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Rucker HR, Kaçar B. Enigmatic evolution of microbial nitrogen fixation: insights from Earth's past. Trends Microbiol 2024; 32:554-564. [PMID: 37061455 DOI: 10.1016/j.tim.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 04/17/2023]
Abstract
The evolution of nitrogen fixation undoubtedly altered nearly all corners of the biosphere, given the essential role of nitrogen in the synthesis of biomass. To date, there is no unified view on what planetary conditions gave rise to nitrogen fixation or how these conditions have sustained it evolutionarily. Intriguingly, the concentrations of metals that nitrogenases require to function have changed throughout Earth's history. In this review, we describe the interconnection of the metal and nitrogen cycles with nitrogenase evolution and the importance of ancient ecology in the formation of the modern nitrogen cycle. We argue that exploration of the nitrogen cycle's deep past will provide insights into humanity's immediate environmental challenges centered on nitrogen availability.
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Affiliation(s)
- Holly R Rucker
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA.
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2
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Jung P, Briegel-Williams L, Werner L, Jost E, Schultz M, Nürnberg DJ, Grube M, Lakatos M. A direct PCR approach with low-biomass insert opens new horizons for molecular sciences on cryptogam communities. Appl Environ Microbiol 2024; 90:e0002424. [PMID: 38349146 PMCID: PMC10952543 DOI: 10.1128/aem.00024-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 03/21/2024] Open
Abstract
Molecular sequence data have transformed research on cryptogams (e.g., lichens, microalgae, fungi, and symbionts thereof) but methods are still strongly hampered by the small size and intermingled growth of the target organisms, poor cultivability and detrimental effects of their secondary metabolites. Here, we aim to showcase examples on which a modified direct PCR approach for diverse aspects of molecular work on environmental samples concerning biocrusts, biofilms, and cryptogams gives new options for the research community. Unlike traditional approaches, this methodology only requires biomass equivalent to colonies and fragments of 0.2 mm in diameter, which can be picked directly from the environmental sample, and includes a quick DNA lysis followed by a standardized PCR cycle that allows co-cycling of various organisms/target regions in the same run. We demonstrate that this modified method can (i) amplify the most widely used taxonomic gene regions and those used for applied and environmental sciences from single colonies and filaments of free-living cyanobacteria, bryophytes, fungi, and lichens, including their mycobionts, chlorobionts, and cyanobionts from both isolates and in situ material during co-cycling; (ii) act as a tool to confirm that the dominant lichen photobiont was isolated from the original sample; and (iii) optionally remove inhibitory secondary lichen substances. Our results represent examples which highlight the method's potential for future applications covering mycology, phycology, biocrusts, and lichenology, in particular.IMPORTANCECyanobacteria, green algae, lichens, and other cryptogams play crucial roles in complex microbial systems such as biological soil crusts of arid biomes or biofilms in caves. Molecular investigations on environmental samples or isolates of these microorganisms are often hampered by their dense aggregation, small size, or metabolism products which complicate DNA extraction and subsequent PCRs. Our work presents various examples of how a direct DNA extraction and PCR method relying on low biomass inserts can overcome these common problems and discusses additional applications of the workflow including adaptations.
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Affiliation(s)
- Patrick Jung
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Laura Briegel-Williams
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Lina Werner
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Emily Jost
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Matthias Schultz
- Institute for Plant Science and Microbiology, Herbarium Hamburgense, University of Hamburg, Hamburg, Germany
| | - Dennis J. Nürnberg
- Institute of Experimental Physics, Freie Universität Berlin, Berlin, Germany
- Dahlem Centre for Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Martin Grube
- Institute of Biology, University of Graz, Graz, Austria
| | - Michael Lakatos
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
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3
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Magain N, Miadlikowska J, Goffinet B, Goward T, Pardo-De la Hoz C, Jüriado I, Simon A, Mercado-Díaz J, Barlow T, Moncada B, Lücking R, Spielmann A, Canez L, Wang L, Nelson P, Wheeler T, Lutzoni F, Sérusiaux E. High species richness in the lichen genus Peltigera ( Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science. PERSOONIA 2023; 51:1-88. [PMID: 38665978 PMCID: PMC11041898 DOI: 10.3767/persoonia.2023.51.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 10/10/2022] [Indexed: 04/28/2024]
Abstract
Applying molecular methods to fungi establishing lichenized associations with green algae or cyanobacteria has repeatedly revealed the existence of numerous phylogenetic taxa overlooked by classical taxonomic approaches. Here, we report taxonomical conclusions based on multiple species delimitation and validation analyses performed on an eight-locus dataset that includes world-wide representatives of the dolichorhizoid and scabrosoid clades in section Polydactylon of the genus Peltigera. Following the recommendations resulting from a consensus species delimitation approach and additional species validation analysis (BPP) performed in this study, we present a total of 25 species in the dolichorhizoid clade and nine in the scabrosoid clade, including respectively 18 and six species that are new to science and formally described. Additionally, one combination and three varieties (including two new to science) are proposed in the dolichorhizoid clade. The following 24 new species are described: P. appalachiensis, P. asiatica, P. borealis, P. borinquensis, P. chabanenkoae, P. clathrata, P. elixii, P. esslingeri, P. flabellae, P. gallowayi, P. hawaiiensis, P. holtanhartwigii, P. itatiaiae, P. hokkaidoensis, P. kukwae, P. massonii, P. mikado, P. nigriventris, P. orientalis, P. rangiferina, P. sipmanii, P. stanleyensis, P. vitikainenii and P. willdenowii; the following new varieties are introduced: P. kukwae var. phyllidiata and P. truculenta var. austroscabrosa; and the following new combination is introduced: P. hymenina var. dissecta. Each species from the dolichorhizoid and scabrosoid clades is morphologically and chemically described, illustrated, and characterised with ITS sequences. Identification keys are provided for the main biogeographic regions where species from the two clades occur. Morphological and chemical characters that are commonly used for species identification in the genus Peltigera cannot be applied to unambiguously recognise most molecularly circumscribed species, due to high variation of thalli formed by individuals within a fungal species, including the presence of distinct morphs in some cases, or low interspecific variation in others. The four commonly recognised morphospecies: P. dolichorhiza, P. neopolydactyla, P. pulverulenta and P. scabrosa in the dolichorhizoid and scabrosoid clades represent species complexes spread across multiple and often phylogenetically distantly related lineages. Geographic origin of specimens is often helpful for species recognition; however, ITS sequences are frequently required for a reliable identification. Citation: Magain N, Miadlikowska J, Goffinet B, et al. 2023. High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science. Persoonia 51: 1-88. doi: 10.3767/persoonia.2023.51.01.
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Affiliation(s)
- N. Magain
- Evolution and Conservation Biology, InBioS Research Center, University of Liège, Sart Tilman B22, Quartier vallée 1, Chemin de la vallée 4, B-4000 Liège, Belgium
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - J. Miadlikowska
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - B. Goffinet
- Ecology and Evolutionary Biology, Unit 3043, University of Connecticut, 75 North Eagleville road, Storrs CT, 06269-3043 USA
| | - T. Goward
- Beaty Biodiversity Museum, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - C.J. Pardo-De la Hoz
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - I. Jüriado
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu 50409, Estonia; Institute of Agricultural & Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 5, Tartu 51006, Estonia
| | - A. Simon
- Evolution and Conservation Biology, InBioS Research Center, University of Liège, Sart Tilman B22, Quartier vallée 1, Chemin de la vallée 4, B-4000 Liège, Belgium
- Ecology and Evolutionary Biology, Unit 3043, University of Connecticut, 75 North Eagleville road, Storrs CT, 06269-3043 USA
| | - J.A. Mercado-Díaz
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois, 60605 USA
| | - T. Barlow
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - B. Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Cra. 4 No. 26B-54, Torre de Laboratorios, Herbario, Bogotá, Colombia; current address: Botanischer Garten, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
| | - R. Lücking
- Botanischer Garten, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
| | - A. Spielmann
- Laboratòrio de Botanica / Liquenologia, Instituto de Biociencias, Universidade Federal de Mato Grosso do Sul, Campo Grande – MS, Brazil
| | - L. Canez
- Laboratòrio de Botanica / Liquenologia, Instituto de Biociencias, Universidade Federal de Mato Grosso do Sul, Campo Grande – MS, Brazil
| | - L.S. Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, CAS, Kunming 650201, China
| | - P. Nelson
- Natural and Behavioral Sciences Division, University of Maine – Fort Kent, Fort Kent, ME, USA
| | - T. Wheeler
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - F. Lutzoni
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - E. Sérusiaux
- Evolution and Conservation Biology, InBioS Research Center, University of Liège, Sart Tilman B22, Quartier vallée 1, Chemin de la vallée 4, B-4000 Liège, Belgium
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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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5
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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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Cleveland CC, Reis CRG, Perakis SS, Dynarski KA, Batterman SA, Crews TE, Gei M, Gundale MJ, Menge DNL, Peoples MB, Reed SC, Salmon VG, Soper FM, Taylor BN, Turner MG, Wurzburger N. Exploring the Role of Cryptic Nitrogen Fixers in Terrestrial Ecosystems: A Frontier in Nitrogen Cycling Research. Ecosystems 2022. [DOI: 10.1007/s10021-022-00804-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Chen Y, Wang Q, Zhu J, Xi Y, Zhang Q, Dai G, He N, Yu G. Atmospheric Wet Iron, Molybdenum, and Vanadium Deposition in Chinese Terrestrial Ecosystems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:12898-12905. [PMID: 36026692 DOI: 10.1021/acs.est.2c03213] [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: 06/15/2023]
Abstract
Iron (Fe), molybdenum (Mo), and vanadium (V) are the main components of the three known biological nitrogenases, which constrain nitrogen fixation and affect ecosystem productivity. Atmospheric deposition is an important pathway of these trace metals into ecosystems. Here, we explored the deposition flux, spatiotemporal pattern, and influencing factors of atmospheric wet Fe, Mo, and V deposition based on China Wet Deposition Observation Network (ChinaWD) data from 2016 to 2020. Our results showed that atmospheric wet Fe, Mo, and V deposition was 7.77 ± 7.24, 0.16 ± 0.11, and 0.13 ± 0.12 mg m-2 a-1 in Chinese terrestrial ecosystems, respectively, and revealed obvious spatial patterns but no significant annual trends. Wet Fe deposition was significantly correlated with the soil Fe content. Mo and V deposition was more affected by anthropogenic activities than Fe deposition. Wet Mo deposition was significantly affected by Mo ore reserves and waste incineration. V deposition was significantly correlated with domestic biomass burning. This study quantified wet Fe, Mo, and V deposition in China for the first time, and the implications of atmospheric trace metal deposition on biological nitrogen fixation were discussed.
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Affiliation(s)
- Yanran Chen
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Qiufeng Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Jianxing Zhu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing 100101, China
| | - Yue Xi
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Qiongyu Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Guanhua Dai
- Research Station of Changbai Mountain Forest Ecosystems, Chinese Academy of Sciences, Antu 133613, China
| | - Nianpeng He
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
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8
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Rnf and Fix Have Specific Roles during Aerobic Nitrogen Fixation in Azotobacter vinelandii. Appl Environ Microbiol 2022; 88:e0104922. [PMID: 36000884 PMCID: PMC9469703 DOI: 10.1128/aem.01049-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biological nitrogen fixation requires large amounts of energy in the form of ATP and low potential electrons to overcome the high activation barrier for cleavage of the dinitrogen triple bond. The model aerobic nitrogen-fixing bacteria, Azotobacter vinelandii, generates low potential electrons in the form of reduced ferredoxin (Fd) and flavodoxin (Fld) using two distinct mechanisms via the enzyme complexes Rnf and Fix. Both Rnf and Fix are expressed during nitrogen fixation, but deleting either rnf1 or fix genes has little effect on diazotrophic growth. However, deleting both rnf1 and fix eliminates the ability to grow diazotrophically. Rnf and Fix both use NADH as a source of electrons, but overcoming the energetics of NADH's endergonic reduction of Fd/Fld is accomplished through different mechanisms. Rnf harnesses free energy from the chemiosmotic potential, whereas Fix uses electron bifurcation to effectively couple the endergonic reduction of Fd/Fld to the exergonic reduction of quinone. Different reaction stoichiometries and condition-specific differential gene expression indicate specific roles for the two reactions. This work's complementary physiological studies and thermodynamic modeling reveal how Rnf and Fix balance redox homeostasis in various conditions. Specifically, the Fix complex is required for efficient growth under low oxygen concentrations, while Rnf is presumed to maintain reduced Fd/Fld production for nitrogenase under standard conditions. This work provides a framework for understanding how the production of low potential electrons sustains robust nitrogen fixation in various conditions. IMPORTANCE The availability of fixed nitrogen is critical for life in many ecosystems, from extreme environments to agriculture. Due to the energy demands of biological nitrogen fixation, organisms must tailor their metabolism during diazotrophic growth to deliver the energy requirements to nitrogenase in the form of ATP and low potential electrons. Therefore, a complete understanding of diazotrophic energy metabolism and redox homeostasis is required to understand the impact on ecological communities or to promote crop growth in agriculture through engineered diazotrophs.
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9
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Vanadium in groundwater aquifers increases the risk of MAC pulmonary infection in O’ahu, Hawai’i. Environ Epidemiol 2022; 6:e220. [DOI: 10.1097/ee9.0000000000000220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/15/2022] [Accepted: 06/15/2022] [Indexed: 11/25/2022] Open
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Renaudin M, Laforest-Lapointe I, Bellenger JP. Unraveling global and diazotrophic bacteriomes of boreal forest floor feather mosses and their environmental drivers at the ecosystem and at the plant scale in North America. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155761. [PMID: 35533858 DOI: 10.1016/j.scitotenv.2022.155761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 06/14/2023]
Abstract
Feather mosses are abundant cryptogams of the boreal forest floor and shelter a broad diversity of bacteria who have important ecological functions (e.g., decomposition, nutrient cycling). In particular, nitrogen (N2-) fixation performed by feather moss-associated diazotrophs constitutes an important entry of nitrogen in the boreal forest ecosystem. However, the composition of the feather moss bacteriome and its environmental drivers are still unclear. Using cDNA amplicon sequencing of the 16S rRNA and nifH genes and cyanobacterial biomass quantification, we explored the active global and diazotrophic bacterial communities of two dominant feather moss species (i) at the ecosystem scale, along a 500-km climatic and nutrient deposition gradient in the North American boreal forest, and (ii) at the plant scale, along the moss shoot senescence gradient. We found that cyanobacteria were major actors of the feather moss bacteriome, accounting for 33% of global bacterial communities and 65% of diazotrophic communities, and that several cyanobacterial and methanotrophic genera were contributing to N2-fixation. Moreover, we showed that bacteria were occupying ecological niches along the moss shoot, with phototrophs being dominant in the apical part and methanotrophs being dominant in the basal part. Finally, climate (temperature, precipitation), environmental variables (moss species, month, tree density) and nutrients (nitrogen, phosphorus, molybdenum, vanadium, iron) strongly shaped global and diazotrophic bacteriomes. In summary, this work presents evidence that the feather moss bacteriome plays crucial roles in supporting moss growth, health, and decomposition, as well as in the boreal forest carbon and nitrogen cycles. This study also highlights the substantial effects of climate and nutrients on the feather moss bacteriome, suggesting the importance of understanding the impacts of global change on moss-associated bacterial growth and activity.
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Affiliation(s)
- Marie Renaudin
- Centre Sève, Département de Chimie, Université de Sherbrooke, J1K 2R1 Sherbrooke, QC, Canada.
| | | | - Jean-Philippe Bellenger
- Centre Sève, Département de Chimie, Université de Sherbrooke, J1K 2R1 Sherbrooke, QC, Canada.
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11
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Chen KH, Nelson J. A scoping review of bryophyte microbiota: diverse microbial communities in small plant packages. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4496-4513. [PMID: 35536989 DOI: 10.1093/jxb/erac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
Plant health depends not only on the condition of the plant itself but also on its diverse community of microbes, or microbiota. Just like the better-studied angiosperms, bryophytes (mosses, liverworts, and hornworts) harbor diverse communities of bacteria, archaea, fungi, and other microbial eukaryotes. Bryophytes are increasingly recognized as important model systems for understanding plant evolution, development, physiology, and symbiotic interactions. Much of the work on bryophyte microbiota in the past focused on specific symbiont types for each bryophyte group, but more recent studies are taking a broader view acknowledging the coexistence of diverse microbial communities in bryophytes. Therefore, this review integrates studies of bryophyte microbes from both perspectives to provide a holistic view of the existing research for each bryophyte group and on key themes. The systematic search also reveals the taxonomic and geographic biases in this field, including a severe under-representation of the tropics, very few studies on viruses or eukaryotic microbes beyond fungi, and a focus on mycorrhizal fungi studies in liverworts. Such gaps may have led to errors in conclusions about evolutionary patterns in symbiosis. This analysis points to a wealth of future research directions that promise to reveal how the distinct life cycles and physiology of bryophytes interact with their microbiota.
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Affiliation(s)
- Ko-Hsuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jessica Nelson
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
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12
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Permin A, Horwath AB, Metcalfe DB, Priemé A, Rousk K. ‘High nitrogen‐fixing rates associated with ground‐covering mosses in a tropical mountain cloud forest will decrease drastically in a future climate’. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Aya Permin
- Terrestrial Ecology Section, Department of Biology University of Copenhagen Copenhagen Denmark
- Center for Permafrost (CENPERM) University of Copenhagen Copenhagen Denmark
| | - Aline B. Horwath
- Biological and Environmental Sciences, Faculty of Natural Sciences University of Stirling Stirling UK
| | - Daniel B. Metcalfe
- Department of Physical Geography and Ecosystem Science Lund University SE Lund Sweden
- Department of Ecology and Environmental Science SE Umeå Sweden
| | - Anders Priemé
- Center for Permafrost (CENPERM) University of Copenhagen Copenhagen Denmark
- Section of Microbiology, Department of Biology University of Copenhagen Copenhagen Denmark
| | - Kathrin Rousk
- Terrestrial Ecology Section, Department of Biology University of Copenhagen Copenhagen Denmark
- Center for Permafrost (CENPERM) University of Copenhagen Copenhagen Denmark
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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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de Vries S, de Vries J. Evolutionary genomic insights into cyanobacterial symbioses in plants. QUANTITATIVE PLANT BIOLOGY 2022; 3:e16. [PMID: 37077989 PMCID: PMC10095879 DOI: 10.1017/qpb.2022.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 05/03/2023]
Abstract
Photosynthesis, the ability to fix atmospheric carbon dioxide, was acquired by eukaryotes through symbiosis: the plastids of plants and algae resulted from a cyanobacterial symbiosis that commenced more than 1.5 billion years ago and has chartered a unique evolutionary path. This resulted in the evolutionary origin of plants and algae. Some extant land plants have recruited additional biochemical aid from symbiotic cyanobacteria; these plants associate with filamentous cyanobacteria that fix atmospheric nitrogen. Examples of such interactions can be found in select species from across all major lineages of land plants. The recent rise in genomic and transcriptomic data has provided new insights into the molecular foundation of these interactions. Furthermore, the hornwort Anthoceros has emerged as a model system for the molecular biology of cyanobacteria-plant interactions. Here, we review these developments driven by high-throughput data and pinpoint their power to yield general patterns across these diverse symbioses.
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Affiliation(s)
- Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Authors for correspondence: Sophie de Vries E-mail: Jan de Vries E-mail:
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goettingen, Germany
- Authors for correspondence: Sophie de Vries E-mail: Jan de Vries E-mail:
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15
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Metabolic Model of the Nitrogen-Fixing Obligate Aerobe Azotobacter vinelandii Predicts Its Adaptation to Oxygen Concentration and Metal Availability. mBio 2021; 12:e0259321. [PMID: 34903060 PMCID: PMC8686835 DOI: 10.1128/mbio.02593-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is considerable interest in promoting biological nitrogen fixation (BNF) as a mechanism to reduce the inputs of nitrogenous fertilizers in agriculture, but considerable fundamental knowledge gaps still need to be addressed. BNF is catalyzed by nitrogenase, which requires a large input of energy in the form of ATP and low potential electrons. Diazotrophs that respire aerobically have an advantage in meeting the ATP demands of BNF but face challenges in protecting nitrogenase from inactivation by oxygen. Here, we constructed a genome-scale metabolic model of the nitrogen-fixing bacterium Azotobacter vinelandii, which uses a complex respiratory protection mechanism to consume oxygen at a high rate to keep intracellular conditions microaerobic. Our model accurately predicts growth rate under high oxygen and substrate concentrations, consistent with a large electron flux directed to the respiratory protection mechanism. While a partially decoupled electron transport chain compensates for some of the energy imbalance under high-oxygen conditions, it does not account for all substrate intake, leading to increased maintenance rates. Interestingly, the respiratory protection mechanism is required for accurate predictions even when ammonia is supplemented during growth, suggesting that the respiratory protection mechanism might be a core principle of metabolism and not just used for nitrogenase protection. We have also shown that rearrangement of flux through the electron transport system allows A. vinelandii to adapt to different oxygen concentrations, metal availability, and genetic disruption, which cause an ammonia excretion phenotype. Accurately determining the energy balance in an aerobic nitrogen-fixing metabolic model is required for future engineering approaches.
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16
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Pessoa JC, Santos MF, Correia I, Sanna D, Sciortino G, Garribba E. Binding of vanadium ions and complexes to proteins and enzymes in aqueous solution. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214192] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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17
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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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18
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The relationship of C and N stable isotopes to high-latitude moss-associated N 2 fixation. Oecologia 2021; 197:283-295. [PMID: 34319437 DOI: 10.1007/s00442-021-05005-7] [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: 02/11/2021] [Accepted: 07/23/2021] [Indexed: 10/20/2022]
Abstract
Moss-associated N2 fixation by epiphytic microbes is a key biogeochemical process in nutrient-limited high-latitude ecosystems. Abiotic drivers, such as temperature and moisture, and the identity of host mosses are critical sources of variation in N2 fixation rates. An understanding of the potential interaction between these factors is essential for predicting N inputs as moss communities change with the climate. To further understand the drivers and results of N2 fixation rate variation, we obtained natural abundance values of C and N isotopes and an associated rate of N2 fixation with 15N2 gas incubations in 34 moss species collected in three regions across Alaska, USA. We hypothesized that δ15N values would increase toward 0‰ with higher N2 fixation to reflect the increasing contribution of fixed N2 in moss biomass. Second, we hypothesized that δ13C and N2 fixation would be positively related, as enriched δ13C signatures reflect abiotic conditions favorable to N2 fixation. We expected that the magnitude of these relationships would vary among types of host mosses, reflecting differences in anatomy and habitat. We found little support for our first hypothesis, with only a modest positive relationship between N2 fixation rates and δ15N in a structural equation model. We found a significant positive relationship between δ13C and N2 fixation only in Hypnales, where the probability of N2 fixation activity reached 95% when δ13C values exceeded - 30.4‰. We conclude that moisture and temperature interact strongly with host moss identity in determining the extent to which abiotic conditions impact associated N2 fixation rates.
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Li Q, Zhang H, Zhang L, Chen S. Functional analysis of multiple nifB genes of Paenibacillus strains in synthesis of Mo-, Fe- and V-nitrogenases. Microb Cell Fact 2021; 20:139. [PMID: 34281551 PMCID: PMC8287671 DOI: 10.1186/s12934-021-01629-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/10/2021] [Indexed: 12/16/2022] Open
Abstract
Background Biological nitrogen fixation is catalyzed by Mo-, V- and Fe-nitrogenases that are encoded by nif, vnf and anf genes, respectively. NifB is the key protein in synthesis of the cofactors of all nitrogenases. Most diazotrophic Paenibacillus strains have only one nifB gene located in a compact nif gene cluster (nifBHDKENX(orf1)hesAnifV). But some Paenibacillus strains have multiple nifB genes and their functions are not known. Results A total of 138 nifB genes are found in the 116 diazotrophic Paenibacillus strains. Phylogeny analysis shows that these nifB genes fall into 4 classes: nifBI class including the genes (named as nifB1 genes) that are the first gene within the compact nif gene cluster, nifBII class including the genes (named as nifB2 genes) that are adjacent to anf or vnf genes, nifBIII class whose members are designated as nifB3 genes and nifBIV class whose members are named as nifB4 genes are scattered on genomes. Functional analysis by complementation of the ∆nifB mutant of P. polymyxa which has only one nifB gene has shown that both nifB1 and nifB2 are active in synthesis of Mo-nitrogenase, while nifB3 and nifB4 genes are not. Deletion analysis also has revealed that nifB1 of Paenibacillus sabinae T27 is involved in synthesis of Mo-nitrogenase, while nifB3 and nifB4 genes are not. Complementation of the P. polymyxa ∆nifBHDK mutant with the four reconstituted operons: nifB1anfHDGK, nifB2anfHDGK, nifB1vnfHDGK and nifB2vnfHDGK, has shown both that nifB1 and nifB2 were able to support synthesis of Fe- or V-nitrogenases. Transcriptional results obtained in the original Paenibacillus strains are consistent with the complementation results. Conclusions The multiple nifB genes of the diazotrophic Paenibacillus strains are divided into 4 classes. The nifB1 located in a compact nif gene cluster (nifBHDKENX(orf1)hesAnifV) and the nifB2 genes being adjacent to nif or anf or vnf genes are active in synthesis of Mo-, Fe and V-nitrogenases, but nifB3 and nifB4 are not. The reconstituted anf system comprising 8 genes (nifBanfHDGK and nifXhesAnifV) and vnf system comprising 10 genes (nifBvnfHDGKEN and nifXhesAnifV) support synthesis of Fe-nitrogenase and V-nitrogenase in Paenibacillus background, respectively. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01629-9.
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Affiliation(s)
- Qin Li
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China.,Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Haowei Zhang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Liqun Zhang
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China.
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20
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Abstract
Species of the floating, freshwater fern Azolla form a well-characterized symbiotic association with the non-culturable cyanobacterium Nostoc azollae, which fixes nitrogen for the plant. However, several cyanobacterial strains have over the years been isolated and cultured from Azolla from all over the world. The genomes of 10 of these strains were sequenced and compared with each other, with other symbiotic cyanobacterial strains, and with similar strains that were not isolated from a symbiotic association. The 10 strains fell into three distinct groups: six strains were nearly identical to the non-symbiotic strain, Nostoc (Anabaena) variabilis ATCC 29413; three were similar to the symbiotic strain, Nostoc punctiforme, and one, Nostoc sp. 2RC, was most similar to non-symbiotic strains of Nostoc linckia. However, Nostoc sp. 2RC was unusual because it has three sets of nitrogenase genes; it has complete gene clusters for two distinct Mo-nitrogenases and an alternative V-nitrogenase. Genes for Mo-nitrogenase, sugar transport, chemotaxis and pili characterized all the symbiotic strains. Several of the strains infected the liverwort Blasia, including N. variabilis ATCC 29413, which did not originate from Azolla but rather from a sewage pond. However, only Nostoc sp. 2RC, which produced highly motile hormogonia, was capable of high-frequency infection of Blasia. Thus, some of these strains, which grow readily in the laboratory, may be useful in establishing novel symbiotic associations with other plants.
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Affiliation(s)
- Brenda S. Pratte
- Department of Biology, University of Missouri–St. Louis, One University Blvd, St. Louis, MO 63121, USA
| | - Teresa Thiel
- Department of Biology, University of Missouri–St. Louis, One University Blvd, St. Louis, MO 63121, USA
- *Correspondence: Teresa Thiel,
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21
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White DJ, Levy LS. Vanadium: environmental hazard or environmental opportunity? A perspective on some key research needs. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:527-534. [PMID: 33908931 DOI: 10.1039/d0em00470g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Vanadium remains an important microalloying element in the metallurgical industry and has more recently become important in energy storage. Such applications provide important opportunities in carbon reduction initiatives. They must be exploited safely and therefore understanding the toxicological profile of vanadium and its compounds, and ensuring ongoing regulatory efforts are appropriate is vital. This perspective details some of the technical challenges and common misconceptions in vanadium chemistry and toxicology and outlines knowledge gaps and areas of research that the authors believe must be addressed to achieve full benefit within a scientifically sound regulatory framework.
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Affiliation(s)
- David J White
- David White Chemical and Metallurgical Consulting, Tewkesbury, Gloucestershire, UK.
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22
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Parison K, Gies-Elterlein J, Trncik C, Einsle O. Expression, Isolation, and Characterization of Vanadium Nitrogenase from Azotobacter vinelandii. Methods Mol Biol 2021; 2353:97-121. [PMID: 34292546 DOI: 10.1007/978-1-0716-1605-5_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nitrogenases are the sole enzymes known to mediate biological nitrogen fixation, an essential process for sustaining life on earth. Among the three known variants, molybdenum nitrogenase is the best-studied to date. Recent work on the alternative vanadium nitrogenase provided important insights into the mechanism of nitrogen fixation since this enzyme differs from its molybdenum counterpart in some important aspects. Here, we present a protocol to obtain unmodified vanadium nitrogenase in high yield and purity from the paradigmatic diazotroph Azotobacter vinelandii, including procedures for cell cultivation, purification, and protein characterization.
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Affiliation(s)
- Katharina Parison
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | | | - Christian Trncik
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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23
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Inomura K, Deutsch C, Masuda T, Prášil O, Follows MJ. Quantitative models of nitrogen-fixing organisms. Comput Struct Biotechnol J 2020; 18:3905-3924. [PMID: 33335688 PMCID: PMC7733014 DOI: 10.1016/j.csbj.2020.11.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 10/26/2022] Open
Abstract
Nitrogen-fixing organisms are of importance to the environment, providing bioavailable nitrogen to the biosphere. Quantitative models have been used to complement the laboratory experiments and in situ measurements, where such evaluations are difficult or costly. Here, we review the current state of the quantitative modeling of nitrogen-fixing organisms and ways to enhance the bridge between theoretical and empirical studies.
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Affiliation(s)
- Keisuke Inomura
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Curtis Deutsch
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Takako Masuda
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, Třeboň, Czech Republic
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, Třeboň, Czech Republic
| | - Michael J. Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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24
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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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25
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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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26
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Abstract
The enzyme molybdenum nitrogenase converts atmospheric nitrogen gas to ammonia and is of critical importance for the cycling of nitrogen in the biosphere and for the sustainability of life. Alternative vanadium and iron-only nitrogenases that are homologous to molybdenum nitrogenases are also found in archaea and bacteria, but they have a different transition metal, either vanadium or iron, at their active sites. So far alternative nitrogenases have only been found in microbes that also have molybdenum nitrogenase. They are less widespread than molybdenum nitrogenase in bacteria and archaea, and they are less efficient. The presumption has been that alternative nitrogenases are fail-safe enzymes that are used in situations where molybdenum is limiting. Recent work indicates that vanadium nitrogenase may play a role in the global biological nitrogen cycle and iron-only nitrogenase may contribute products that shape microbial community interactions in nature.
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Affiliation(s)
- Caroline S Harwood
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA;
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27
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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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Muggia L, Nelsen MP, Kirika PM, Barreno E, Beck A, Lindgren H, Lumbsch HT, Leavitt SD. Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): An impetus for developing an integrated taxonomy. Mol Phylogenet Evol 2020; 149:106821. [PMID: 32294545 DOI: 10.1016/j.ympev.2020.106821] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 12/16/2022]
Abstract
Lichens provide valuable systems for studying symbiotic interactions. In lichens, these interactions are frequently described in terms of availability, selectivity and specificity of the mycobionts and photobionts towards one another. The lichen-forming, green algal genus Trebouxia Puymaly is among the most widespread photobiont, associating with a broad range of lichen-forming fungi. To date, 29 species have been described, but studies consistently indicate that the vast majority of species-level lineages still lack formal description, and new, previously unrecognized lineages are frequently reported. To reappraise the diversity and the evolutionary relationships of species-level lineages in Trebouxia, we assembled DNA sequence data from over 1600 specimens, compiled from a range of sequences from previously published studies, axenic algal cultures, and lichens collected from poorly sampled regions. From these samples, we selected representatives of the currently known genetic diversity in the lichenized Trebouxia and inferred a phylogeny from multi-locus sequence data (ITS, rbcL, cox2). We demonstrate that the current formally described species woefully underrepresent overall species-level diversity in this important lichen-forming algal genus. We anticipate that an integrative taxonomic approach, incorporating morphological and physiological data from axenic cultures with genetic data, will be required to establish a robust, comprehensive taxonomy for Trebouxia. The data presented here provide an important impetus and reference dataset for more reliably characterizing diversity in lichenized algae and in using lichens to investigate the evolution of symbioses and holobionts.
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Affiliation(s)
- Lucia Muggia
- University of Trieste, Department of Life Sciences, via Giorgieri 10, 34127 Trieste, Italy
| | | | - Paul M Kirika
- Botany Department, EA Herbarium, National Museums of Kenya, P.O. Box 40658-00100, Nairobi, Kenya
| | - Eva Barreno
- Botánica, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Fac. CC. Biológicas, Universitat de València, C/ Dr. Moliner, 50. 46100-Burjassot, Valencia, Spain
| | - Andreas Beck
- Botanische Staatssammlung München, SNSB-BSM, Menzinger Str. 67, D-80638 Munich, Germany
| | | | | | - Steven D Leavitt
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, UT, USA.
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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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