Heffner
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Meret Aeppli
- Environmental Engineering Institute IIE-ENAC, Laboratory SOIL, Ecole Polytechnique Fédérale de Lausanne (EPFL), Valais Wallis, CH 1950 Sion, Switzerland
| | - Wenyu Gu
- Environmental Engineering Institute IIE-ENAC, Laboratory MICROBE, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH 1015 Lausanne, Switzerland
| | - Pil Joo Kim
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Marcus A Horn
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Adrian Ho
- Nestlè Research, Route du Jorat 57, CH 1000 Lausanne 26, Switzerland
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16
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Qian X, Ma C, Zhang H, Liu K. Bioseparation of rare earth elements and high value-added biomaterials applications. Bioorg Chem 2024; 143:107040. [PMID: 38141331 DOI: 10.1016/j.bioorg.2023.107040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/24/2023] [Accepted: 12/15/2023] [Indexed: 12/25/2023]
Abstract
Rare earth elements (REEs) are a group of critical minerals and extensively employed in new material manufacturing. However, separation of lanthanides is difficult because of their similar chemical natures. Current lanthanide leaching and separation methods require hazardous compounds, resulting in severe environmental concerns. Bioprocessing of lanthanides offers an emerging class of tools for REE separation due to mild leaching conditions and highly selective separation scenarios. In the course of biopreparation, engineered microbes not only dissolve REEs from ores but also allow for selective separation of the lanthanides. In this review, we present an overview of recent advances in microbes and proteins used for the biomanufacturing of lanthanides and discuss high value-added applications of REE-derived biomaterials. We begin by introducing the fundamental interactions between natural microbes and REEs. Then we discuss the rational design of chassis microbes for bioleaching and biosorption. We also highlight the investigations on REE binding proteins and their applications in the synthesis of high value-added biomaterials. Finally, future opportunities and challenges for the development of next generation lanthanide-binding biological systems are discussed.
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Affiliation(s)
- Xining Qian
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Chao Ma
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China; Xiangfu Laboratory, Building 5, No.828 Zhongxing Road, Xitang Town, Jiashan, Jiaxing, Zhejiang 314102, China.
| | - Hongjie Zhang
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China; Xiangfu Laboratory, Building 5, No.828 Zhongxing Road, Xitang Town, Jiashan, Jiaxing, Zhejiang 314102, China
| | - Kai Liu
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China; Xiangfu Laboratory, Building 5, No.828 Zhongxing Road, Xitang Town, Jiashan, Jiaxing, Zhejiang 314102, China
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17
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Bakhti A, Shokouhi Z, Mohammadipanah F. Modulation of proteins by rare earth elements as a biotechnological tool. Int J Biol Macromol 2024; 258:129072. [PMID: 38163500 DOI: 10.1016/j.ijbiomac.2023.129072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 12/24/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Although rare earth element (REE) complexes are often utilized in bioimaging due to their photo- and redox stability, magnetic and optical characteristics, they are also applied for pharmaceutical applications due to their interaction with macromolecules namely proteins. The possible implications induced by REEs through modification in the function or regulatory activity of the proteins trigger a variety of applications for these elements in biomedicine and biotechnology. Lanthanide complexes have particularly been applied as anti-biofilm agents, cancer inhibitors, potential inflammation inhibitors, metabolic elicitors, and helper agents in the cultivation of unculturable strains, drug delivery, tissue engineering, photodynamic, and radiation therapy. This paper overviews emerging applications of REEs in biotechnology, especially in biomedical imaging, tumor diagnosis, and treatment along with their potential toxic effects. Although significant advances in applying REEs have been made, there is a lack of comprehensive studies to identify the potential of all REEs in biotechnology since only four elements, Eu, Ce, Gd, and La, among 17 REEs have been mostly investigated. However, in depth research on ecotoxicology, environmental behavior, and biological functions of REEs in the health and disease status of living organisms is required to fill the vital gaps in our understanding of REEs applications.
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Affiliation(s)
- Azam Bakhti
- Department of Microbial Biotechnology, Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455 Tehran, Iran
| | - Zahra Shokouhi
- Department of Microbial Biotechnology, Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455 Tehran, Iran
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455 Tehran, Iran.
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18
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Behrsing T, Blair VL, Jaroschik F, Deacon GB, Junk PC. Rare Earths-The Answer to Everything. Molecules 2024; 29:688. [PMID: 38338432 PMCID: PMC10856286 DOI: 10.3390/molecules29030688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 01/24/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Rare earths, scandium, yttrium, and the fifteen lanthanoids from lanthanum to lutetium, are classified as critical metals because of their ubiquity in daily life. They are present in magnets in cars, especially electric cars; green electricity generating systems and computers; in steel manufacturing; in glass and light emission materials especially for safety lighting and lasers; in exhaust emission catalysts and supports; catalysts in artificial rubber production; in agriculture and animal husbandry; in health and especially cancer diagnosis and treatment; and in a variety of materials and electronic products essential to modern living. They have the potential to replace toxic chromates for corrosion inhibition, in magnetic refrigeration, a variety of new materials, and their role in agriculture may expand. This review examines their role in sustainability, the environment, recycling, corrosion inhibition, crop production, animal feedstocks, catalysis, health, and materials, as well as considering future uses.
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Affiliation(s)
- Thomas Behrsing
- School of Chemistry, Monash University, Melbourne, VIC 3800, Australia; (T.B.); (V.L.B.); (G.B.D.)
| | - Victoria L. Blair
- School of Chemistry, Monash University, Melbourne, VIC 3800, Australia; (T.B.); (V.L.B.); (G.B.D.)
| | | | - Glen B. Deacon
- School of Chemistry, Monash University, Melbourne, VIC 3800, Australia; (T.B.); (V.L.B.); (G.B.D.)
| | - Peter C. Junk
- College of Science & Engineering, James Cook University, Townsville, QLD 4811, Australia
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19
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Liu R, Wei Z, Dong W, Wang R, Adams JM, Yang L, Krause SMB. Unraveling the impact of lanthanum on methane consuming microbial communities in rice field soils. Front Microbiol 2024; 15:1298154. [PMID: 38322316 PMCID: PMC10844099 DOI: 10.3389/fmicb.2024.1298154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024] Open
Abstract
The discovery of the lanthanide requiring enzymes in microbes was a significant scientific discovery that opened a whole new avenue of biotechnological research of this important group of metals. However, the ecological impact of lanthanides on microbial communities utilizing methane (CH4) remains largely unexplored. In this study, a laboratory microcosm model experiment was performed using rice field soils with different pH origins (5.76, 7.2, and 8.36) and different concentrations of La3+ in the form of lanthanum chloride (LaCl3). Results clearly showed that CH4 consumption was inhibited by the addition of La3+ but that the response depended on the soil origin and pH. 16S rRNA gene sequencing revealed the genus Methylobacter, Methylosarcina, and Methylocystis as key players in CH4 consumption under La3+ addition. We suggest that the soil microbiome involved in CH4 consumption can generally tolerate addition of high concentrations of La3+, and adjustments in community composition ensured ecosystem functionality over time. As La3+ concentrations increase, the way that the soil microbiome reacts may not only differ within the same environment but also vary when comparing different environments, underscoring the need for further research into this subject.
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Affiliation(s)
- Ruyan Liu
- School of Ecology and Environmental Sciences, East China Normal University, Shanghai, China
| | - Ziting Wei
- School of Ecology and Environmental Sciences, East China Normal University, Shanghai, China
| | - Wanying Dong
- School of Ecology and Environmental Sciences, East China Normal University, Shanghai, China
| | - Rui Wang
- School of Ecology and Environmental Sciences, East China Normal University, Shanghai, China
| | - Jonathan M. Adams
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, China
| | - Lin Yang
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, China
| | - Sascha M. B. Krause
- School of Ecology and Environmental Sciences, East China Normal University, Shanghai, China
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20
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Larrinaga WB, Cotruvo JA, Worrell BT, Eaton SS, Eaton GR. Electron Paramagnetic Resonance, Electronic Ground State, and Electron Spin Relaxation of Seven Lanthanide Ions Bound to Lanmodulin and the Bioinspired Chelator, 3,4,3-LI(1,2-HOPO). Chemistry 2023; 29:e202303215. [PMID: 37802965 DOI: 10.1002/chem.202303215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/08/2023]
Abstract
The electron paramagnetic resonance (EPR) spectra of lanthanide(III) ions besides Gd3+ , bound to small-molecule and protein chelators, are uncharacterized. Here, the EPR properties of 7 lanthanide(III) ions bound to the natural lanthanide-binding protein, lanmodulin (LanM), and the synthetic small-molecule chelator, 3,4,3-LI(1,2-HOPO) ("HOPO"), were systematically investigated. Echo-detected pulsed EPR spectra reveal intense signals from ions for which the normal continuous-wave first-derivative spectra are negligibly different from zero. Spectra of Kramers lanthanide ions Ce3+ , Nd3+ , Sm3+ , Er3+ , and Yb3+ , and non-Kramers Tb3+ and Tm3+ , bound to LanM are more similar to the ions in dilute aqueous:ethanol solution than to those coordinated with HOPO. Lanmodulins from two bacteria, with distinct metal-binding sites, had similar spectra for Tb3+ but different spectra for Nd3+ . Spin echo dephasing rates (1/Tm ) are faster for lanthanides than for most transition metals and limited detection of echoes to temperatures below ~6 to 12 K. Dephasing rates were environment dependent and decreased in the order water:ethanol>LanM>HOPO, which is attributed to decreasing librational motion. These results demonstrate that the EPR spectra and relaxation times of lanthanide(III) ions are sensitive to coordination environment, motivating wider application of these methods for characterization of both small-molecule and biomolecule interactions with lanthanides.
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Affiliation(s)
- Wyatt B Larrinaga
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Joseph A Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Brady T Worrell
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, 80208, United States
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, 80208, United States
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, 80208, United States
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21
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Deblonde GJP, Morrison K, Mattocks JA, Cotruvo JA, Zavarin M, Kersting AB. Impact of a Biological Chelator, Lanmodulin, on Minor Actinide Aqueous Speciation and Transport in the Environment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:20830-20843. [PMID: 37897703 DOI: 10.1021/acs.est.3c06033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/30/2023]
Abstract
Minor actinides are major contributors to the long-term radiotoxicity of nuclear fuels and other radioactive wastes. In this context, understanding their interactions with natural chelators and minerals is key to evaluating their transport behavior in the environment. The lanmodulin family of metalloproteins is produced by ubiquitous bacteria and Methylorubrum extorquens lanmodulin (LanM) was recently identified as one of nature's most selective chelators for trivalent f-elements. Herein, we investigated the behavior of neptunium, americium, and curium in the presence of LanM, carbonate ions, and common minerals (calcite, montmorillonite, quartz, and kaolinite). We show that LanM's aqueous complexes with Am(III) and Cm(III) remain stable in carbonate-bicarbonate solutions. Furthermore, the sorption of Am(III) to these minerals is strongly impacted by LanM, while Np(V) sorption is not. With calcite, even a submicromolar concentration of LanM leads to a significant reduction in the Am(III) distribution coefficient (Kd, from >104 to ∼102 mL/g at pH 8.5), rendering it even more mobile than Np(V). Thus, LanM-type chelators can potentially increase the mobility of trivalent actinides and lanthanide fission products under environmentally relevant conditions. Monitoring biological chelators, including metalloproteins, and their biogenerators should therefore be considered during the evaluation of radioactive waste repository sites and the risk assessment of contaminated sites.
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Affiliation(s)
- Gauthier J-P Deblonde
- Physical and Life Sciences Directorate, Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Glenn T. Seaborg Institute, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Keith Morrison
- Physical and Life Sciences Directorate, Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Glenn T. Seaborg Institute, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Joseph A Mattocks
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Joseph A Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Mavrik Zavarin
- Glenn T. Seaborg Institute, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Annie B Kersting
- Glenn T. Seaborg Institute, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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22
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Newton SL, Franke A, Zahl A, Molinaro G, Kenwright A, Smith DJ, Ivanovic-Burmazovic I, Britton MM, Peacock AFA. Understanding the mechanism by which Gd(III) coiled coils achieve magnetic resonance relaxivity - a study into the water coordination chemistry. Dalton Trans 2023; 52:15665-15668. [PMID: 37882137 DOI: 10.1039/d3dt02909c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
A class of Gd(III) coiled coils achieve high MRI relaxivity, in part due to their slow rotational correlation time. However, extending their length is unable to further enhance performance, as the mechanism by which relaxivity is achieved is dominated by the presence of three inner sphere waters in rapid exchange, through an associative mechanism.
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Affiliation(s)
- S L Newton
- School of Chemistry, University of Birmingham, Edgbaston, B15 2TT, UK.
- PSIBS, School of Chemistry, University of Birmingham, Edgbaston, B15 2TT, UK
| | - A Franke
- Department Chemie und Pharmazie, Universität Erlangen-Nürnberg, D-91058, Erlangen, Germany
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - A Zahl
- Department Chemie und Pharmazie, Universität Erlangen-Nürnberg, D-91058, Erlangen, Germany
| | - G Molinaro
- School of Chemistry, University of Birmingham, Edgbaston, B15 2TT, UK.
| | - A Kenwright
- School of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - D J Smith
- School of Mathematics, University of Birmingham, Edgbaston, B15 2TT, UK
| | - I Ivanovic-Burmazovic
- Department Chemie und Pharmazie, Universität Erlangen-Nürnberg, D-91058, Erlangen, Germany
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - M M Britton
- School of Chemistry, University of Birmingham, Edgbaston, B15 2TT, UK.
| | - A F A Peacock
- School of Chemistry, University of Birmingham, Edgbaston, B15 2TT, UK.
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23
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24
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Awala SI, Gwak JH, Kim Y, Seo C, Strazzulli A, Kim SG, Rhee SK. Methylacidiphilum caldifontis gen. nov., sp. nov., a thermoacidophilic methane-oxidizing bacterium from an acidic geothermal environment, and descriptions of the family Methylacidiphilaceae fam. nov. and order Methylacidiphilales ord. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37791995 DOI: 10.1099/ijsem.0.006085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
Strain IT6T, a thermoacidophilic and facultative methane-oxidizing bacterium, was isolated from a mud-water mixture collected from Pisciarelli hot spring in Pozzuoli, Italy. The novel strain is white when grown in liquid or solid media and forms Gram-negative rod-shaped, non-flagellated, non-motile cells. It conserves energy by aerobically oxidizing methane and hydrogen while deriving carbon from carbon dioxide fixation. Strain IT6T had three complete pmoCAB operons encoding particulate methane monooxygenase and genes encoding group 1d and 3b [NiFe] hydrogenases. Simple carbon-carbon substrates such as ethanol, 2-propanol, acetone, acetol and propane-1,2-diol were used as alternative electron donors and carbon sources. Optimal growth occurred at 50-55°C and between pH 2.0-3.0. The major fatty acids were C18 : 0, C15 : 0 anteiso, C14 : 0 iso, C16 : 0 and C14 : 0, and the main polar lipids were phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, diphosphatidylglycerol, some unidentified phospholipids and glycolipids, and other unknown polar lipids. Strain IT6T has a genome size of 2.19 Mbp and a G+C content of 40.70 mol%. Relative evolutionary divergence using 120 conserved single-copy marker genes (bac120) and phylogenetic analyses based on bac120 and 16S rRNA gene sequences showed that strain IT6T is affiliated with members of the proposed order 'Methylacidiphilales' of the class Verrucomicrobiia in the phylum Verrucomicrobiota. It shared a 16S rRNA gene sequence identity of >96 % with cultivated isolates in the genus 'Methylacidiphilum' of the family 'Methylacidiphilaceae', which are thermoacidophilic methane-oxidizing bacteria. 'Methylacidiphilum sp.' Phi (100 %), 'Methylacidiphilum infernorum' V4 (99.02 %) and 'Methylacidiphilum sp.' RTK17.1 (99.02 %) were its closest relatives. Its physiological and genomic properties were consistent with those of other isolated 'Methylacidiphilum' species. Based on these results, we propose the name Methylacidiphilum caldifontis gen. nov., sp. nov. to accommodate strain IT6T (=KCTC 92103T=JCM 39288T). We also formally propose that the names Methylacidiphilaceae fam. nov. and Methylacidiphilales ord. nov. to accommodate the genus Methylacidiphilum gen. nov.
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Affiliation(s)
- Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Yongman Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Chanmee Seo
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126, Naples, Italy
| | - Song-Gun Kim
- University of Science and Technology, Yuseong-gu, Daejeon 305-850, Republic of Korea
- Biological Resource Center/ Korean Collection for Type Culture (KCTC), Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
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Quiton-Tapia S, Balboa S, Omil F, Garrido JM, Suarez S. How efficiently does a metabolically enhanced system with denitrifying anaerobic methane oxidizing microorganisms remove antibiotics? ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122033. [PMID: 37348697 DOI: 10.1016/j.envpol.2023.122033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/26/2023] [Accepted: 06/10/2023] [Indexed: 06/24/2023]
Abstract
In this work, the novel N-damo (Nitrite dependent anaerobic methane oxidation) process was investigated at high biomass activities for its potential to remove simultaneously nitrite and methane, as well as selected antibiotics commonly found in sewage in trace amounts. For this purpose, two MBRs were operated at three high nitrite loading rates (NLRs), namely 76 ± 9.9, 161.5 ± 11.4 and 215.2 ± 24.2 mg N-NO⁻2 L-1 d-1, at long-term operation. The MBRs performance achieved a significantly high nitrite removal activity for an N-damo process (specific denitrifying activity of up to 540 mg N-NO⁻2 g-1 VSS d-1), even comparable to heterotrophic denitrification values. In this study, we have implemented a novel operational strategy that sets our work apart from previous studies with similar bioreactors. Specifically, we have introduced Cerium as a trace element in the feeding medium, which serves as a key differentiating factor. It allowed maintaining a stable reactor operation at high NLRs. Microbial community composition evidenced that both MBRs were dominated with N-damo bacteria (67-87% relative abundance in period III and I, respectively). However, a decrease in functional N-damo bacteria (Candidatus Methylomirabilis) abundance was observed during the increase in biomass activity and concentration, concomitantly with an increase of the other minor families (Hypomicrobiaceae and Xanthobacteraceae). Most of the selected antibiotics showed high biotransformation such as sulfamethoxazole, trimethoprim, cefalexin and azithromycin, whereas others such as roxithromycin and clarithromycin were only partially degraded (20-35%). On the contrary, ciprofloxacin showed almost no removal. Despite the metabolic enhancement, no apparent increase on the antibiotic removal was observed throughout the operation, suggesting that microbiological composition was of greater influence than its primary metabolic activity on the removal of antibiotics.
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Affiliation(s)
- Silvana Quiton-Tapia
- CRETUS Institute. Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, Rúa Lope Gómez de Marzoa, E-15782, Santiago de Compostela, Spain.
| | - Sabela Balboa
- CRETUS Institute. Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, Rúa Lope Gómez de Marzoa, E-15782, Santiago de Compostela, Spain.
| | - Francisco Omil
- CRETUS Institute. Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, Rúa Lope Gómez de Marzoa, E-15782, Santiago de Compostela, Spain.
| | - Juan Manuel Garrido
- CRETUS Institute. Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, Rúa Lope Gómez de Marzoa, E-15782, Santiago de Compostela, Spain.
| | - Sonia Suarez
- CRETUS Institute. Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, Rúa Lope Gómez de Marzoa, E-15782, Santiago de Compostela, Spain.
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Dedysh SN. Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new? Syst Appl Microbiol 2023; 46:126439. [PMID: 37413783 DOI: 10.1016/j.syapm.2023.126439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/17/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.
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Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
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27
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Ratnadevi CM, Erikstad HA, Kruse T, Birkeland NK. Methylacidiphilum kamchatkense gen. nov., sp. nov., an extremely acidophilic and moderately thermophilic methanotroph belonging to the phylum Verrucomicrobiota. Int J Syst Evol Microbiol 2023; 73. [PMID: 37755432 DOI: 10.1099/ijsem.0.006060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
The thermo-acidophilic aerobic methanotrophic Verrucomicrobia bacterium, designated strain Kam1T was isolated from an acidic geothermal mud spring in Kamchatka, Russia. Kam1T is Gram-stain-negative, with non-motile cells and non-spore-forming rods, and a diameter of 0.45-0.65 µm and length of 0.8-1.0 µm. Its growth is optimal at the temperature of 55 °C (range, 37-60 °C) and pH of 2.5 (range, pH 1-6), and its maximal growth rate is ~0.11 h-1 (doubling time ~6.3 h). Its cell wall contains peptidoglycan with meso-diaminopimelic acid. In addition to growing on methane and methanol, strain Kam1T grows on acetone and 2-propanol. Phylogenetically, it forms a distinct group together with other Methylacidiphilum strains and with the candidate genus Methylacidimicrobium as a sister group. These findings support the classification of the strain Kam1T as a representative of a novel species and genus of the phylum Verrucomicrobiota. For this strain, we propose the name Methylacidiphilum kamchatkense sp. nov. as the type species within Methylacidiphilum gen. nov. Strain Kam1T (JCM 30608T=KCTC 4682T) is the type strain.
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Affiliation(s)
| | - Helge-André Erikstad
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway
| | - Thomas Kruse
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway
- Present address: NORCE, Industrial biotechnology, Prof. Olav Hanssensvei 15, 4021 Stavanger, Norway
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28
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Houghton KM, Carere CR, Stott MB, McDonald IR. Thermophilic methane oxidation is widespread in Aotearoa-New Zealand geothermal fields. Front Microbiol 2023; 14:1253773. [PMID: 37720161 PMCID: PMC10502179 DOI: 10.3389/fmicb.2023.1253773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023] Open
Abstract
Geothermal areas represent substantial point sources for greenhouse gas emissions such as methane. While it is known that methanotrophic microorganisms act as a biofilter, decreasing the efflux of methane in most soils to the atmosphere, the diversity and the extent to which methane is consumed by thermophilic microorganisms in geothermal ecosystems has not been widely explored. To determine the extent of biologically mediated methane oxidation at elevated temperatures, we set up 57 microcosms using soils from 14 Aotearoa-New Zealand geothermal fields and show that moderately thermophilic (>40°C) and thermophilic (>60°C) methane oxidation is common across the region. Methane oxidation was detected in 54% (n = 31) of the geothermal soil microcosms tested at temperatures up to 75°C (pH 1.5-8.1), with oxidation rates ranging from 0.5 to 17.4 μmol g-1 d-1 wet weight. The abundance of known aerobic methanotrophs (up to 60.7% Methylacidiphilum and 11.2% Methylothermus) and putative anaerobic methanotrophs (up to 76.7% Bathyarchaeota) provides some explanation for the rapid rates of methane oxidation observed in microcosms. However, not all methane oxidation was attributable to known taxa; in some methane-consuming microcosms we detected methanotroph taxa in conditions outside of their known temperature range for growth, and in other examples, we observed methane oxidation in the absence of known methanotrophs through 16S rRNA gene sequencing. Both of these observations suggest unidentified methane oxidizing microorganisms or undescribed methanotrophic syntrophic associations may also be present. Subsequent enrichment cultures from microcosms yielded communities not predicted by the original diversity studies and showed rates inconsistent with microcosms (≤24.5 μmol d-1), highlighting difficulties in culturing representative thermophilic methanotrophs. Finally, to determine the active methane oxidation processes, we attempted to elucidate metabolic pathways from two enrichment cultures actively oxidizing methane using metatranscriptomics. The most highly expressed genes in both enrichments (methane monooxygenases, methanol dehydrogenases and PqqA precursor peptides) were related to methanotrophs from Methylococcaceae, Methylocystaceae and Methylothermaceae. This is the first example of using metatranscriptomics to investigate methanotrophs from geothermal environments and gives insight into the metabolic pathways involved in thermophilic methanotrophy.
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Affiliation(s)
- Karen M. Houghton
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
| | - Carlo R. Carere
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
| | - Matthew B. Stott
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
| | - Ian R. McDonald
- Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
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Sweeney KJ, Han X, Müller UF. A ribozyme that uses lanthanides as cofactor. Nucleic Acids Res 2023; 51:7163-7173. [PMID: 37326001 PMCID: PMC10415125 DOI: 10.1093/nar/gkad513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/10/2023] [Accepted: 06/13/2023] [Indexed: 06/17/2023] Open
Abstract
To explore how an early, RNA-based life form could have functioned, in vitro selection experiments have been used to develop catalytic RNAs (ribozymes) with relevant functions. We previously identified ribozymes that use the prebiotically plausible energy source cyclic trimetaphosphate (cTmp) to convert their 5'-hydroxyl group to a 5'-triphosphate. While these ribozymes were developed in the presence of Mg2+, we tested here whether lanthanides could also serve as catalytic cofactors because lanthanides are ideal catalytic cations for this reaction. After an in vitro selection in the presence of Yb3+, several active sequences were isolated, and the most active RNA was analyzed in more detail. This ribozyme required lanthanides for activity, with highest activity at a 10:1 molar ratio of cTmp : Yb3+. Only the four heaviest lanthanides gave detectable signals, indicating a high sensitivity of ribozyme catalysis to the lanthanide ion radius. Potassium and Magnesium did not facilitate catalysis alone but they increased the lanthanide-mediated kOBS by at least 100-fold, with both K+ and Mg2+ modulating the ribozyme's secondary structure. Together, these findings show that RNA is able to use the unique properties of lanthanides as catalytic cofactor. The results are discussed in the context of early life forms.
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Affiliation(s)
- Kevin J Sweeney
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Xu Han
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Ulrich F Müller
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
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30
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Peres FV, Paula FS, Bendia AG, Gontijo JB, de Mahiques MM, Pellizari VH. Assessment of prokaryotic communities in Southwestern Atlantic deep-sea sediments reveals prevalent methanol-oxidising Methylomirabilales. Sci Rep 2023; 13:12782. [PMID: 37550336 PMCID: PMC10406867 DOI: 10.1038/s41598-023-39415-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
Continental slopes can play a significant contribution to marine productivity and carbon cycling. These regions can harbour distinct geological features, such as salt diapirs and pockmarks, in which their depressions may serve as natural sediment traps where different compounds can accumulate. We investigated the prokaryotic communities in surface (0-2 cm) and subsurface (18-20 or 22-24 cm) sediments from a salt diapir and pockmark field in Santos Basin, Southwest Atlantic Ocean. Metabarcoding of 16 samples revealed that surface sediments were dominated by the archaeal class Nitrososphaeria, while the bacterial class Dehalococcoidia was the most prevalent in subsurface samples. Sediment strata were found to be a significant factor explaining 27% of the variability in community composition. However, no significant difference was observed among geomorphological features. We also performed a metagenomic analysis of three surface samples and analysed the highest quality metagenome-assembled genome retrieved, which belonged to the family CSP1-5, phylum Methylomirabilota. This non-methanotrophic methylotroph contains genes encoding for methanol oxidation and Calvin Cycle pathways, along with diverse functions that may contribute to its adaptation to deep-sea habitats and to oscillating environmental conditions. By integrating metabarcoding and metagenomic approaches, we reported that CSP1-5 is prevalent in the sediment samples from Santos Basin slope, indicating the potential importance of methanol metabolism in this region. Finally, using a phylogenetic approach integrating 16S rRNA sequences assigned to Methylomirabilota in this study with those from a public database, we argued that CSP1-5 public sequences might be misclassified as Methylomirabilaceae (the methanotrophic clade) and, therefore, the role of these organisms and the methanol cycling could also be neglected in other environments.
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Affiliation(s)
- Francielli V Peres
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
| | - Fabiana S Paula
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil.
| | - Amanda G Bendia
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
| | - Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Centre for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Michel M de Mahiques
- Department of Physical, Chemical and Geological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, Brazil
| | - Vivian H Pellizari
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
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31
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Iguchi S, Tokunaga T, Kamon E, Takenaka Y, Koshimizu S, Watanabe M, Ishimizu T. Lanthanum Supplementation Alleviates Tomato Root Growth Suppression under Low Light Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:2663. [PMID: 37514277 PMCID: PMC10384870 DOI: 10.3390/plants12142663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]
Abstract
Supplementation with rare earth elements (REEs) such as lanthanum and cerium has been shown to promote plant elongation and/or increase crop yields. On the other hand, there are reports that REE supplementation of plants has no such effect. The appropriate modes for REE utilization and the underlying mechanism are not fully understood. In this study, we investigated how REE supplementation of plants under low light stress affects plant growth and gene expression. Under low light stress conditions, tomato root elongation was observed to be reduced by about half. This suppression of root elongation was found to be considerably alleviated by 20 mM lanthanum ion supplementation. This effect was plant-species-dependent and nutrient-condition-dependent. Under low light stress, the expression of the genes for phytochrome-interacting factor, which induces auxin synthesis, and several auxin-synthesis-related proteins were markedly upregulated by lanthanum ion supplementation. Thus, we speculate that REE supplementation of plants results in auxin-induced cell elongation and alleviates growth suppression under stress conditions.
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Affiliation(s)
- Syo Iguchi
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Tatsuya Tokunaga
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Eri Kamon
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Yuto Takenaka
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | | | - Masao Watanabe
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Takeshi Ishimizu
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
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32
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Soleimanifar M, Rodriguez-Freire L. Biointeraction of cerium oxide and neodymium oxide nanoparticles with pure culture methylobacterium extorquens AM1. CHEMOSPHERE 2023:139113. [PMID: 37270036 DOI: 10.1016/j.chemosphere.2023.139113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/05/2023]
Abstract
Rare earth elements (REE) are valuable raw materials in our modern life. Extensive REE application from electronic devices to medical instruments and wind turbines, and non-uniform distribution of these resources around the world, make them strategically and economically important for countries. Current REE physical and chemical mining and recycling methods could have negative environmental consequences, and biologically-mediated techniques could be applied to overcome this issue. In this study, the bioextraction of cerium oxide and neodymium oxide nanoparticles (REE-NP) by a pure culture Methylobacterium extorquens AM1 (ATCC®14718™) was investigated in batch experiments. Results show that adding up to 1000 ppm CeO2 or Nd2O3 nanoparticles (REE-NP) did not seem to affect the bacterial growth over 14-days contact time. Effect of methylamine hydrochloride as an essential electron donor and carbon source for microbial oxidation and growth was also observed inasmuch as there was approximately no growth when it does not exist in the medium. Although very low concentrations of cerium and neodymium in the liquid phase were measured, concentrations of 45 μg/gcell Ce and 154 μg/gcell Nd could be extracted by M. extorquens AM1. Furthermore, SEM-EDS and STEM-EDS confirmed surface and intracellular accumulation of nanoparticles. These results confirmed the ability of M. extorquens to accumulate REE nanoparticles.
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Affiliation(s)
- Maedeh Soleimanifar
- John A. Reif, Jr. Department of Civil & Environmental Engineering, New Jersey Institute of Technology, 07102, Newark, NJ, United States.
| | - Lucia Rodriguez-Freire
- John A. Reif, Jr. Department of Civil & Environmental Engineering, New Jersey Institute of Technology, 07102, Newark, NJ, United States
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33
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Banta S. How a protein differentiates between rare-earth elements. Nature 2023; 618:35-36. [PMID: 37259005 DOI: 10.1038/d41586-023-01739-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Mattocks JA, Jung JJ, Lin CY, Dong Z, Yennawar NH, Featherston ER, Kang-Yun CS, Hamilton TA, Park DM, Boal AK, Cotruvo JA. Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer. Nature 2023; 618:87-93. [PMID: 37259003 PMCID: PMC10232371 DOI: 10.1038/s41586-023-05945-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/13/2023] [Indexed: 06/02/2023]
Abstract
Technologically critical rare-earth elements are notoriously difficult to separate, owing to their subtle differences in ionic radius and coordination number1-3. The natural lanthanide-binding protein lanmodulin (LanM)4,5 is a sustainable alternative to conventional solvent-extraction-based separation6. Here we characterize a new LanM, from Hansschlegelia quercus (Hans-LanM), with an oligomeric state sensitive to rare-earth ionic radius, the lanthanum(III)-induced dimer being >100-fold tighter than the dysprosium(III)-induced dimer. X-ray crystal structures illustrate how picometre-scale differences in radius between lanthanum(III) and dysprosium(III) are propagated to Hans-LanM's quaternary structure through a carboxylate shift that rearranges a second-sphere hydrogen-bonding network. Comparison to the prototypal LanM from Methylorubrum extorquens reveals distinct metal coordination strategies, rationalizing Hans-LanM's greater selectivity within the rare-earth elements. Finally, structure-guided mutagenesis of a key residue at the Hans-LanM dimer interface modulates dimerization in solution and enables single-stage, column-based separation of a neodymium(III)/dysprosium(III) mixture to >98% individual element purities. This work showcases the natural diversity of selective lanthanide recognition motifs, and it reveals rare-earth-sensitive dimerization as a biological principle by which to tune the performance of biomolecule-based separation processes.
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Affiliation(s)
- Joseph A Mattocks
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Jonathan J Jung
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Chi-Yun Lin
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Ziye Dong
- Critical Materials Institute, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Emily R Featherston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Christina S Kang-Yun
- Critical Materials Institute, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Timothy A Hamilton
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Dan M Park
- Critical Materials Institute, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Amie K Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
| | - Joseph A Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
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35
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Prejanò M, Toscano M, Marino T. Periodicity of the Affinity of Lanmodulin for Trivalent Lanthanides and Actinides: Structural and Electronic Insights from Quantum Chemical Calculations. Inorg Chem 2023; 62:7461-7470. [PMID: 37128767 DOI: 10.1021/acs.inorgchem.3c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Lanmodulin (LanM) is the first identified macrochelator that has naturally evolved to sequester ions of rare earth elements (REEs) such as Y and all lanthanides, reversibly. This natural protein showed a 106 times better affinity for lanthanide cations than for Ca, which is a naturally abundant and biologically relevant element. Recent experiments have shown that its metal ion binding activity can be further extended to some actinides, like Np, Pu, and Am. For this reason, it was thought that LanM could be adopted for the separation of REE ions and actinides, thus increasing the interest in its potential use for industry-oriented applications. In this work, a systematic study of the affinity of LanM for lanthanides and actinides has been carried out, taking into account all trivalent ions belonging to the 4f (from La to Lu) and 5f (from Ac to Lr) series, starting from their chemistry in solution. On the basis of a recently published nuclear magnetic resonance structure, a model of the LanM-binding site was built and a detailed structural and electronic description of initial aquo- and LanM-metal ion complexes was provided. The obtained binding energies are in agreement with the available experimental data. A possible reason that could explain the origin of the affinity of LanM for these metal ions is also discussed.
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Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via P. Bucci, 87036 Rende, Italy
| | - Marirosa Toscano
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via P. Bucci, 87036 Rende, Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via P. Bucci, 87036 Rende, Italy
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Schmollinger S, Chen S, Merchant SS. Quantitative elemental imaging in eukaryotic algae. Metallomics 2023; 15:mfad025. [PMID: 37186252 PMCID: PMC10209819 DOI: 10.1093/mtomcs/mfad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/03/2023] [Indexed: 05/17/2023]
Abstract
All organisms, fundamentally, are made from the same raw material, namely the elements of the periodic table. Biochemical diversity is achieved by how these elements are utilized, for what purpose, and in which physical location. Determining elemental distributions, especially those of trace elements that facilitate metabolism as cofactors in the active centers of essential enzymes, can determine the state of metabolism, the nutritional status, or the developmental stage of an organism. Photosynthetic eukaryotes, especially algae, are excellent subjects for quantitative analysis of elemental distribution. These microbes utilize unique metabolic pathways that require various trace nutrients at their core to enable their operation. Photosynthetic microbes also have important environmental roles as primary producers in habitats with limited nutrient supplies or toxin contaminations. Accordingly, photosynthetic eukaryotes are of great interest for biotechnological exploitation, carbon sequestration, and bioremediation, with many of the applications involving various trace elements and consequently affecting their quota and intracellular distribution. A number of diverse applications were developed for elemental imaging, allowing subcellular resolution, with X-ray fluorescence microscopy (XFM, XRF) being at the forefront, enabling quantitative descriptions of intact cells in a non-destructive method. This Tutorial Review summarizes the workflow of a quantitative, single-cell elemental distribution analysis of a eukaryotic alga using XFM.
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Affiliation(s)
- Stefan Schmollinger
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Si Chen
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Sabeeha S Merchant
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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Firsova YE, Mustakhimov II, Torgonskaya ML. Compartment-related aspects of XoxF protein functionality in Methylorubrum extorquens DM4 analysed using its cytoplasmic targeting. Antonie Van Leeuwenhoek 2023; 116:393-413. [PMID: 36719530 DOI: 10.1007/s10482-023-01811-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/16/2023] [Indexed: 02/01/2023]
Abstract
The impact of periplasmic localisation on the functioning of the XoxF protein was evaluated in the well-studied dichloromethane-utilising methylotroph Methylorubrum extorquens DM4, which harbors only one paralogue of the xoxF gene. It was found that the cytoplasmic targeting of XoxF by expression of the corresponding gene without the sequence encoding the N-terminal signal peptide does not impair the activation and lanthanide-dependent regulation of the MxaFI-methanol dehydrogenase genes. Analysis of the viability of ΔxoxF cells complemented with the full-length and truncated xoxF gene also showed that the expression of cytoplasmically targeted XoxF even increases the resistance to acids. These results contradict the proposed function of the XoxF protein as an extracytoplasmic signal sensor. At the same time, the observed dynamics of growth with methanol, as well as with dichloromethane of strains expressing cytoplasmic-targeted XoxF, indicate the probable enzymatic activity of lanthanide-dependent methanol dehydrogenase in this compartment. Herewith, the only available substrate for this enzyme in cells growing with dichloromethane was formaldehyde, which is produced during the primary metabolism of the mentioned halogenated toxicant directly in the cytosol. These findings suggest that the maturation of XoxF-methanol dehydrogenase may occur already in the cytoplasm, while the factors changing affinity of this enzyme for formaldehyde are apparently absent there. Together with the demonstrated functioning of an enhancer-like upstream activating sequence in the promoter region of the xoxF gene in M. extorquens DM4, the obtained information enriches our understanding of the regulation, synthesis and role of the XoxF protein.
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Affiliation(s)
- Yulia E Firsova
- Laboratory of Radioactive Isotopes, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research of Russian Academy of Sciences, 142290, Pushchino, Russia
| | - Ildar I Mustakhimov
- Laboratory of Radioactive Isotopes, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research of Russian Academy of Sciences, 142290, Pushchino, Russia
| | - Maria L Torgonskaya
- Laboratory of Radioactive Isotopes, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research of Russian Academy of Sciences, 142290, Pushchino, Russia
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Wait EE, Gourary J, Liu C, Spoerke ED, Rempe SB, Ren P. Development of AMOEBA Polarizable Force Field for Rare-Earth La 3+ Interaction with Bioinspired Ligands. J Phys Chem B 2023; 127:1367-1375. [PMID: 36735638 PMCID: PMC9957963 DOI: 10.1021/acs.jpcb.2c07237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Rare-earth metals (REMs) are crucial for many important industries, such as power generation and storage, in addition to cancer treatment and medical imaging. One promising new REM refinement approach involves mimicking the highly selective and efficient binding of REMs observed in relatively recently discovered proteins. However, realizing any such bioinspired approach requires an understanding of the biological recognition mechanisms. Here, we developed a new classical polarizable force field based on the AMOEBA framework for modeling a lanthanum ion (La3+) interacting with water, acetate, and acetamide, which have been found to coordinate the ion in proteins. The parameters were derived by comparing to high-level ab initio quantum mechanical (QM) calculations that include relativistic effects. The AMOEBA model, with advanced atomic multipoles and electronic polarization, is successful in capturing both the QM distance-dependent La3+-ligand interaction energies and experimental hydration free energy. A new scheme for pairwise polarization damping (POLPAIR) was developed to describe the polarization energy in La3+ interactions with both charged and neutral ligands. Simulations of La3+ in water showed water coordination numbers and ion-water distances consistent with previous experimental and theoretical findings. Water residence time analysis revealed both fast and slow kinetics in water exchange around the ion. This new model will allow investigation of fully solvated lanthanum ion-protein systems using GPU-accelerated dynamics simulations to gain insights on binding selectivity, which may be applied to the design of synthetic analogues.
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Affiliation(s)
- Elizabeth E. Wait
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Justin Gourary
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Erik D. Spoerke
- Electronic, Optical, and Nano Materials Department, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Susan B. Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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Wang C, Qiao S, Zhou J. Strategy of nitrate removal in anaerobic ammonia oxidation-dependent processes. CHEMOSPHERE 2023; 313:137586. [PMID: 36529177 DOI: 10.1016/j.chemosphere.2022.137586] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 12/10/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
The anaerobic ammonium oxidation (anammox), a microbial process that is considered as a low-cost and high efficient wastewater treatment, has received extensive attention with an attractive application prospect. The anammox process reduces nitrite (NO2-) to nitrogen gas (N2) with ammonium (NH4+) as the electron donor. However, some nitrate (NO3-) equivalent to 11% of total nitrogen (TN) is generated in this process, which limits the development of anammox. To overcome this problem, many efforts have been made in this regard, mainly combining with other biological treatment methods (denitrification, denitrifying anaerobic methane oxidation, etc.), introducing the substance into anammox process, etc. Herein, we summarized a detailed review of previous researches on the removal of NO3- in the anammox-dependent processes. It is hoped that this review could serve as valuable guidance in future research and practical applications of anammox.
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Affiliation(s)
- Chao Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Sen Qiao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
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Identification of a TonB-Dependent Receptor Involved in Lanthanide Switch by the Characterization of Laboratory-Adapted Methylosinus trichosporium OB3b. Appl Environ Microbiol 2023; 89:e0141322. [PMID: 36645275 PMCID: PMC9888264 DOI: 10.1128/aem.01413-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Two methanol dehydrogenases (MDHs), MxaFI and XoxF, have been characterized in methylotrophic and methanotrophic bacteria. MxaFI contains a calcium ion in its active site, whereas XoxF contains a lanthanide ion. Importantly, the expression of MxaFI and XoxF is inversely regulated by lanthanide bioavailability, i.e., the "lanthanide switch." To reveal the genetic and environmental factors affecting the lanthanide switch, we focused on two Methylosinus trichosporium OB3b mutants isolated during routine cultivation. In these mutants, MxaF was constitutively expressed, but lanthanide-dependent XoxF1 was not, even in the presence of 25 μM cerium ions, which is sufficient for XoxF expression in the wild type. Genotyping showed that both mutants harbored a loss-of-function mutation in the CQW49_RS02145 gene, which encodes a TonB-dependent receptor. Gene disruption and complementation experiments demonstrated that CQW49_RS02145 was required for XoxF1 expression in the presence of 25 μM cerium ions. Phylogenetic analysis indicated that CQW49_RS02145 was homologous to the Methylorubrum extorquens AM1 lanthanide transporter gene (lutH). These findings suggest that CQW49_RS02145 is involved in lanthanide uptake across the outer membrane. Furthermore, we demonstrated that supplementation with cerium and glycerol caused severe growth arrest in the wild type. CQW49_RS02145 underwent adaptive laboratory evolution in the presence of cerium and glycerol ions, resulting in a mutation that partially mitigated the growth arrest. This finding implies that loss-of-function mutations in CQW49_RS02145 can be attributed to residual glycerol from the frozen stock. IMPORTANCE Lanthanides are widely used in many industrial applications, including catalysts, magnets, and polishing. Recently, lanthanide-dependent metabolism was characterized in methane-utilizing bacteria. Despite the global demand for lanthanides, few studies have investigated the mechanism of lanthanide uptake by these bacteria. In this study, we identify a lanthanide transporter in Methylosinus trichosporium OB3b and indicate the potential interaction between intracellular lanthanide and glycerol. Understanding the genetic and environmental factors affecting lanthanide uptake should not only help improve the use of lanthanides for the bioconversion of methane into valuable products like methanol but also be of value for developing biomining to extract lanthanides under neutral conditions.
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Abstract
Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.
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Affiliation(s)
- Kaleigh A Remick
- Department of Microbiology, Cornell University, New York, NY, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, New York, NY, United States.
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Friedman R. Estimating the Gibbs Hydration Energies of Actinium and Trans-Plutonium Actinides. Chemphyschem 2023; 24:e202200516. [PMID: 36149643 PMCID: PMC10100388 DOI: 10.1002/cphc.202200516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/23/2022] [Indexed: 01/20/2023]
Abstract
The use of actinides for medical, scientific and technological purposes has gained momentum in the recent years. This creates a need to understand their interactions with biomolecules, both at the interface and as they become complexed. Calculation of the Gibbs binding energies of the ions to biomolecules, i. e., the Gibbs energy change associated with a transfer of an ion from the water phase to its binding site, could help to understand the actinides' toxicities and to design agents that bind them with high affinities. To this end, there is a need to obtain accurate reference values for actinide hydration, that for most actinides are not available from experiment. In this study, a set of ionic radii is developed that enables future calculations of binding energies for Pu3+ and five actinides with renewed scientific and technological interest: Ac3+ , Am3+ , Cm3+ , Bk3+ and Cf3+ . Reference hydration energies were calculated using quantum chemistry and ion solvation theory and agree well for all ions except Ac3+ , where ion solvation theory seems to underestimate the magnitude of the Gibbs hydration energy. The set of radii and reference energies that are presented here provide means to calculate binding energies for actinides and biomolecules.
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Affiliation(s)
- Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, SE-391 82, Sweden
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Xie R, Takashino M, Igarashi K, Kitagawa W, Kato S. Transcriptional Regulation of Methanol Dehydrogenases in the Methanotrophic Bacterium Methylococcus capsulatus Bath by Soluble and Insoluble Lanthanides. Microbes Environ 2023; 38:ME23065. [PMID: 38092408 PMCID: PMC10728633 DOI: 10.1264/jsme2.me23065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/18/2023] [Indexed: 12/18/2023] Open
Abstract
The effects of soluble and insoluble lanthanides on gene expression in Methylococcus capsulatus Bath were investigated. Genes for lanthanide-containing methanol dehydrogenases (XoxF-MDHs) and their calcium-containing counterparts (MxaFI-MDHs) were up- and down-regulated, respectively, by supplementation with soluble lanthanide chlorides, indicating that M. capsulatus has the "lanthanide switch" observed in other methanotrophs. Insoluble lanthanide oxides also induced the lanthanide switch and were dissolved by the spent medium of M. capsulatus, suggesting the presence of lanthanide-chelating compounds. A transcriptome ana-lysis indicated that a gene cluster for the synthesis of an enterobactin-like metal chelator contributed to the dissolution of insoluble lanthanides.
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Affiliation(s)
- Ruoyun Xie
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060–8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
| | - Motoko Takashino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
| | - Wataru Kitagawa
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060–8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
| | - Souichiro Kato
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060–8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
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Kajjumba GW, Marti EJ. A review of the application of cerium and lanthanum in phosphorus removal during wastewater treatment: Characteristics, mechanism, and recovery. CHEMOSPHERE 2022; 309:136462. [PMID: 36162516 DOI: 10.1016/j.chemosphere.2022.136462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Owing to their strong bond with anions, rare earth elements (REEs) are prime contenders in wastewater treatment to meet the stringent phosphorus (P) effluent quality requirements. REEs outcompete traditional metals to abate phosphorus. The application of lanthanides in wastewater treatment is mainly through adsorption, where REEs are incorporated into a carrier matrix to improve the adsorption capacity. As coagulants, information on the performance of lanthanides is lacking. In this review, the performance of major water coagulants (iron and aluminum) is discussed and compared to two lanthanides: cerium and lanthanum. The use of lanthanides as adsorbents and as coagulants is elucidated during P treatment. The recovery of P and REEs is also discussed. Where details were lacking in the literature, experiments were conducted to fill these research gaps. Using REEs as adsorbents limits their P precipitation potential; as coagulants, REE capacity is 520.79 mg P/g La3+ and 469.96 mg P/g Ce3+. In addition, as coagulants, they are not affected by pH (3.0 < pH < 10.0); however, carbonates and sulfate are the major species that can reduce the performance of REEs during P treatment. REE-P precipitation is orchestrated through the formation of an REE-PO4 bond. Unfortunately, this strong bond between lanthanides and phosphate makes phosphate recovery almost impractical. If the goal is to recover REEs and reuse P in other applications like fertilizers, REEs are not the best candidates. We recommend additional research dedicated to understanding lanthanide coagulants in typical wastewater treatment facilities and their release from phosphate precipitates under different environmental conditions.
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Affiliation(s)
- George William Kajjumba
- Department of Civil and Environmental Engineering and Construction, University of Nevada, 4505 S. Maryland Pkwy, Las Vegas, NV, 89154, USA.
| | - Erica J Marti
- Department of Civil and Environmental Engineering and Construction, University of Nevada, 4505 S. Maryland Pkwy, Las Vegas, NV, 89154, USA.
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Nijman TPA, Lemmens M, Lurling M, Kosten S, Welte C, Veraart AJ. Phosphorus control and dredging decrease methane emissions from shallow lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157584. [PMID: 35882339 DOI: 10.1016/j.scitotenv.2022.157584] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Freshwater ecosystems are an important source of the greenhouse gas methane (CH4), and their emissions are expected to increase due to eutrophication. Two commonly applied management techniques to reduce eutrophication are the addition of phosphate-binding lanthanum modified bentonite (LMB, trademark Phoslock©) and dredging, but their effect on CH4 emissions is still poorly understood. Here, this study researched how LMB and dredging affected CH4 emissions using a full-factorial mesocosm design monitored for 18 months. The effect was tested by measuring diffusive and ebullitive CH4 fluxes, plant community composition, methanogen and methanotroph activity and community composition, and a range of physicochemical water and sediment variables. LMB addition decreased total CH4 emissions, while dredging showed a trend towards decreasing CH4 emissions. Total CH4 emissions in all mesocosms were much higher in the summer of the second year, likely because of higher algal decomposition and organic matter availability. First, LMB addition lowered CH4 emissions by decreasing P-availability, which reduced coverage of the floating fern Azolla filiculoides, and thereby prevented anoxia and decreased surface water NH4+ concentrations, lowering CH4 production rates. Second, dredging decreased CH4 emissions in the first summer, possibly it removed the methanogenic community, and in the second year by preventing autumn and winter die-off of the rooted macrophyte Potamogeton cripsus. Finally, methanogen community composition was related to surface water NH4+ and O2, and porewater total phosphorus, while methanotroph community composition was related to organic matter content. To conclude, LMB addition and dredging not only improve water quality, but also decrease CH4 emissions, mitigating climate change.
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Affiliation(s)
- Thomas P A Nijman
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
| | - Maxime Lemmens
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Miquel Lurling
- Aquatic Ecology & Water Quality Management Group, Department of Environmental Sciences, Wageningen University, Droevendaalsesteeg 3a, 6708 PB Wageningen, the Netherlands
| | - Sarian Kosten
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Cornelia Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
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Pütz E, Gazanis A, Keltsch NG, Jegel O, Pfitzner F, Heermann R, Ternes TA, Tremel W. Communication Breakdown: Into the Molecular Mechanism of Biofilm Inhibition by CeO 2 Nanocrystal Enzyme Mimics and How It Can Be Exploited. ACS NANO 2022; 16:16091-16108. [PMID: 36174231 DOI: 10.1021/acsnano.2c04377] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Bacterial biofilm formation is a huge problem in industry and medicine. Therefore, the discovery of anti-biofilm agents may hold great promise. Biofilm formation is usually a consequence of bacterial cell-cell communication, a process called quorum sensing (QS). CeO2 nanocrystals (NCs) have been established as haloperoxidase (HPO) mimics and ecologically beneficial biofilm inhibitors. They were suggested to interfere with QS, a mechanism termed quorum quenching (QQ), but their molecular mechanism remained elusive. We show that CeO2 NCs are effective QQ agents, inactivating QS signals by bromination. Catalytic bromination of 3-oxo-C12-AHL a QS signaling compound used by Pseudomonas aeruginosa, was detected in the presence of CeO2 NCs, bromide ions, and hydrogen peroxide. Brominated acyl-homoserine lactones (AHLs) no longer act as QS signals but were not detected in the bacterial cultures. Externally added brominated AHLs also disappeared in P. aeruginosa cultures within minutes of their addition, indicating that they are rapidly degraded by the bacteria. Moreover, we detected the catalytic bromination of 2-heptyl-1-hydroxyquinolin-4(1H)-one (HQNO), a multifunctional non-AHL QS signal from P. aeruginosa with antibacterial and algicidal properties controlling the expression of many virulence genes. Brominated HQNO was not degraded by the bacteria in vivo. The repression of the Pseudomonas quinolone signal (PQS) production and biofilm formation in P. aeruginosa through the catalytic formation of Br-HQNO on surfaces with coatings containing CeO2 enzyme mimics validates the non-toxic strategy for the development of anti-infectives.
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Affiliation(s)
- Eva Pütz
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Athanasios Gazanis
- Mikrobiologie und Biotechnologie, Institut für Molekulare PhysiologieJohannes Gutenberg-Universität Mainz, Biozentrum II, Hanns-Dieter-Hüsch-Weg 17, D-55128 Mainz, Germany
| | - Nils Gert Keltsch
- Bundesanstalt für Gewässerkunde, Am Mainzer Tor 1, D-56068 Koblenz, Germany
| | - Olga Jegel
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Felix Pfitzner
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Ralf Heermann
- Mikrobiologie und Biotechnologie, Institut für Molekulare PhysiologieJohannes Gutenberg-Universität Mainz, Biozentrum II, Hanns-Dieter-Hüsch-Weg 17, D-55128 Mainz, Germany
| | - Thomas A Ternes
- Bundesanstalt für Gewässerkunde, Am Mainzer Tor 1, D-56068 Koblenz, Germany
| | - Wolfgang Tremel
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
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Neira G, Vergara E, Holmes DS. Genome-guided prediction of acid resistance mechanisms in acidophilic methanotrophs of phylogenetically deep-rooted Verrucomicrobia isolated from geothermal environments. Front Microbiol 2022; 13:900531. [PMID: 36212841 PMCID: PMC9543262 DOI: 10.3389/fmicb.2022.900531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Verrucomicrobia are a group of microorganisms that have been proposed to be deeply rooted in the Tree of Life. Some are methanotrophs that oxidize the potent greenhouse gas methane and are thus important in decreasing atmospheric concentrations of the gas, potentially ameliorating climate change. They are widespread in various environments including soil and fresh or marine waters. Recently, a clade of extremely acidophilic Verrucomicrobia, flourishing at pH < 3, were described from high-temperature geothermal ecosystems. This novel group could be of interest for studies about the emergence of life on Earth and to astrobiologists as homologs for possible extraterrestrial life. In this paper, we describe predicted mechanisms for survival of this clade at low pH and suggest its possible evolutionary trajectory from an inferred neutrophilic ancestor. Extreme acidophiles are defined as organisms that thrive in extremely low pH environments (≤ pH 3). Many are polyextremophiles facing high temperatures and high salt as well as low pH. They are important to study for both providing fundamental insights into biological mechanisms of survival and evolution in such extreme environments and for understanding their roles in biotechnological applications such as industrial mineral recovery (bioleaching) and mitigation of acid mine drainage. They are also, potentially, a rich source of novel genes and pathways for the genetic engineering of microbial strains. Acidophiles of the Verrucomicrobia phylum are unique as they are the only known aerobic methanotrophs that can grow optimally under acidic (pH 2–3) and moderately thermophilic conditions (50–60°C). Three moderately thermophilic genera, namely Methylacidiphilum, Methylacidimicrobium, and Ca. Methylacidithermus, have been described in geothermal environments. Most of the investigations of these organisms have focused on their methane oxidizing capabilities (methanotrophy) and use of lanthanides as a protein cofactor, with no extensive study that sheds light on the mechanisms that they use to flourish at extremely low pH. In this paper, we extend the phylogenetic description of this group of acidophiles using whole genome information and we identify several mechanisms, potentially involved in acid resistance, including “first line of defense” mechanisms that impede the entry of protons into the cell. These include the presence of membrane-associated hopanoids, multiple copies of the outer membrane protein (Slp), and inner membrane potassium channels (kup, kdp) that generate a reversed membrane potential repelling the intrusion of protons. Acidophilic Verrucomicrobia also display a wide array of proteins potentially involved in the “second line of defense” where protons that evaded the first line of defense and entered the cell are expelled or neutralized, such as the glutamate decarboxylation (gadAB) and phosphate-uptake systems. An exclusive N-type ATPase F0-F1 was identified only in acidophiles of Verrucomicrobia and is predicted to be a specific adaptation in these organisms. Phylogenetic analyses suggest that many predicted mechanisms are evolutionarily conserved and most likely entered the acidophilic lineage of Verrucomicrobia by vertical descent from a common ancestor. However, it is likely that some defense mechanisms such as gadA and kup entered the acidophilic Verrucomicrobia lineage by horizontal gene transfer.
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Affiliation(s)
- Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- *Correspondence: David S. Holmes
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Tabuchi R, Takezawa H, Fujita M. Selective Confinement of Rare‐Earth‐Metal Hydrates by a Capped Metallo‐Cage under Aqueous Conditions. Angew Chem Int Ed Engl 2022; 61:e202208866. [DOI: 10.1002/anie.202208866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Ryosuke Tabuchi
- Department of Applied Chemistry School of Engineering The University of Tokyo Mitsui Link Lab Kashiwanoha 1, FS CREATION 6-6-2 Kashiwanoha Kashiwa Chiba 227-0882 Japan
| | - Hiroki Takezawa
- Department of Applied Chemistry School of Engineering The University of Tokyo Mitsui Link Lab Kashiwanoha 1, FS CREATION 6-6-2 Kashiwanoha Kashiwa Chiba 227-0882 Japan
| | - Makoto Fujita
- Department of Applied Chemistry School of Engineering The University of Tokyo Mitsui Link Lab Kashiwanoha 1, FS CREATION 6-6-2 Kashiwanoha Kashiwa Chiba 227-0882 Japan
- Division of Advanced Molecular Science Institute for Molecular Science (IMS) 5-1 Higashiyama, Myodaiji Okazaki Aichi 444-8787 Japan
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Maret W. The quintessence of metallomics: a harbinger of a different life science based on the periodic table of the bioelements. Metallomics 2022; 14:mfac051. [PMID: 35820043 PMCID: PMC9406523 DOI: 10.1093/mtomcs/mfac051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022]
Abstract
This year marks the 20th anniversary of the field of metallomics. As a landmark in time, it is an occasion to reflect on the past, present, and future of this integrated field of biometal sciences. A fundamental bias is one reason for having metallomics as a scientific discipline. The focus of biochemistry on the six non-metal chemical elements, collectively known with the acronym SPONCH (sulphur, phosphorus, oxygen, nitrogen, carbon, hydrogen), glosses over the fact that the lower quantities of many other elements have qualities that made them instrumental in the evolution of life and pivotal in numerous life processes. The metallome, alongside the genome, proteome, lipidome, and glycome, should be regarded as a fifth pillar of elemental-vis-à-vis molecular-building blocks in biochemistry. Metallomics as 'global approaches to metals in the biosciences' considers the biological significance of most chemical elements in the periodic table, not only the ones essential for life, but also the non-essential ones that are present in living matter-some at higher concentrations than the essential ones. The non-essential elements are bioactive with either positive or negative effects. Integrating the significance of many more chemical elements into the life sciences requires a transformation in learning and teaching with a focus on elemental biology in addition to molecular biology. It should include the dynamic interactions between the biosphere and the geosphere and how the human footprint is changing the ecology globally and exposing us to many additional chemical elements that become new bioelements.
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Affiliation(s)
- Wolfgang Maret
- Metal Metabolism Group, Department of Nutritional Sciences, School of Life Course and Population Sciences, King's College London,London, UK
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Abstract
Wetlands are the major natural source of methane, an important greenhouse gas. The sulfur and methane cycles in wetlands are linked—e.g., a strong sulfur cycle can inhibit methanogenesis. Although there has historically been a clear distinction drawn between methane and sulfur oxidizers, here, we isolated a methanotroph that also performed respiratory oxidization of sulfur compounds. We experimentally demonstrated that thiotrophy and methanotrophy are metabolically compatible, and both metabolisms could be expressed simultaneously in a single microorganism. These findings suggest that mixotrophic methane/sulfur-oxidizing bacteria are a previously overlooked component of environmental methane and sulfur cycles. This creates a framework for a better understanding of these redox cycles in natural and engineered wetlands. Natural and anthropogenic wetlands are major sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic bacteria at the oxic–anoxic interface, a zone of intense redox cycling of carbon, sulfur, and nitrogen compounds. Here, we report on the isolation of an aerobic methanotrophic bacterium, ‘Methylovirgula thiovorans' strain HY1, which possesses metabolic capabilities never before found in any methanotroph. Most notably, strain HY1 is the first bacterium shown to aerobically oxidize both methane and reduced sulfur compounds for growth. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are responsible for methane and methanol oxidation, respectively. Various pathways for respiratory sulfur oxidation were present, including the Sox–rDsr pathway and the S4I system. Strain HY1 employed the Calvin–Benson–Bassham cycle for CO2 fixation during chemolithoautotrophic growth on reduced sulfur compounds. Proteomic and microrespirometry analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of the respective substrates. Methane and thiosulfate could therefore be independently or simultaneously oxidized. The discovery of this versatile bacterium demonstrates that methanotrophy and thiotrophy are compatible in a single microorganism and underpins the intimate interactions of methane and sulfur cycles in oxic–anoxic interface environments.
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