1
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Srivastava S, Dong H, Baars O, Sheng Y. Bioavailability of mineral-associated trace metals as cofactors for nitrogen fixation by Azotobacter vinelandii. GEOBIOLOGY 2023; 21:507-519. [PMID: 36852450 DOI: 10.1111/gbi.12552] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/28/2023] [Accepted: 02/12/2023] [Indexed: 06/13/2023]
Abstract
Life on Earth depends on N2 -fixing microbes to make ammonia from atmospheric N2 gas by the nitrogenase enzyme. Most nitrogenases use Mo as a cofactor; however, V and Fe are also possible. N2 fixation was once believed to have evolved during the Archean-Proterozoic times using Fe as a cofactor. However, δ15 N values of paleo-ocean sediments suggest Mo and V cofactors despite their low concentrations in the paleo-oceans. This apparent paradox is based on an untested assumption that only soluble metals are bioavailable. In this study, laboratory experiments were performed to test the bioavailability of mineral-associated trace metals to a model N2 -fixing bacterium Azotobacter vinelandii. N2 fixation was observed when Mo in molybdenite, V in cavansite, and Fe in ferrihydrite were used as the sole sources of cofactors, but the rate of N2 fixation was greatly reduced. A physical separation between minerals and cells further reduced the rate of N2 fixation. Biochemical assays detected five siderophores, including aminochelin, azotochelin, azotobactin, protochelin, and vibrioferrin, as possible chelators to extract metals from minerals. The results of this study demonstrate that mineral-associated trace metals are bioavailable as cofactors of nitrogenases to support N2 fixation in those environments that lack soluble trace metals and may offer a partial answer to the paradox.
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Affiliation(s)
- Shreya Srivastava
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, USA
| | - Hailiang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, USA
| | - Oliver Baars
- Department of Entomology and Plant Pathology, North Carolina State University, North Carolina, Raleigh, USA
| | - Yizhi Sheng
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, USA
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2
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Sheng Y, Baars O, Guo D, Whitham J, Srivastava S, Dong H. Mineral-Bound Trace Metals as Cofactors for Anaerobic Biological Nitrogen Fixation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7206-7216. [PMID: 37116091 DOI: 10.1021/acs.est.3c01371] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nitrogenase is the only known biological enzyme capable of reducing N2 to bioavailable NH3. Most nitrogenases use Mo as a metallocofactor, while alternative cofactors V and Fe are also viable. Both geological and bioinformatic evidence suggest an ancient origin of Mo-based nitrogenase in the Archean, despite the low concentration of dissolved Mo in the Archean oceans. This apparent paradox would be resolvable if mineral-bound Mo were bioavailable for nitrogen fixation by ancient diazotrophs. In this study, the bioavailability of mineral-bound Mo, V, and Fe was determined by incubating an obligately anaerobic diazotroph Clostridium kluyveri with Mo-, V-, and Fe-bearing minerals (molybdenite, cavansite, and ferrihydrite, respectively) and basalt under diazotrophic conditions. The results showed that C. kluyveri utilized mineral-associated metals to express nitrogenase genes and fix nitrogen, as measured by the reverse transcription quantitative polymerase chain reaction and acetylene reduction assay, respectively. C. kluyveri secreted chelating molecules to extract metals from the minerals. As a result of microbial weathering, mineral surface chemistry significantly changed, likely due to surface coating by microbial exudates for metal extraction. These results provide important support for the ancient origin of Mo-based nitrogenase, with profound implications for coevolution of the biosphere and geosphere.
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Affiliation(s)
- Yizhi Sheng
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio 45056, United States
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Oliver Baars
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Dongyi Guo
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio 45056, United States
| | - Jason Whitham
- Department of Plant and Molecular Biology, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Shreya Srivastava
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio 45056, United States
| | - Hailiang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio 45056, United States
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3
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Darnajoux R, Inomura K, Zhang X. A diazotrophy-ammoniotrophy dual growth model for the sulfate reducing bacterium Desulfovibrio vulgaris var. Hildenborough. Comput Struct Biotechnol J 2023; 21:3136-3148. [PMID: 37293241 PMCID: PMC10244686 DOI: 10.1016/j.csbj.2023.05.007] [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: 01/31/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 06/10/2023] Open
Abstract
Sulfate reducing bacteria (SRB) comprise one of the few prokaryotic groups in which biological nitrogen fixation (BNF) is common. Recent studies have highlighted SRB roles in N cycling, particularly in oligotrophic coastal and benthic environments where they could contribute significantly to N input. Most studies of SRB have focused on sulfur cycling and SRB growth models have primarily aimed at understanding the effects of electron sources, with N usually provided as fixed-N (nitrate, ammonium). Mechanistic links between SRB nitrogen-fixing metabolism and growth are not well understood, particularly in environments where fixed-N fluctuates. Here, we investigate diazotrophic growth of the model sulfate reducer Desulfovibrio vulgaris var. Hildenborough under anaerobic heterotrophic conditions and contrasting N availabilities using a simple cellular model with dual ammoniotrophic and diazotrophic modes. The model was calibrated using batch culture experiments with varying initial ammonium concentrations (0-3000 µM) and acetylene reduction assays of BNF activity. The model confirmed the preferential usage of ammonium over BNF for growth and successfully reproduces experimental data, with notably clear bi-phasic growth curves showing an initial ammoniotrophic phase followed by onset of BNF. Our model enables quantification of the energetic cost of each N acquisition strategy and indicates the existence of a BNF-specific limiting phenomenon, not directly linked to micronutrient (Mo, Fe, Ni) concentration, by-products (hydrogen, hydrogen sulfide), or fundamental model metabolic parameters (death rate, electron acceptor stoichiometry). By providing quantitative predictions of environment and metabolism, this study contributes to a better understanding of anaerobic heterotrophic diazotrophs in environments with fluctuating N conditions.
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Affiliation(s)
- Romain Darnajoux
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
- High Meadow Environmental Institute, Princeton University, Princeton, NJ 08544, USA
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
- High Meadow Environmental Institute, Princeton University, Princeton, NJ 08544, USA
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4
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Quantification of biological nitrogen fixation by Mo-independent complementary nitrogenases in environmental samples with low nitrogen fixation activity. Sci Rep 2022; 12:22011. [PMID: 36539445 PMCID: PMC9768154 DOI: 10.1038/s41598-022-24860-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Biological nitrogen fixation (BNF) by canonical molybdenum and complementary vanadium and iron-only nitrogenase isoforms is the primary natural source of newly fixed nitrogen. Understanding controls on global nitrogen cycling requires knowledge of the isoform responsible for environmental BNF. The isotopic acetylene reduction assay (ISARA), which measures carbon stable isotope (13C/12C) fractionation between ethylene and acetylene in acetylene reduction assays, is one of the few methods that can quantify isoform-specific BNF fluxes. Application of classical ISARA has been challenging because environmental BNF activity is often too low to generate sufficient ethylene for isotopic analyses. Here we describe a high sensitivity method to measure ethylene δ13C by in-line coupling of ethylene preconcentration to gas chromatography-combustion-isotope ratio mass spectrometry (EPCon-GC-C-IRMS). Ethylene requirements in samples with 10% v/v acetylene are reduced from > 500 to ~ 20 ppmv (~ 2 ppmv with prior offline acetylene removal). To increase robustness by reducing calibration error, single nitrogenase-isoform Azotobacter vinelandii mutants and environmental sample assays rely on a common acetylene source for ethylene production. Application of the Low BNF activity ISARA (LISARA) method to low nitrogen-fixing activity soils, leaf litter, decayed wood, cryptogams, and termites indicates complementary BNF in most sample types, calling for additional studies of isoform-specific BNF.
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5
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Darnajoux R, Bradley R, Bellenger JP. In Vivo Temperature Dependency of Molybdenum and Vanadium Nitrogenase Activity in the Heterocystous Cyanobacteria Anabaena variabilis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2760-2769. [PMID: 35073047 DOI: 10.1021/acs.est.1c05279] [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: 06/14/2023]
Abstract
The reduction of atmospheric dinitrogen by nitrogenase is a key component of terrestrial nitrogen cycling. Nitrogenases exist in several isoforms named after the metal present within their active center: the molybdenum (Mo), the vanadium (V), and the iron (Fe)-only nitrogenase. While earlier in vitro studies hint that the relative contribution of V nitrogenase to total BNF could be temperature-dependent, the effect of temperature on in vivo activity remains to be investigated. In this study, we characterize the in vivo effect of temperature (3-42 °C) on the activities of Mo nitrogenase and V nitrogenase in the heterocystous cyanobacteria Anabaena variabilis ATTC 29413 using the acetylene reduction assay by cavity ring-down absorption spectroscopy. We demonstrate that V nitrogenase becomes as efficient as Mo nitrogenase at temperatures below 10-15 °C. At temperatures above 22 °C, BNF seems to be limited by O2 availability to respiration in both enzymes. Furthermore, Anabaena variabilis cultures grown in Mo or V media achieved similar growth rates at temperatures below 20 °C. Considering the average temperature on earth is 15 °C, our findings further support the role of V nitrogenase as a viable backup enzymatic system for BNF in natural ecosystems.
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Affiliation(s)
- Romain Darnajoux
- Département de Chimie, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
- Centre Sève, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Robert Bradley
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
- Centre Sève, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Jean-Philippe Bellenger
- Département de Chimie, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
- Centre Sève, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
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6
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Smethurst DGJ, Shcherbik N. Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules. J Biol Chem 2021; 297:101374. [PMID: 34732319 PMCID: PMC8633580 DOI: 10.1016/j.jbc.2021.101374] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 02/08/2023] Open
Abstract
Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth's atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.
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Affiliation(s)
- Daniel G J Smethurst
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
| | - Natalia Shcherbik
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
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7
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Doydora SA, Baars O, Harrington JM, Duckworth OW. Salicylate coordination in metal-protochelin complexes. Biometals 2021; 35:87-98. [PMID: 34837588 DOI: 10.1007/s10534-021-00352-7] [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: 08/09/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022]
Abstract
Molybdenum (Mo) is an essential trace element for bacteria that is utilized in myriad metalloenzymes that directly couple to the biogeochemical cycling of nitrogen, sulfur, and carbon. In particular, Mo is found in the most common nitrogenase enzyme, and the scarcity and low bioavailability of Mo in soil may be a critical factor that contributes to the limitation of nitrogen fixation in forests and agroenvironments. To overcome this scarcity, microbes produce exudates that specifically chelate scarce metals, promoting their solubilization and uptake. Here, we have determined the structure and stability constants of Mo bound by protochelin, a siderophore produced by bacteria under Mo-depleted conditions. Spectrophotometric titration spectra indicated a coordination shift from a catecholate to salicylate binding mode for MoVI-protochelin (Mo-Proto) complexes at pH < 5. pKa values obtained from analysis of titrations were 4.8 ± 0.3 for MoVIO2H3Proto- and 3.3 ± 0.1 for MoVIO2H4Proto. The occurrence of negatively charged Mo-Proto complexes at pH 6 was also confirmed by mass spectrometry. K-edge Extended X-ray absorption fine structure spectroscopy confirmed the change in Mo coordination at low pH, and structural fitting provides insights into the physical architecture of complexes at neutral and acidic pH. These findings suggest that Mo can be chelated by protochelin across a wide environmental pH range, with a coordination shift occurring at pH < 5. This chelation and associated coordination shift may impact biological availability and mineral surface retention of Mo under acidic conditions.
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Affiliation(s)
- Sarah A Doydora
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Oliver Baars
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - James M Harrington
- RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709-2194, USA
| | - Owen W Duckworth
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
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8
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Yu GH, Kuzyakov Y, Luo Y, Goodman BA, Kappler A, Liu FF, Sun FS. Molybdenum Bioavailability and Asymbiotic Nitrogen Fixation in Soils are Raised by Iron (Oxyhydr)oxide-Mediated Free Radical Production. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14979-14989. [PMID: 34677955 DOI: 10.1021/acs.est.1c04240] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nitrogen (N) fixation in soils is closely linked to microbially mediated molybdenum (Mo) cycling. Therefore, elucidating the mechanisms and factors that affect Mo bioavailability is crucial for understanding N fixation. Here, we demonstrate that long-term (26 years) manure fertilization increased microbial diversity and content of short-range ordered iron (oxyhydr)oxides that raised Mo bioavailability (by 2.8 times) and storage (by ∼30%) and increased the abundance of nifH genes (by ∼14%) and nitrogenase activity (by ∼60%). Nanosized iron (oxyhydr)oxides (ferrihydrite, goethite, and hematite nanoparticles) play a dual role in soil Mo cycling: (i) in concert with microorganisms, they raise Mo bioavailability by catalyzing hydroxyl radical (HO•) production via the Fenton reactions and (ii) they increase Mo retention by association with the nanosized iron (oxyhydr)oxides. In summary, long-term manure fertilization raised the stock and bioavailability of Mo (and probably also of other micronutrients) by increasing iron (oxyhydr)oxide reactivity and intensified asymbiotic N fixation through an increased abundance of nifH genes and nitrogenase activity. This work provides a strategy for increasing biological N fixation in agricultural ecosystems.
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Affiliation(s)
- Guang-Hui Yu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, Göttingen 37073, Germany
- Agro-Technological Institute, RUDN University, Moscow 117198, Russia
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Bernard A Goodman
- College of Physical Science and Technology, Guangxi University, Nanning 530004, China
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen 72076, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infections, Tübingen 72076, Germany
| | - Fei-Fei Liu
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fu-Sheng Sun
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China
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9
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Hemkemeyer M, Schwalb SA, Heinze S, Joergensen RG, Wichern F. Functions of elements in soil microorganisms. Microbiol Res 2021; 252:126832. [PMID: 34508963 DOI: 10.1016/j.micres.2021.126832] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.
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Affiliation(s)
- Michael Hemkemeyer
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany.
| | - Sanja A Schwalb
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
| | - Stefanie Heinze
- Department of Soil Science & Soil Ecology, Ruhr-University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Rainer Georg Joergensen
- Department of Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, 37213 Witzenhausen, Germany
| | - Florian Wichern
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
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10
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Saiz E, Sgouridis F, Drijfhout FP, Peichl M, Nilsson MB, Ullah S. Chronic Atmospheric Reactive Nitrogen Deposition Suppresses Biological Nitrogen Fixation in Peatlands. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1310-1318. [PMID: 33389989 DOI: 10.1021/acs.est.0c04882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Biological nitrogen fixation (BNF) represents the natural pathway by which mosses meet their demands for bioavailable/reactive nitrogen (Nr) in peatlands. However, following intensification of nitrogen fertilizer and fossil fuel use, atmospheric Nr deposition has increased exposing peatlands to Nr loading often above the ecological threshold. As BNF is energy intensive, therefore, it is unclear whether BNF shuts down when Nr availability is no longer a rarity. We studied the response of BNF under a gradient of Nr deposition extending over decades in three peatlands in the U.K., and at a background deposition peatland in Sweden. Experimental nitrogen fertilization plots in the Swedish site were also evaluated for BNF activity. In situ BNF activity of peatlands receiving Nr deposition of 6, 17, and 27 kg N ha-1 yr-1 was not shut down but rather suppressed by 54, 69, and 74%, respectively, compared to the rates under background Nr deposition of ∼2 kg N ha-1 yr-1. These findings were corroborated by similar BNF suppression at the fertilization plots in Sweden. Therefore, contribution of BNF in peatlands exposed to chronic Nr deposition needs accounting when modeling peatland's nitrogen pools, given that nitrogen availability exerts a key control on the carbon capture of peatlands, globally.
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Affiliation(s)
- Ernesto Saiz
- School of Geography, Geology, and the Environment, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Fotis Sgouridis
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, United Kingdom
| | - Falko P Drijfhout
- Chemical Ecology Group, School of Physical and Chemical Sciences, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Matthias Peichl
- Department of Forest Ecology & Management, Swedish University of Agricultural Sciences, Umeå 750 07, Sweden
| | - Mats B Nilsson
- Department of Forest Ecology & Management, Swedish University of Agricultural Sciences, Umeå 750 07, Sweden
| | - Sami Ullah
- School of Geography, Earth, and Environmental Sciences, and Birmingham Institute of Forest Research, University of Birmingham, Birmingham B15 2TT, United Kingdom
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11
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Kügler S, Cooper RE, Boessneck J, Küsel K, Wichard T. Rhizobactin B is the preferred siderophore by a novel Pseudomonas isolate to obtain iron from dissolved organic matter in peatlands. Biometals 2020; 33:415-433. [PMID: 33026607 PMCID: PMC7676072 DOI: 10.1007/s10534-020-00258-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 09/30/2020] [Indexed: 01/12/2023]
Abstract
Bacteria often release diverse iron-chelating compounds called siderophores to scavenge iron from the environment for many essential biological processes. In peatlands, where the biogeochemical cycle of iron and dissolved organic matter (DOM) are coupled, bacterial iron acquisition can be challenging even at high total iron concentrations. We found that the bacterium Pseudomonas sp. FEN, isolated from an Fe-rich peatland in the Northern Bavarian Fichtelgebirge (Germany), released an unprecedented siderophore for its genus. High-resolution mass spectrometry (HR-MS) using metal isotope-coded profiling (MICP), MS/MS experiments, and nuclear magnetic resonance spectroscopy (NMR) identified the amino polycarboxylic acid rhizobactin and a novel derivative at even higher amounts, which was named rhizobactin B. Interestingly, pyoverdine-like siderophores, typical for this genus, were not detected. With peat water extract (PWE), studies revealed that rhizobactin B could acquire Fe complexed by DOM, potentially through a TonB-dependent transporter, implying a higher Fe binding constant of rhizobactin B than DOM. The further uptake of Fe-rhizobactin B by Pseudomonas sp. FEN suggested its role as a siderophore. Rhizobactin B can complex several other metals, including Al, Cu, Mo, and Zn. The study demonstrates that the utilization of rhizobactin B can increase the Fe availability for Pseudomonas sp. FEN through ligand exchange with Fe-DOM, which has implications for the biogeochemical cycling of Fe in this peatland.
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Affiliation(s)
- Stefan Kügler
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Rebecca E Cooper
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Johanna Boessneck
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
- The German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, 07743, Jena, Germany.
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12
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Wong MY, Neill C, Marino R, Silvério D, Howarth RW. Molybdenum, phosphorus, and pH do not constrain nitrogen fixation in a tropical forest in the southeastern Amazon. Ecology 2020; 102:e03211. [PMID: 32981087 DOI: 10.1002/ecy.3211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 07/06/2020] [Accepted: 08/06/2020] [Indexed: 01/09/2023]
Abstract
High rates of biological nitrogen fixation (BNF) are commonly reported for tropical forests, but most studies have been conducted in regions that receive substantial inputs of molybdenum (Mo) from atmospheric dust and sea-salt aerosols. Even in these regions, the low availability of Mo can constrain free-living BNF catalyzed by heterotrophic bacteria and archaea. We hypothesized that in regions where atmospheric inputs of Mo are low and soils are highly weathered, such as the southeastern Amazon, Mo would constrain BNF. We also hypothesized that the high soil acidity, characteristic of the Amazon Basin, would further constrain Mo availability and therefore soil BNF. We conducted two field experiments across the wet and dry seasons, adding Mo, phosphorus (P), and lime alone and in combination to the forest floor in the southeastern Amazon. We sampled soils and litter immediately, and then weeks and months after the applications, and measured Mo and P availability through resin extractions and BNF with the acetylene reduction assay. The experimental additions of Mo and P increased their availability and the lime increased soil pH. While the combination of Mo and P increased BNF at some time points, BNF rates did not increase strongly or consistently across the study as a whole, suggesting that Mo, P, and soil pH are not the dominant controls over BNF. In a separate short-term laboratory experiment, BNF did not respond strongly to Mo and P even when labile carbon was added. We postulate that high nitrogen (N) availability in this area of the Amazon, as indicated by the stoichiometry of soils and vegetation and the high nitrate soil stocks, likely suppresses BNF at this site. These patterns may also extend across highly weathered soils with high N availability in other topographically stable regions of the tropics.
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Affiliation(s)
- Michelle Y Wong
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853, USA
| | | | - Roxanne Marino
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Divino Silvério
- Instituto de Pesquisa Ambiental da Amazônia (IPAM), Canarana, Mato Grosso, 78640-000, Brazil.,Departamento de Biologia, Universidade Federal Rural da Amazônia-UFRA, Capitão Poço, Pará, 68650-000, Brazil
| | - Robert W Howarth
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853, USA.,Woods Hole Research Center, Falmouth, Massachusetts, 02450, USA
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13
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Luxem KE, Leavitt WD, Zhang X. Large Hydrogen Isotope Fractionation Distinguishes Nitrogenase-Derived Methane from Other Methane Sources. Appl Environ Microbiol 2020; 86:e00849-20. [PMID: 32709722 PMCID: PMC7499036 DOI: 10.1128/aem.00849-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/16/2020] [Indexed: 02/01/2023] Open
Abstract
Biological nitrogen fixation is catalyzed by the enzyme nitrogenase. Two forms of this metalloenzyme, the vanadium (V)- and iron (Fe)-only nitrogenases, were recently found to reduce small amounts of carbon dioxide (CO2) into the potent greenhouse gas methane (CH4). Here, we report carbon (13C/12C) and hydrogen (2H/1H) stable isotopic compositions and fractionations of methane generated by V- and Fe-only nitrogenases in the metabolically versatile nitrogen fixer Rhodopseudomonas palustris The stable carbon isotope fractionation imparted by both forms of alternative nitrogenase are within the range observed for hydrogenotrophic methanogenesis (13αCO2/CH4 = 1.051 ± 0.002 for V-nitrogenase and 1.055 ± 0.001 for Fe-only nitrogenase; values are means ± standard errors). In contrast, the hydrogen isotope fractionations (2αH2O/CH4 = 2.071 ± 0.014 for V-nitrogenase and 2.078 ± 0.018 for Fe-only nitrogenase) are the largest of any known biogenic or geogenic pathway. The large 2αH2O/CH4 shows that the reaction pathway nitrogenases use to form methane strongly discriminates against 2H, and that 2αH2O/CH4 distinguishes nitrogenase-derived methane from all other known biotic and abiotic sources. These findings on nitrogenase-derived methane will help constrain carbon and nitrogen flows in microbial communities and the role of the alternative nitrogenases in global biogeochemical cycles.IMPORTANCE All forms of life require nitrogen for growth. Many different kinds of microbes living in diverse environments make inert nitrogen gas from the atmosphere bioavailable using a special enzyme, nitrogenase. Nitrogenase has a wide substrate range, and, in addition to producing bioavailable nitrogen, some forms of nitrogenase also produce small amounts of the greenhouse gas methane. This is different from other microbes that produce methane to generate energy. Until now, there was no good way to determine when microbes with nitrogenases are making methane in nature. Here, we present an isotopic fingerprint that allows scientists to distinguish methane from microbes making it for energy versus those making it as a by-product of nitrogen acquisition. With this new fingerprint, it will be possible to improve our understanding of the relationship between methane production and nitrogen acquisition in nature.
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Affiliation(s)
- Katja E Luxem
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire, USA
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey, USA
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14
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Bing H, Zhong Z, Wang X, Zhu H, Wu Y. Spatiotemporal distribution of vanadium in the flooding soils mediated by entrained-sediment flow and altitude in the Three Gorges Reservoir. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 724:138246. [PMID: 32247140 DOI: 10.1016/j.scitotenv.2020.138246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/20/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
The re-emergence of vanadium (V) as a toxic metal has been highlighted recently due to its long-standing environmental and health hazard. This work targeted the world largest reservoir-Three Gorges Reservoir (TGR) to explore the spatial variation of V in the flooding soils from 2014 to 2018; meanwhile, the typical riparian zones with different altitudes and land-uses at the middle reach of the TGR were selected to decipher the key drivers on the V distribution. The results showed that the concentrations of soil V in the mainstream markedly exceeded local background, but they did not vary significantly with time except a marked increase at the upper-middle reaches. Spatially, the concentrations of soil V increased towards the dam, and the increase trend became increasingly significant with time. At the typical riparian zone, the concentrations of soil V decreased strikingly with altitude despite the difference in the land-uses, and a marked change-point occurred at 160-165 m. The soil V dominated by residual fraction, followed by oxidizable and reducible fractions, and then the minimal acid-soluble fraction. The contamination and eco-risk of V in the soils were low with similar spatiotemporal variation to its concentrations. Entrained-sediment flow and particle size rather than pH and organic matters led to the spatiotemporal variation in the distribution of soil V in the mainstream, and the driving effects tended to be more predominant with time. Altitude-regulated alteration of soil properties including particle sizes and iron/manganese (hydr)oxides with different flooding duration dominated the vertical distribution of V over the local land-uses at the riparian zone. Our results reveal the hotspots of V contamination in the riparian soils of the TGR and highlight unceasing focus on the variation in the distribution and dynamic migration of soil V due to its levels out of limits and changing soil conditions.
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Affiliation(s)
- Haijian Bing
- The Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Zhilin Zhong
- The Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxiao Wang
- School of Land and Resources, China West Normal University, Nanchong 637000, China
| | - He Zhu
- The Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yanhong Wu
- The Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China.
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15
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Zhang X, Ward BB, Sigman DM. Global Nitrogen Cycle: Critical Enzymes, Organisms, and Processes for Nitrogen Budgets and Dynamics. Chem Rev 2020; 120:5308-5351. [DOI: 10.1021/acs.chemrev.9b00613] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Bess B. Ward
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Daniel M. Sigman
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
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16
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Morphological, elemental, and boron isotopic insights into pathophysiology of diseased coral growth anomalies. Sci Rep 2020; 10:8252. [PMID: 32427852 PMCID: PMC7237652 DOI: 10.1038/s41598-020-65118-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/15/2020] [Indexed: 11/08/2022] Open
Abstract
Coral growth anomalies (GAs) are tumor-like lesions that are detrimental to colony fitness and are commonly associated with high human population density, yet little is known about the disease pathology or calcification behavior. SEM imagery, skeletal trace elements and boron isotopes (δ11B) have been combined as a novel approach to study coral disease. Low Mg/Ca, and high U/Ca, Mo/Ca, and V/Ca potentially suggest a decreased abundance of "centers of calcification" and nitrogen-fixation in GAs. Estimates of carbonate system parameters from δ11B and B/Ca measurements indicate reduced pH (-0.05 units) and [CO32-] within GA calcifying fluid. We theorize GAs re-allocate resources away from internal pH upregulation to sustain elevated tissue growth, resulting in a porous and fragile skeleton. Our findings show that dystrophic calcification processes could explain structural differences seen in GA skeletons and highlight the use of skeletal geochemistry to shed light on disease pathophysiology in corals.
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17
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Abreu I, Mihelj P, Raimunda D. Transition metal transporters in rhizobia: tuning the inorganic micronutrient requirements to different living styles. Metallomics 2020; 11:735-755. [PMID: 30734808 DOI: 10.1039/c8mt00372f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A group of bacteria known as rhizobia are key players in symbiotic nitrogen fixation (SNF) in partnership with legumes. After a molecular exchange, the bacteria end surrounded by a plant membrane forming symbiosomes, organelle-like structures, where they differentiate to bacteroids and fix nitrogen. This symbiotic process is highly dependent on dynamic nutrient exchanges between the partners. Among these are transition metals (TM) participating as inorganic and organic cofactors of fundamental enzymes. While the understanding of how plant transporters facilitate TMs to the very near environment of the bacteroid is expanding, our knowledge on how bacteroid transporters integrate to TM homeostasis mechanisms in the plant host is still limited. This is significantly relevant considering the low solubility and scarcity of TMs in soils, and the in crescendo gradient of TM bioavailability rhizobia faces during the infection and bacteroid differentiation processes. In the present work, we review the main metal transporter families found in rhizobia, their role in free-living conditions and, when known, in symbiosis. We focus on discussing those transporters which could play a significant role in TM-dependent biochemical and physiological processes in the bacteroid, thus paving the way towards an optimized SNF.
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Affiliation(s)
- Isidro Abreu
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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18
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Luxem KE, Kraepiel AML, Zhang L, Waldbauer JR, Zhang X. Carbon substrate re-orders relative growth of a bacterium using Mo-, V-, or Fe-nitrogenase for nitrogen fixation. Environ Microbiol 2020; 22:1397-1408. [PMID: 32090445 PMCID: PMC7187303 DOI: 10.1111/1462-2920.14955] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/07/2020] [Indexed: 01/21/2023]
Abstract
Biological nitrogen fixation is catalyzed by the molybdenum (Mo), vanadium (V) and iron (Fe)‐only nitrogenase metalloenzymes. Studies with purified enzymes have found that the ‘alternative’ V‐ and Fe‐nitrogenases generally reduce N2 more slowly and produce more byproduct H2 than the Mo‐nitrogenase, leading to an assumption that their usage results in slower growth. Here we show that, in the metabolically versatile photoheterotroph Rhodopseudomonas palustris, the type of carbon substrate influences the relative rates of diazotrophic growth based on different nitrogenase isoforms. The V‐nitrogenase supports growth as fast as the Mo‐nitrogenase on acetate but not on the more oxidized substrate succinate. Our data suggest that this is due to insufficient electron flux to the V‐nitrogenase isoform on succinate compared with acetate. Despite slightly faster growth based on the V‐nitrogenase on acetate, the wild‐type strain uses exclusively the Mo‐nitrogenase on both carbon substrates. Notably, the differences in H2:N2 stoichiometry by alternative nitrogenases (~1.5 for V‐nitrogenase, ~4–7 for Fe‐nitrogenase) and Mo‐nitrogenase (~1) measured here are lower than prior in vitro estimates. These results indicate that the metabolic costs of V‐based nitrogen fixation could be less significant for growth than previously assumed, helping explain why alternative nitrogenase genes persist in diverse diazotroph lineages and are broadly distributed in the environment.
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Affiliation(s)
- Katja E Luxem
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Anne M L Kraepiel
- Princeton Environmental Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Lichun Zhang
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.,Princeton Environmental Institute, Princeton University, Princeton, NJ, 08544, USA
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19
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Molybdenum threshold for ecosystem scale alternative vanadium nitrogenase activity in boreal forests. Proc Natl Acad Sci U S A 2019; 116:24682-24688. [PMID: 31727845 PMCID: PMC6900544 DOI: 10.1073/pnas.1913314116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Biological nitrogen fixation (BNF) is responsible for large new N inputs to terrestrial ecosystems, particularly in pristine, high-latitude areas undergoing rapid global change. The most common form of nitrogenase requires molybdenum (Mo) and Mo limitation of BNF is ubiquitous. Mo-free alternative forms of nitrogenase exist, but their roles in environmental BNF have remained uncertain. This study on N2-fixing cyanolichens provides extensive field evidence, at an ecosystem scale, that vanadium (V)-based nitrogenase greatly contributes to BNF when Mo availability is limited. Mo exposure data in circumboreal forests further suggest that V-based BNF is widespread. The results showcase the resilience of BNF to micronutrient limitation and reveal strong links between the biogeochemical cycle of macronutrients and micronutrients in terrestrial ecosystems. Biological nitrogen fixation (BNF) by microorganisms associated with cryptogamic covers, such as cyanolichens and bryophytes, is a primary source of fixed nitrogen in pristine, high-latitude ecosystems. On land, low molybdenum (Mo) availability has been shown to limit BNF by the most common form of nitrogenase (Nase), which requires Mo in its active site. Vanadium (V) and iron-only Nases have been suggested as viable alternatives to countering Mo limitation of BNF; however, field data supporting this long-standing hypothesis have been lacking. Here, we elucidate the contribution of vanadium nitrogenase (V-Nase) to BNF by cyanolichens across a 600-km latitudinal transect in eastern boreal forests of North America. Widespread V-Nase activity was detected (∼15–50% of total BNF rates), with most of the activity found in the northern part of the transect. We observed a 3-fold increase of V-Nase contribution during the 20-wk growing season. By including the contribution of V-Nase to BNF, estimates of new N input by cyanolichens increase by up to 30%. We find that variability in V-based BNF is strongly related to Mo availability, and we identify a Mo threshold of ∼250 ng·glichen−1 for the onset of V-based BNF. Our results provide compelling ecosystem-scale evidence for the use of the V-Nase as a surrogate enzyme that contributes to BNF when Mo is limiting. Given widespread findings of terrestrial Mo limitation, including the carbon-rich circumboreal belt where global change is most rapid, additional consideration of V-based BNF is required in experimental and modeling studies of terrestrial biogeochemistry.
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20
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Iron Homeostasis in Bacillus subtilis Requires Siderophore Production and Biofilm Formation. Appl Environ Microbiol 2019; 85:AEM.02439-18. [PMID: 30446551 PMCID: PMC6344612 DOI: 10.1128/aem.02439-18] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 11/07/2018] [Indexed: 12/05/2022] Open
Abstract
Iron acquisition is of fundamental importance for microorganisms, since this metal is generally poorly bioavailable under natural conditions. In the environment, most bacteria are found tightly packed within multicellular communities named biofilms. Here, using the soil Gram-positive bacterium Bacillus subtilis, we show that biofilm formation and the production of siderophores, i.e., small molecules specifically binding metals, are both essential to ensure Fe uptake from the medium and maintain cellular Fe homeostasis. The biofilm matrix appears to play an important role favoring the efficient usage of siderophores. Taken together, our results demonstrate a close link between biofilm formation and iron acquisition in B. subtilis, allowing a better comprehension of how bacteria can cope with metal limitation under environmental conditions. Iron (Fe) is the most important metal in biology. Despite its abundance, Fe is mostly present as a ferric form in soils, strongly limiting its bioavailability. To overcome the challenge of Fe acquisition, many microorganisms produce siderophores to retrieve Fe from natural sources. Another ubiquitous feature of bacteria in natural environments is biofilm formation. Previous studies showed that external Fe strongly influenced biofilm formation in several bacteria, suggesting that this microenvironment plays a mechanistic role in micronutrient acquisition for bacteria. Here, we applied a complementary set of analytical methods and deletion mutants to evaluate the role of biofilm formation, siderophore production, and their interaction in Fe homeostasis in Bacillus subtilis. We observed that Fe homeostasis, i.e., active growth at a constant intracellular Fe concentration, requires both siderophore production and biofilm formation. Also, we report that in B. subtilis, both biofilm formation and siderophore production are required to achieve active Fe acquisition from the medium and to sustain normal growth. Furthermore, we provide evidence that the formation of biofilm slightly enhances the kinetics of Fe complexation by catechol siderophores and markedly improves siderophore use efficiency. These results provide new perspectives on the mechanism underlying siderophore-based acquisition of Fe in biofilm-forming bacteria. IMPORTANCE Iron acquisition is of fundamental importance for microorganisms, since this metal is generally poorly bioavailable under natural conditions. In the environment, most bacteria are found tightly packed within multicellular communities named biofilms. Here, using the soil Gram-positive bacterium Bacillus subtilis, we show that biofilm formation and the production of siderophores, i.e., small molecules specifically binding metals, are both essential to ensure Fe uptake from the medium and maintain cellular Fe homeostasis. The biofilm matrix appears to play an important role favoring the efficient usage of siderophores. Taken together, our results demonstrate a close link between biofilm formation and iron acquisition in B. subtilis, allowing a better comprehension of how bacteria can cope with metal limitation under environmental conditions.
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21
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Deicke M, Mohr JF, Roy S, Herzsprung P, Bellenger JP, Wichard T. Metallophore profiling of nitrogen-fixingFrankiaspp. to understand metal management in the rhizosphere of actinorhizal plants. Metallomics 2019; 11:810-821. [DOI: 10.1039/c8mt00344k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Frankiaspp. are widespread nitrogen-fixing and metallophore releasing soil bacteria, which often live in symbiosis with a broad spectrum of hosts.
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Affiliation(s)
- Michael Deicke
- Friedrich Schiller University Jena
- Institute for Inorganic and Analytical Chemistry
- 07743 Jena
- Germany
| | - Jan Frieder Mohr
- Friedrich Schiller University Jena
- Institute for Inorganic and Analytical Chemistry
- 07743 Jena
- Germany
| | - Sébastien Roy
- Centre SÈVE
- Département de Biologie
- Faculté des Sciences
- Université de Sherbrooke
- Canada
| | - Peter Herzsprung
- UFZ – Helmholtz Centre for Environmental Research
- Department Lake Research
- 39114 Magdeburg
- Germany
| | | | - Thomas Wichard
- Friedrich Schiller University Jena
- Institute for Inorganic and Analytical Chemistry
- 07743 Jena
- Germany
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22
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McRose DL, Seyedsayamdost MR, Morel FMM. Multiple siderophores: bug or feature? J Biol Inorg Chem 2018; 23:983-993. [PMID: 30264174 DOI: 10.1007/s00775-018-1617-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/04/2018] [Indexed: 12/31/2022]
Abstract
It is common for bacteria to produce chemically diverse sets of small Fe-binding molecules called siderophores. Studies of siderophore bioinorganic chemistry have firmly established the role of these molecules in Fe uptake and provided great insight into Fe complexation. However, we still do not fully understand why microbes make so many siderophores. In many cases, the release of small structural variants or siderophore fragments has been ignored, or considered as an inefficiency of siderophore biosynthesis. Yet, in natural settings, microbes live in complex consortia and it has become increasingly clear that the secondary metabolite repertoires of microbes reflect this dynamic environment. Multiple siderophore production may, therefore, provide a window into microbial life in the wild. This minireview focuses on three biochemical routes by which multiple siderophores can be released by the same organism-multiple biosynthetic gene clusters, fragment release, and precursor-directed biosynthesis-and highlights emergent themes related to each. We also emphasize the plurality of reasons for multiple siderophore production, which include enhanced iron uptake via synergistic siderophore use, microbial warfare and cooperation, and non-classical functions such as the use of siderophores to take up metals other than Fe.
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Affiliation(s)
- Darcy L McRose
- Department of Geosciences, Princeton University, Princeton, USA.
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, USA.,Department of Molecular Biology, Princeton University, Princeton, USA
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23
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Winbourne JB, Houlton BZ. Plant-soil feedbacks on free-living nitrogen fixation over geological time. Ecology 2018; 99:2496-2505. [PMID: 30076606 DOI: 10.1002/ecy.2486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 07/04/2018] [Accepted: 07/23/2018] [Indexed: 11/09/2022]
Abstract
Free-living heterotrophic nitrogen fixation (FNF) is a widespread nitrogen input pathway in terrestrial ecosystems. However, questions remain over the relative influence of co-occurring controls on patterns of heterotrophic FNF activity, especially across generalized stages of primary succession, from biomass accumulation to retrogressive phases. Here, we experimentally test two alternative hypotheses regarding FNF rates during ecosystem development: (H1) site (i.e., changes in soil fertility during succession) is the primary driver of leaf-litter FNF rates, vs. (H2) leaf-litter chemistry is the primary determinant of FNF activity across a broad range of ecosystem conditions. We evaluated these hypotheses across a well-studied soil chronosequence in California (i.e., the Ecological Staircase), which spans ~1 million years of ecosystem development and displays extreme ranges in plant-soil nutrient conditions, culminating in the nutrient depleted and stunted Pygmy forest. Across this successional gradient, we implemented a reciprocal leaf-litter transplant and a common garden litter bag decomposition experiment with senesced needles of Pinus muricata. Our results support H1: rates of FNF were similar for all leaf-litter types decomposed at the same site regardless of initial leaf-litter C and nutrient contents. FNF rates sharply declined from the maximal to retrogressive stage of succession. Trends in P dynamics during decomposition suggest an important role of P in regulating FNF. For example, P. muricata litter collected from the infertile Pygmy site displayed substantially higher FNF rates when decomposed at the fertile site, in part by immobilizing significant quantities of P from the soil at the fertile site. Conversely, P. muricata litter collected from the fertile site decomposed more slowly at the Pygmy site, with concomitant declines in FNF rates that matched those of Pygmy site litter decomposed in situ. These results are consistent with the idea that, over millennia, long-term declines in P availability feedback to constrain FNF rates, in part explaining the emergence of extremely nutrient-poor and retrograded ecosystems.
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Affiliation(s)
- Joy B Winbourne
- Department of Land, Air, and Water Resources, University of California, Davis, California, 95616, USA.,Department of Earth and Environment, Boston University, Boston, Massachusetts, 02215, USA
| | - Benjamin Z Houlton
- Department of Land, Air, and Water Resources, University of California, Davis, California, 95616, USA
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24
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Kisková J, Perháčová Z, Vlčko L, Sedláková J, Kvasnová S, Pristaš P. The Bacterial Population of Neutral Mine Drainage Water of Elizabeth's Shaft (Slovinky, Slovakia). Curr Microbiol 2018; 75:988-996. [PMID: 29532150 PMCID: PMC7160218 DOI: 10.1007/s00284-018-1472-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 03/05/2018] [Indexed: 11/25/2022]
Abstract
Although neutral mine drainage is the less frequent subject of the interest than acid mine drainage, it can have adverse environmental effects caused mainly by precipitation of dissolved Fe. The aim of the study was to characterize the composition of bacterial population in environment with high concentration of iron and sulfur compounds represented by neutral mine drainage water of Elizabeth's shaft, Slovinky (Slovakia). Direct microscopic observations, cultivation methods, and 454 pyrosequencing of the 16S rRNA gene amplicons were used to examine the bacterial population. Microscopic observations identified iron-oxidizing Proteobacteria of the genera Gallionella and Leptothrix which occurrence was not changed during the years 2008-2014. Using 454 pyrosequencing, there were identified members of 204 bacterial genera that belonged to 25 phyla. Proteobacteria (69.55%), followed by Chloroflexi (10.31%) and Actinobacteria (4.24%) dominated the bacterial community. Genera Azotobacter (24.52%) and Pseudomonas (14.15%), followed by iron-oxidizing Proteobacteria Dechloromonas (11%) and Methyloversatilis (8.53%) were most abundant within bacterial community. Typical sulfur bacteria were detected with lower frequency, e.g., Desulfobacteraceae (0.25%), Desulfovibrionaceae (0.16%), or Desulfobulbaceae (0.11%). Our data indicate that the composition of bacterial community of the Elizabeth's shaft drainage water reflects observed neutral pH, high level of iron and sulfur ions in this aquatic habitat.
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Affiliation(s)
- Jana Kisková
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, 041 54, Košice, Slovakia.
| | - Zuzana Perháčová
- Department of Biology and General Ecology, Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, 960 53, Zvolen, Slovakia
| | - Ladislav Vlčko
- Department of Biology and General Ecology, Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, 960 53, Zvolen, Slovakia
| | - Jana Sedláková
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, 041 54, Košice, Slovakia
| | - Simona Kvasnová
- Department of Biology and Ecology, Faculty of Natural Science, Matej Bel University, 974 01, Banská Bystrica, Slovakia
| | - Peter Pristaš
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, 041 54, Košice, Slovakia
- Institute of Animal Physiology, Centre of Biosciences of Slovak Academy of Sciences, 041 01, Košice, Slovakia
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25
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Noar JD, Bruno-Bárcena JM. Azotobacter vinelandii: the source of 100 years of discoveries and many more to come. MICROBIOLOGY-SGM 2018. [PMID: 29533747 DOI: 10.1099/mic.0.000643] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Azotobacter vinelandii has been studied for over 100 years since its discovery as an aerobic nitrogen-fixing organism. This species has proved useful for the study of many different biological systems, including enzyme kinetics and the genetic code. It has been especially useful in working out the structures and mechanisms of different nitrogenase enzymes, how they can function in oxic environments and the interactions of nitrogen fixation with other aspects of metabolism. Interest in studying A. vinelandii has waned in recent decades, but this bacterium still possesses great potential for new discoveries in many fields and commercial applications. The species is of interest for research because of its genetic pliability and natural competence. Its features of particular interest to industry are its ability to produce multiple valuable polymers - bioplastic and alginate in particular; its nitrogen-fixing prowess, which could reduce the need for synthetic fertilizer in agriculture and industrial fermentations, via coculture; its production of potentially useful enzymes and metabolic pathways; and even its biofuel production abilities. This review summarizes the history and potential for future research using this versatile microbe.
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Affiliation(s)
- Jesse D Noar
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Jose M Bruno-Bárcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
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Molybdenum-Based Diazotrophy in a Sphagnum Peatland in Northern Minnesota. Appl Environ Microbiol 2017; 83:AEM.01174-17. [PMID: 28667112 DOI: 10.1128/aem.01174-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 06/28/2017] [Indexed: 11/20/2022] Open
Abstract
Microbial N2 fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO2 and are susceptible to the changing climate. The objectives of this study were (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in an ombrotrophic Sphagnum-dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O2, CO2, and CH4) on potential rates of diazotrophy measured by acetylene (C2H2) reduction and 15N2 incorporation. A molecular analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated by Alphaproteobacteria (Bradyrhizobiaceae and Beijerinckiaceae). Despite higher concentrations of dissolved vanadium ([V] 11 nM) than molybdenum ([Mo] 3 nM) in surface peat, a combination of metagenomic, amplicon sequencing, and activity measurements indicated that Mo-containing nitrogenases dominate over the V-containing form. Acetylene reduction was only detected in surface peat exposed to light, with the highest rates observed in peat collected from hollows with the highest water contents. Incorporation of 15N2 was suppressed 90% by O2 and 55% by C2H2 and was unaffected by CH4 and CO2 amendments. These results suggest that peatland diazotrophy is mediated by a combination of C2H2-sensitive and C2H2-insensitive microbes that are more active at low concentrations of O2 and show similar activity at high and low concentrations of CH4 IMPORTANCE Previous studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy in Sphagnum-dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process, remain in question. Our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy and that members of the Alphaproteobacteria (Rhizobiales) catalyze this process at the bog surface using the molybdenum-based form of the nitrogenase enzyme.
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McRose DL, Baars O, Morel FMM, Kraepiel AML. Siderophore production in
Azotobacter vinelandii
in response to Fe‐, Mo‐ and V‐limitation. Environ Microbiol 2017; 19:3595-3605. [DOI: 10.1111/1462-2920.13857] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/08/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Darcy L. McRose
- Department of GeosciencesPrinceton UniversityPrinceton NJ 08544 USA
| | - Oliver Baars
- Department of GeosciencesPrinceton UniversityPrinceton NJ 08544 USA
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Rousk K, Degboe J, Michelsen A, Bradley R, Bellenger JP. Molybdenum and phosphorus limitation of moss-associated nitrogen fixation in boreal ecosystems. THE NEW PHYTOLOGIST 2017; 214:97-107. [PMID: 27883187 DOI: 10.1111/nph.14331] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/15/2016] [Indexed: 05/27/2023]
Abstract
Biological nitrogen fixation (BNF) performed by moss-associated cyanobacteria is one of the main sources of new nitrogen (N) input in pristine, high-latitude ecosystems. Yet, the nutrients that limit BNF remain elusive. Here, we tested whether this important ecosystem function is limited by the availability of molybdenum (Mo), phosphorus (P), or both. BNF in dominant mosses was measured with the acetylene reduction assay (ARA) at different time intervals following Mo and P additions, in both laboratory microcosms with mosses from a boreal spruce forest and field plots in subarctic tundra. We further used a 15 N2 tracer technique to assess the ARA to N2 fixation conversion ratios at our subarctic site. BNF was up to four-fold higher shortly after the addition of Mo, in both the laboratory and field experiments. A similar positive response to Mo was found in moss colonizing cyanobacterial biomass. As the growing season progressed, nitrogenase activity became progressively more P limited. The ARA : 15 N2 ratios increased with increasing Mo additions. These findings show that N2 fixation activity as well as cyanobacterial biomass in dominant feather mosses from boreal forests and subarctic tundra are limited by Mo availability.
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Affiliation(s)
- Kathrin Rousk
- Department of Biology, Terrestrial Ecology Section, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Center for Permafrost (CENPERM), University of Copenhagen, Øster Voldgade 10, 1350, Copenhagen, Denmark
| | - Jefferson Degboe
- Centre Sève, Département de Chimie, Université de Sherbrooke, Sherbrooke, J1K 2R1, QC, Canada
| | - Anders Michelsen
- Department of Biology, Terrestrial Ecology Section, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Center for Permafrost (CENPERM), University of Copenhagen, Øster Voldgade 10, 1350, Copenhagen, Denmark
| | - Robert Bradley
- Département de Biologie, Université de Sherbrooke, Sherbrooke, J1K 2R1, QC, Canada
| | - Jean-Philippe Bellenger
- Centre Sève, Département de Chimie, Université de Sherbrooke, Sherbrooke, J1K 2R1, QC, Canada
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Winbourne JB, Brewer SW, Houlton BZ. Iron controls over di-nitrogen fixation in karst tropical forest. Ecology 2017; 98:773-781. [DOI: 10.1002/ecy.1700] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Joy B. Winbourne
- Department of Land, Air and Water Resources; University of California, Davis; One Shields Avenue Davis California 95616 USA
| | - Steven W. Brewer
- Belize Foundation for Research and Environmental Education; PO Box 129 Punta Gorda Todelo Belize
- Copperhead Consulting; 11641 Richmond Rd. Paint Lick Kentucky 40461 USA
| | - Benjamin Z. Houlton
- Department of Land, Air and Water Resources; University of California, Davis; One Shields Avenue Davis California 95616 USA
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Darnajoux R, Zhang X, McRose DL, Miadlikowska J, Lutzoni F, Kraepiel AML, Bellenger JP. Biological nitrogen fixation by alternative nitrogenases in boreal cyanolichens: importance of molybdenum availability and implications for current biological nitrogen fixation estimates. THE NEW PHYTOLOGIST 2017; 213:680-689. [PMID: 27588707 DOI: 10.1111/nph.14166] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/26/2016] [Indexed: 05/03/2023]
Abstract
Cryptogamic species and their associated cyanobacteria have attracted the attention of biogeochemists because of their critical roles in the nitrogen cycle through symbiotic and asymbiotic biological fixation of nitrogen (BNF). BNF is mediated by the nitrogenase enzyme, which, in its most common form, requires molybdenum at its active site. Molybdenum has been reported as a limiting nutrient for BNF in many ecosystems, including tropical and temperate forests. Recent studies have suggested that alternative nitrogenases, which use vanadium or iron in place of molybdenum at their active site, might play a more prominent role in natural ecosystems than previously recognized. Here, we studied the occurrence of vanadium, the role of molybdenum availability on vanadium acquisition and the contribution of alternative nitrogenases to BNF in the ubiquitous cyanolichen Peltigera aphthosa s.l. We confirmed the use of the alternative vanadium-based nitrogenase in the Nostoc cyanobiont of these lichens and its substantial contribution to BNF in this organism. We also showed that the acquisition of vanadium is strongly regulated by the abundance of molybdenum. These findings show that alternative nitrogenase can no longer be neglected in natural ecosystems, particularly in molybdenum-limited habitats.
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Affiliation(s)
- Romain Darnajoux
- Centre Sève, Département de Chimie, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
| | - Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Darcy L McRose
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | | | | | - Anne M L Kraepiel
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Jean-Philippe Bellenger
- Centre Sève, Département de Chimie, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
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Noumsi CJ, Pourhassan N, Darnajoux R, Deicke M, Wichard T, Burrus V, Bellenger JP. Effect of organic matter on nitrogenase metal cofactors homeostasis in Azotobacter vinelandii under diazotrophic conditions. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:76-84. [PMID: 26549632 DOI: 10.1111/1758-2229.12353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 10/30/2015] [Accepted: 10/30/2015] [Indexed: 06/05/2023]
Abstract
Biological nitrogen fixation can be catalysed by three isozymes of nitrogenase: molybdenum (Mo)-nitrogenase, vanadium (V)-nitrogenase and iron-only (Fe)-nitrogenase. The activity of these isozymes strongly depends on their metal cofactors, molybdenum, vanadium and iron, and their bioavailability in ecosystems. Here, we show how metal bioavailability can be affected by the presence of tannic acid (organic matter), and the subsequent consequences on diazotrophic growth of the soil bacterium Azotobacter vinelandii. In the presence of tannic acids, A. vinelandii produces a higher amount of metallophores, which coincides with an active, regulated and concomitant acquisition of molybdenum and vanadium under cellular conditions that are usually considered not molybdenum limiting. The associated nitrogenase genes exhibit decreased nifD expression and increased vnfD expression. Thus, in limiting bioavailable metal conditions, A. vinelandii takes advantage of its nitrogenase diversity to ensure optimal diazotrophic growth.
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Affiliation(s)
- Christelle Jouogo Noumsi
- Département de Chimie, Faculté des sciences, Université de Sherbrooke, 2500 boul. de l'université, Sherbrooke, Québec, J1K 2R1, Canada
- Laboratory of Bacterial Molecular Genetics, Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boul. de l'université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Nina Pourhassan
- Département de Chimie, Faculté des sciences, Université de Sherbrooke, 2500 boul. de l'université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Romain Darnajoux
- Département de Chimie, Faculté des sciences, Université de Sherbrooke, 2500 boul. de l'université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Michael Deicke
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Vincent Burrus
- Laboratory of Bacterial Molecular Genetics, Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boul. de l'université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Jean-Philippe Bellenger
- Département de Chimie, Faculté des sciences, Université de Sherbrooke, 2500 boul. de l'université, Sherbrooke, Québec, J1K 2R1, Canada
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Marks JA, Pett-Ridge JC, Perakis SS, Allen JL, McCune B. Response of the nitrogen-fixing lichenLobaria pulmonariato phosphorus, molybdenum, and vanadium. Ecosphere 2015. [DOI: 10.1890/es15-00140.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Darnajoux R, Constantin J, Miadlikowska J, Lutzoni F, Bellenger JP. Is vanadium a biometal for boreal cyanolichens? THE NEW PHYTOLOGIST 2014; 202:765-771. [PMID: 24641550 DOI: 10.1111/nph.12777] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 02/17/2014] [Indexed: 06/03/2023]
Abstract
Molybdenum (Mo) nitrogenase has long been considered the predominant isoenzyme responsible for dinitrogen fixation worldwide. Recent findings have challenged the paradigm of Mo hegemony, and highlighted the role of alternative nitrogenases, such as the vanadium-nitrogenase. Here, we first characterized homeostasis of vanadium (V) along with other metals in situ in the dinitrogen fixing cyanolichen Peltigera aphthosa. These lichens were sampled in natural sites exposed to various levels of atmospheric metal deposition. These results were compared with laboratory experiments where Anabaena variabilis, which is also hosting the V-nitrogenase, and a relatively close relative of the lichen cyanobiont Nostoc, was subjected to various levels of V. We report here that V is preferentially allocated to cephalodia, specialized structures where dinitrogen fixation occurs in tri-membered lichens. This specific allocation is biologically controlled and tightly regulated. Vanadium homeostasis in lichen cephalodia exposed to various V concentrations is comparable to the one observed in Anabaena variabilis and other dinitrogen fixing organisms using V-nitrogenase. Overall, our findings support current hypotheses that V could be a more important factor in mediating nitrogen input in high latitude ecosystems than previously recognized. They invite the reassessment of current theoretical models linking metal dynamics and dinitrogen fixation in boreal and subarctic ecosystems.
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Affiliation(s)
- Romain Darnajoux
- Centre Sève, Département de chimie, Université de Sherbrooke, J1K 2R1, QC, Canada
| | - Jérôme Constantin
- Centre Sève, Département de chimie, Université de Sherbrooke, J1K 2R1, QC, Canada
| | | | - François Lutzoni
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708-0338, USA
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Nitrogen isotope fractionation by alternative nitrogenases and past ocean anoxia. Proc Natl Acad Sci U S A 2014; 111:4782-7. [PMID: 24639508 DOI: 10.1073/pnas.1402976111] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biological nitrogen fixation constitutes the main input of fixed nitrogen to Earth's ecosystems, and its isotope effect is a key parameter in isotope-based interpretations of the N cycle. The nitrogen isotopic composition (δ(15)N) of newly fixed N is currently believed to be ∼-1‰, based on measurements of organic matter from diazotrophs using molybdenum (Mo)-nitrogenases. We show that the vanadium (V)- and iron (Fe)-only "alternative" nitrogenases produce fixed N with significantly lower δ(15)N (-6 to -7‰). An important contribution of alternative nitrogenases to N2 fixation provides a simple explanation for the anomalously low δ(15)N (<-2‰) in sediments from the Cretaceous Oceanic Anoxic Events and the Archean Eon. A significant role for the alternative nitrogenases over Mo-nitrogenase is also consistent with evidence of Mo scarcity during these geologic periods, suggesting an additional dimension to the coupling between the global cycles of trace elements and nitrogen.
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36
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Kruft BI, Harrington JM, Duckworth OW, Jarzęcki AA. Quantum mechanical investigation of aqueous desferrioxamine B metal complexes: Trends in structure, binding, and infrared spectroscopy. J Inorg Biochem 2013; 129:150-61. [DOI: 10.1016/j.jinorgbio.2013.08.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 08/23/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
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Deicke M, Bellenger JP, Wichard T. Direct quantification of bacterial molybdenum and iron metallophores with ultra-high-performance liquid chromatography coupled to time-of-flight mass spectrometry. J Chromatogr A 2013; 1298:50-60. [DOI: 10.1016/j.chroma.2013.05.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 04/30/2013] [Accepted: 05/02/2013] [Indexed: 10/26/2022]
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Allard P, Darnajoux R, Phalyvong K, Bellenger JP. Effects of tungsten and titanium oxide nanoparticles on the diazotrophic growth and metals acquisition by Azotobacter vinelandii under molybdenum limiting condition. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:2061-2068. [PMID: 23339336 DOI: 10.1021/es304544k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The acquisition of essential metals, such as the metal cofactors (molybdenum (Mo) and iron (Fe)) of the nitrogenase, the enzyme responsible for the reduction of dinitrogen (N(2)) to ammonium, is critical to N(2) fixing bacteria in soil. The release of metal nanoparticles (MNPs) to the environment could be detrimental to N(2) fixing bacteria by introducing a new source of toxic metals and by interfering with the acquisition of essential metals such as Mo. Since Mo has been reported to limit nonsymbiotic N(2) fixation in many ecosystems from tropical to cold temperate, this question is particularly acute in the context of Mo limitation. Using a combination of microbiology and analytical chemistry techniques, we have evaluated the effect of titanium (Ti) and tungsten (W) oxide nanoparticles on the diazotrophic growth and metals acquisition in pure culture of the ubiquitous N(2) fixing bacterium Azotobacter vinelandii under Mo replete and Mo limiting conditions. We report that under our conditions (≤10 mg·L(-1)) TiO(2) NPs have no effects on the diazotrophic growth of A. vinelandii while WO(3) NPs are highly detrimental to the growth especially under Mo limiting conditions. Our results show that the toxicity of WO(3) NPs to A. vinelandii is due to an interference with the catechol-metalophores assisted uptake of Mo.
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Affiliation(s)
- Patrick Allard
- Département de Chimie, Université de Sherbrooke, 2500 Boul. de l'Université, Sherbrooke, Québec J1K 2R1, Canada
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Glass JB, Poret-Peterson AT, Wolfe-Simon F, Anbar AD. Molybdenum Limitation Induces Expression of the Molybdate-Binding Protein Mop in a Freshwater Nitrogen-Fixing Cyanobacterium. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/aim.2013.36a002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Glass JB, Axler RP, Chandra S, Goldman CR. Molybdenum limitation of microbial nitrogen assimilation in aquatic ecosystems and pure cultures. Front Microbiol 2012; 3:331. [PMID: 22993512 PMCID: PMC3440940 DOI: 10.3389/fmicb.2012.00331] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 08/24/2012] [Indexed: 11/29/2022] Open
Abstract
Molybdenum (Mo) is an essential micronutrient for biological assimilation of nitrogen gas and nitrate because it is present in the cofactors of nitrogenase and nitrate reductase enzymes. Although Mo is the most abundant transition metal in seawater (107 nM), it is present in low concentrations in most freshwaters, typically <20 nM. In 1960, it was discovered that primary productivity was limited by Mo scarcity (2–4 nM) in Castle Lake, a small, meso-oligotrophic lake in northern California. Follow up studies demonstrated that Mo also limited primary productivity in lakes in New Zealand, Alaska, and the Sierra Nevada. Research in the 1970s and 1980s showed that Mo limited primary productivity and nitrate uptake in Castle Lake only during periods of the growing season when nitrate concentrations were relatively high because ammonium assimilation does not require Mo. In the years since, research has shifted to investigate whether Mo limitation also occurs in marine and soil environments. Here we review studies of Mo limitation of nitrogen assimilation in natural microbial communities and pure cultures. We also summarize new data showing that the simultaneous addition of Mo and nitrate causes increased activity of proteins involved in nitrogen assimilation in the hypolimnion of Castle Lake when ammonium is scarce. Furthermore, we suggest that meter-scale Mo and oxygen depth profiles from Castle Lake are consistent with the hypothesis that nitrogen-fixing cyanobacteria in freshwater periphyton communities have higher Mo requirements than other microbial communities. Finally, we present topics for future research related to Mo bioavailability through time and with changing oxidation state.
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Affiliation(s)
- Jennifer B Glass
- School of Earth and Space Exploration, Arizona State University Arizona, AZ, USA
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41
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Wurzburger N, Bellenger JP, Kraepiel AML, Hedin LO. Molybdenum and phosphorus interact to constrain asymbiotic nitrogen fixation in tropical forests. PLoS One 2012; 7:e33710. [PMID: 22470462 PMCID: PMC3309997 DOI: 10.1371/journal.pone.0033710] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 02/15/2012] [Indexed: 11/18/2022] Open
Abstract
Biological di-nitrogen fixation (N2) is the dominant natural source of new nitrogen to land ecosystems. Phosphorus (P) is thought to limit N2 fixation in many tropical soils, yet both molybdenum (Mo) and P are crucial for the nitrogenase reaction (which catalyzes N2 conversion to ammonia) and cell growth. We have limited understanding of how and when fixation is constrained by these nutrients in nature. Here we show in tropical forests of lowland Panama that the limiting element on asymbiotic N2 fixation shifts along a broad landscape gradient in soil P, where Mo limits fixation in P-rich soils while Mo and P co-limit in P-poor soils. In no circumstance did P alone limit fixation. We provide and experimentally test a mechanism that explains how Mo and P can interact to constrain asymbiotic N2 fixation. Fixation is uniformly favored in surface organic soil horizons - a niche characterized by exceedingly low levels of available Mo relative to P. We show that soil organic matter acts to reduce molybdate over phosphate bioavailability, which, in turn, promotes Mo limitation in sites where P is sufficient. Our findings show that asymbiotic N2 fixation is constrained by the relative availability and dynamics of Mo and P in soils. This conceptual framework can explain shifts in limitation status across broad landscape gradients in soil fertility and implies that fixation depends on Mo and P in ways that are more complex than previously thought.
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Affiliation(s)
- Nina Wurzburger
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panama
| | - Jean Philippe Bellenger
- Department of Geosciences, Princeton University, Princeton, New Jersey, United States of America
| | - Anne M. L. Kraepiel
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
| | - Lars O. Hedin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
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Merchant SS, Helmann JD. Elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation. Adv Microb Physiol 2012; 60:91-210. [PMID: 22633059 PMCID: PMC4100946 DOI: 10.1016/b978-0-12-398264-3.00002-4] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microorganisms play a dominant role in the biogeochemical cycling of nutrients. They are rightly praised for their facility for fixing both carbon and nitrogen into organic matter, and microbial driven processes have tangibly altered the chemical composition of the biosphere and its surrounding atmosphere. Despite their prodigious capacity for molecular transformations, microorganisms are powerless in the face of the immutability of the elements. Limitations for specific elements, either fleeting or persisting over eons, have left an indelible trace on microbial genomes, physiology, and their very atomic composition. We here review the impact of elemental limitation on microbes, with a focus on selected genetic model systems and representative microbes from the ocean ecosystem. Evolutionary adaptations that enhance growth in the face of persistent or recurrent elemental limitations are evident from genome and proteome analyses. These range from the extreme (such as dispensing with a requirement for a hard to obtain element) to the extremely subtle (changes in protein amino acid sequences that slightly, but significantly, reduce cellular carbon, nitrogen, or sulfur demand). One near-universal adaptation is the development of sophisticated acclimation programs by which cells adjust their chemical composition in response to a changing environment. When specific elements become limiting, acclimation typically begins with an increased commitment to acquisition and a concomitant mobilization of stored resources. If elemental limitation persists, the cell implements austerity measures including elemental sparing and elemental recycling. Insights into these fundamental cellular properties have emerged from studies at many different levels, including ecology, biological oceanography, biogeochemistry, molecular genetics, genomics, and microbial physiology. Here, we present a synthesis of these diverse studies and attempt to discern some overarching themes.
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Affiliation(s)
- Sabeeha S. Merchant
- Institute for Genomics and Proteomics and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, 14853-8101
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Harrington JM, Bargar JR, Jarzecki AA, Roberts JG, Sombers LA, Duckworth OW. Trace metal complexation by the triscatecholate siderophore protochelin: structure and stability. Biometals 2011; 25:393-412. [PMID: 22187125 DOI: 10.1007/s10534-011-9513-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 12/01/2011] [Indexed: 11/29/2022]
Abstract
Although siderophores are generally viewed as biological iron uptake agents, recent evidence has shown that they may play significant roles in the biogeochemical cycling and biological uptake of other metals. One such siderophore that is produced by A. vinelandii is the triscatecholate protochelin. In this study, we probe the solution chemistry of protochelin and its complexes with environmentally relevant trace metals to better understand its effect on metal uptake and cycling. Protochelin exhibits low solubility below pH 7.5 and degrades gradually in solution. Electrochemical measurements of protochelin and metal-protochelin complexes reveal a ligand half-wave potential of 200 mV. The Fe(III)Proto(3-) complex exhibits a salicylate shift in coordination mode at circumneutral to acidic pH. Coordination of Mn(II) by protochelin above pH 8.0 promotes gradual air oxidation of the metal center to Mn(III), which accelerates at higher pH values. The Mn(III)Proto(3-) complex was found to have a stability constant of log β(110) = 41.6. Structural parameters derived from spectroscopic measurements and quantum mechanical calculations provide insights into the stability of the Fe(III)Proto(3-), Fe(III)H(3)Proto, and Mn(III)Proto(3-) complexes. Complexation of Co(II) by protochelin results in redox cycling of Co, accompanied by accelerated degradation of the ligand at all solution pH values. These results are discussed in terms of the role of catecholate siderophores in environmental trace metal cycling and intracellular metal release.
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Affiliation(s)
- James M Harrington
- Soil Science Department, North Carolina State University, Raleigh, NC 27695-7619, USA
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Reed SC, Cleveland CC, Townsend AR. Functional Ecology of Free-Living Nitrogen Fixation: A Contemporary Perspective. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2011. [DOI: 10.1146/annurev-ecolsys-102710-145034] [Citation(s) in RCA: 358] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sasha C. Reed
- U.S. Geological Survey, Canyonlands Research Station, Moab, Utah 84532;
| | - Cory C. Cleveland
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, Montana 59812
| | - Alan R. Townsend
- Department of Ecology and Evolutionary Biology and the Institute of Arctic and Alpine Research (INSTAAR), University of Colorado, Boulder, Colorado 80309
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