1
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Stenow R, Robertson EK, Kourtchenko O, Whitehouse MJ, Pinder MIM, Benvenuto G, Töpel M, Godhe A, Ploug H. Resting cells of Skeletonema marinoi assimilate organic compounds and respire by dissimilatory nitrate reduction to ammonium in dark, anoxic conditions. Environ Microbiol 2024; 26:e16625. [PMID: 38653479 DOI: 10.1111/1462-2920.16625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 04/05/2024] [Indexed: 04/25/2024]
Abstract
Diatoms can survive long periods in dark, anoxic sediments by forming resting spores or resting cells. These have been considered dormant until recently when resting cells of Skeletonema marinoi were shown to assimilate nitrate and ammonium from the ambient environment in dark, anoxic conditions. Here, we show that resting cells of S. marinoi can also perform dissimilatory nitrate reduction to ammonium (DNRA), in dark, anoxic conditions. Transmission electron microscope analyses showed that chloroplasts were compacted, and few large mitochondria had visible cristae within resting cells. Using secondary ion mass spectrometry and isotope ratio mass spectrometry combined with stable isotopic tracers, we measured assimilatory and dissimilatory processes carried out by resting cells of S. marinoi under dark, anoxic conditions. Nitrate was both respired by DNRA and assimilated into biomass by resting cells. Cells assimilated nitrogen from urea and carbon from acetate, both of which are sources of dissolved organic matter produced in sediments. Carbon and nitrogen assimilation rates corresponded to turnover rates of cellular carbon and nitrogen content ranging between 469 and 10,000 years. Hence, diatom resting cells can sustain their cells in dark, anoxic sediments by slowly assimilating and respiring substrates from the ambient environment.
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Affiliation(s)
- Rickard Stenow
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SE, Sweden
| | | | - Olga Kourtchenko
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SE, Sweden
| | | | - Matthew I M Pinder
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SE, Sweden
| | | | - Mats Töpel
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SE, Sweden
- IVL-Swedish Environmental Research Institute, Gothenburg, SE, Sweden
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SE, Sweden
| | - Helle Ploug
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SE, Sweden
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2
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Wang C, He T, Zhang M, Zheng C, Yang L, Yang L. Review of the mechanisms involved in dissimilatory nitrate reduction to ammonium and the efficacies of these mechanisms in the environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 345:123480. [PMID: 38325507 DOI: 10.1016/j.envpol.2024.123480] [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: 12/08/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Dissimilatory nitrate reduction to ammonium (DNRA) is currently of great interest because it is an important method for recovering nitrogen from wastewater and offers many advantages, over other methods. A full understanding of DNRA requires the mechanisms, pathways, and functional microorganisms involved to be identified. The roles these pathways play and the effectiveness of DNRA in the environment are not well understood. The objectives of this review are to describe our current understanding of the molecular mechanisms and pathways involved in DNRA from the substrate transfer perspective and to summarize the effects of DNRA in the environment. First, the mechanisms and pathways involved in DNRA are described in detail. Second, our understanding of DNRA by actinomycetes is reviewed and gaps in our understanding are identified. Finally, the effects of DNRA in the environment are assessed. This review will help in the development of future research into DNRA to promote the use of DNRA to treat wastewater and recover nitrogen.
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Affiliation(s)
- Cerong Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Tengxia He
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Manman Zhang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Chunxia Zheng
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Li Yang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Lu Yang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
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3
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Gain G, Berne N, Feller T, Godaux D, Cenci U, Cardol P. Induction of photosynthesis under anoxic condition in Thalassiosira pseudonana and Euglena gracilis: interactions between fermentation and photosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1186926. [PMID: 37560033 PMCID: PMC10407231 DOI: 10.3389/fpls.2023.1186926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/28/2023] [Indexed: 08/11/2023]
Abstract
INTRODUCTION In their natural environment, microalgae can be transiently exposed to hypoxic or anoxic environments. Whereas fermentative pathways and their interactions with photosynthesis are relatively well characterized in the green alga model Chlamydomonas reinhardtii, little information is available in other groups of photosynthetic micro-eukaryotes. In C. reinhardtii cyclic electron flow (CEF) around photosystem (PS) I, and light-dependent oxygen-sensitive hydrogenase activity both contribute to restoring photosynthetic linear electron flow (LEF) in anoxic conditions. METHODS Here we analyzed photosynthetic electron transfer after incubation in dark anoxic conditions (up to 24 h) in two secondary microalgae: the marine diatom Thalassiosira pseudonana and the excavate Euglena gracilis. RESULTS Both species showed sustained abilities to prevent over-reduction of photosynthetic electron carriers and to restore LEF. A high and transient CEF around PSI was also observed specifically in anoxic conditions at light onset in both species. In contrast, at variance with C. reinhardtii, no sustained hydrogenase activity was detected in anoxic conditions in both species. DISCUSSION Altogether our results suggest that another fermentative pathway might contribute, along with CEF around PSI, to restore photosynthetic activity in anoxic conditions in E. gracilis and T. pseudonana. We discuss the possible implication of the dissimilatory nitrate reduction to ammonium (DNRA) in T. pseudonana and the wax ester fermentation in E. gracilis.
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Affiliation(s)
- Gwenaëlle Gain
- InBioS – PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, Liège, Belgium
| | - Nicolas Berne
- InBioS – PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, Liège, Belgium
| | - Tom Feller
- InBioS – PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, Liège, Belgium
| | - Damien Godaux
- InBioS – PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, Liège, Belgium
| | - Ugo Cenci
- Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, CNRS, UMR8576 – UGSF, Lille, France
| | - Pierre Cardol
- InBioS – PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, Liège, Belgium
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4
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Marguš M, Ahel M, Čanković M, Ljubešić Z, Terzić S, Hodak Kobasić V, Ciglenečki I. Phytoplankton pigment dynamics in marine lake fluctuating between stratified and holomictic euxinic conditions. MARINE POLLUTION BULLETIN 2023; 191:114931. [PMID: 37075558 DOI: 10.1016/j.marpolbul.2023.114931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 05/03/2023]
Abstract
Biomass dynamics in the marine lake are strongly dependent on seasonal variability in vertical stratification, indicating rapid adaptation of phytoplankton to short-term changes in the water column. A small marine lake (Rogoznica Lake, Croatia), which fluctuates between stably stratified and holomictic euxinic conditions, was used as a model to study the phytoplankton responses to environmental perturbations, in particular the anoxic stress, caused by periodic holomixia. The epilimnion showed significant temporal and vertical variability with a chlorophyll a subsurface maximum with the highest biomass near the chemocline. Fucoxanthin-containing biomass (diatoms) dominated in the epilimnion in colder seasons and was first to recover after holomictic euxinic events. The shift towards the smaller groups prevailed during highly stratified water column conditions in warmer seasons. Results for the hypolimnion were more enigmatic, with high concentrations of alloxanthin, zeaxanthin, and violaxanthin indicating the presence of a viable small-size mixotrophic community under extreme conditions.
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Affiliation(s)
- Marija Marguš
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Marijan Ahel
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Milan Čanković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Zrinka Ljubešić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Senka Terzić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Vedranka Hodak Kobasić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Irena Ciglenečki
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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5
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Blumberg K, Miller M, Ponsero A, Hurwitz B. Ontology-driven analysis of marine metagenomics: what more can we learn from our data? Gigascience 2022; 12:giad088. [PMID: 37941395 PMCID: PMC10632069 DOI: 10.1093/gigascience/giad088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/30/2023] [Accepted: 09/28/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND The proliferation of metagenomic sequencing technologies has enabled novel insights into the functional genomic potentials and taxonomic structure of microbial communities. However, cyberinfrastructure efforts to manage and enable the reproducible analysis of sequence data have not kept pace. Thus, there is increasing recognition of the need to make metagenomic data discoverable within machine-searchable frameworks compliant with the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for data stewardship. Although a variety of metagenomic web services exist, none currently leverage the hierarchically structured terminology encoded within common life science ontologies to programmatically discover data. RESULTS Here, we integrate large-scale marine metagenomic datasets with community-driven life science ontologies into a novel FAIR web service. This approach enables the retrieval of data discovered by intersecting the knowledge represented within ontologies against the functional genomic potential and taxonomic structure computed from marine sequencing data. Our findings highlight various microbial functional and taxonomic patterns relevant to the ecology of prokaryotes in various aquatic environments. CONCLUSIONS In this work, we present and evaluate a novel Semantic Web architecture that can be used to ask novel biological questions of existing marine metagenomic datasets. Finally, the FAIR ontology searchable data products provided by our API can be leveraged by future research efforts.
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Affiliation(s)
- Kai Blumberg
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Matthew Miller
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Alise Ponsero
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Bonnie Hurwitz
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
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6
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Al-Hazmi HE, Hassan GK, Maktabifard M, Grubba D, Majtacz J, Mąkinia J. Integrating conventional nitrogen removal with anammox in wastewater treatment systems: Microbial metabolism, sustainability and challenges. ENVIRONMENTAL RESEARCH 2022; 215:114432. [PMID: 36167115 DOI: 10.1016/j.envres.2022.114432] [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: 07/06/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The various forms of nitrogen (N), including ammonium (NH4+), nitrite (NO2-), and nitrate (NO3-), present in wastewaters can create critical biotic stress and can lead to hazardous phenomena that cause imbalances in biological diversity. Thus, biological nitrogen removal (BNR) from wastewaters is considered to be imperatively urgent. Therefore, anammox-based systems, i.e. partial nitrification and anaerobic ammonium oxidation (PN/anammox) and partial denitrification and anammox (PD/anammox) have been universally acknowledged to consider as alternatives, promising and cost-effective technologies for sustainable N removal from wastewaters compared to nitrification-denitrification processes. This review comprehensively presents and discusses the latest advances in BNR technologies, including traditional nitrification-denitrification and anammox-based systems. To a deep understanding of a better-controlled combining anammox with traditional processes, the microbial community diversity and metabolism, as well as, biomass morphological characteristics were clearly reviewed in the anammox-based systems. Explaining simultaneous microbial competition and control of crucial operation parameters in single-stage anammox-based processes in terms of optimization and economic benefits makes this contribution a different vision from available review papers. The most important sustainability indicators, including global warming potential (GWP), carbon footprint (CF) and energy behaviours were explored to evaluate the sustainability of BNR processes in wastewater treatment. Additionally, the challenges and solutions for BNR processes are extensively discussed. In summary, this review helps facilitate a critical understanding of N removal technologies. It is confirmed that sustainability and saving energy would be achieved by anammox-based systems, thereby could be encouraged future outcomes for a sustainable N removal economy.
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Affiliation(s)
- Hussein E Al-Hazmi
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Ul. Narutowicza 11/12, Gdańsk, 80-233, Poland.
| | - Gamal K Hassan
- Water Pollution Research Department, National Research Centre, 33 Bohouth St, Giza, Dokki, P.O. Box 12622, Egypt
| | - Mojtaba Maktabifard
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Ul. Narutowicza 11/12, Gdańsk, 80-233, Poland
| | - Dominika Grubba
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Ul. Narutowicza 11/12, Gdańsk, 80-233, Poland
| | - Joanna Majtacz
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Ul. Narutowicza 11/12, Gdańsk, 80-233, Poland
| | - Jacek Mąkinia
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Ul. Narutowicza 11/12, Gdańsk, 80-233, Poland
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7
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OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6576764. [DOI: 10.1093/femsec/fiac053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/02/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
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8
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Fenizia S, Weissflog J, Pohnert G. Cysteinolic Acid Is a Widely Distributed Compatible Solute of Marine Microalgae. Mar Drugs 2021; 19:md19120683. [PMID: 34940682 PMCID: PMC8703288 DOI: 10.3390/md19120683] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/23/2022] Open
Abstract
Phytoplankton rely on bioactive zwitterionic and highly polar small metabolites with osmoregulatory properties to compensate changes in the salinity of the surrounding seawater. Dimethylsulfoniopropionate (DMSP) is a main representative of this class of metabolites. Salinity-dependent DMSP biosynthesis and turnover contribute significantly to the global sulfur cycle. Using advanced chromatographic and mass spectrometric techniques that enable the detection of highly polar metabolites, we identified cysteinolic acid as an additional widely distributed polar metabolite in phytoplankton. Cysteinolic acid belongs to the class of marine sulfonates, metabolites that are commonly produced by algae and consumed by bacteria. It was detected in all dinoflagellates, haptophytes, diatoms and prymnesiophytes that were surveyed. We quantified the metabolite in different phytoplankton taxa and revealed that the cellular content can reach even higher concentrations than the ubiquitous DMSP. The cysteinolic acid concentration in the cells of the diatom Thalassiosira weissflogii increases significantly when grown in a medium with elevated salinity. In contrast to the compatible solute ectoine, cysteinolic acid is also found in high concentrations in axenic algae, indicating biosynthesis by the algae and not the associated bacteria. Therefore, we add this metabolite to the family of highly polar metabolites with osmoregulatory characteristics produced by phytoplankton.
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Affiliation(s)
- Simona Fenizia
- Bioorganic Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstrasse 8, D-07743 Jena, Germany;
- MPG Fellow Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany;
| | - Jerrit Weissflog
- MPG Fellow Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany;
| | - Georg Pohnert
- Bioorganic Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstrasse 8, D-07743 Jena, Germany;
- MPG Fellow Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany;
- Correspondence:
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9
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Santin A, Caputi L, Longo A, Chiurazzi M, Ribera d'Alcalà M, Russo MT, Ferrante MI, Rogato A. Integrative omics identification, evolutionary and structural analysis of low affinity nitrate transporters in diatoms, diNPFs. Open Biol 2021; 11:200395. [PMID: 33823659 PMCID: PMC8025304 DOI: 10.1098/rsob.200395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Diatoms are one of the major and most diverse groups of phytoplankton, with chimeric genomes harbouring a combination of genes of bacterial, animal and plant origin. They have developed sophisticated mechanisms to face environmental variations. In marine environments, nutrients concentration shows significant temporal and spatial variability, influencing phytoplankton growth. Among nutrients, nitrogen, present at micromolar levels, is often a limiting resource. Here, we report a comprehensive characterization of the Nitrate Transporter 1/Peptide Transporter Family (NPF) in diatoms, diNPFs. NPFs are well characterized in many organisms where they recognize a broad range of substrates, ranging from short-chained di- and tri-peptides in bacteria, fungi and mammals to a wide variety of molecules including nitrate in higher plants. Scarce information is available for diNPFs. We integrated-omics, phylogenetic, structural and expression analyses, to infer information on their role in diatoms. diNPF genes diverged to produce two distinct clades with strong sequence and structural homology with either bacterial or plant NPFs, with different predicted sub-cellular localization, suggesting that the divergence resulted in functional diversification. Moreover, transcription analysis of diNPF genes under different laboratory and environmental growth conditions suggests that diNPF diversification led to genetic adaptations that might contribute to diatoms ability to flourish in diverse environmental conditions.
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Affiliation(s)
- Anna Santin
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Luigi Caputi
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Antonella Longo
- BioDiscovery Institute, Denton, TX, USA.,Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Maurizio Chiurazzi
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | | | | | | | - Alessandra Rogato
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.,Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy
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10
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Occurrence, Evolution and Specificities of Iron-Sulfur Proteins and Maturation Factors in Chloroplasts from Algae. Int J Mol Sci 2021; 22:ijms22063175. [PMID: 33804694 PMCID: PMC8003979 DOI: 10.3390/ijms22063175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/25/2021] [Accepted: 03/17/2021] [Indexed: 01/08/2023] Open
Abstract
Iron-containing proteins, including iron-sulfur (Fe-S) proteins, are essential for numerous electron transfer and metabolic reactions. They are present in most subcellular compartments. In plastids, in addition to sustaining the linear and cyclic photosynthetic electron transfer chains, Fe-S proteins participate in carbon, nitrogen, and sulfur assimilation, tetrapyrrole and isoprenoid metabolism, and lipoic acid and thiamine synthesis. The synthesis of Fe-S clusters, their trafficking, and their insertion into chloroplastic proteins necessitate the so-called sulfur mobilization (SUF) protein machinery. In the first part, we describe the molecular mechanisms that allow Fe-S cluster synthesis and insertion into acceptor proteins by the SUF machinery and analyze the occurrence of the SUF components in microalgae, focusing in particular on the green alga Chlamydomonas reinhardtii. In the second part, we describe chloroplastic Fe-S protein-dependent pathways that are specific to Chlamydomonas or for which Chlamydomonas presents specificities compared to terrestrial plants, putting notable emphasis on the contribution of Fe-S proteins to chlorophyll synthesis in the dark and to the fermentative metabolism. The occurrence and evolutionary conservation of these enzymes and pathways have been analyzed in all supergroups of microalgae performing oxygenic photosynthesis.
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11
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Merz E, Dick GJ, de Beer D, Grim S, Hübener T, Littmann S, Olsen K, Stuart D, Lavik G, Marchant HK, Klatt JM. Nitrate respiration and diel migration patterns of diatoms are linked in sediments underneath a microbial mat. Environ Microbiol 2020; 23:1422-1435. [PMID: 33264477 DOI: 10.1111/1462-2920.15345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022]
Abstract
Diatoms are among the few eukaryotes known to store nitrate (NO3 - ) and to use it as an electron acceptor for respiration in the absence of light and O2 . Using microscopy and 15 N stable isotope incubations, we studied the relationship between dissimilatory nitrate/nitrite reduction to ammonium (DNRA) and diel vertical migration of diatoms in phototrophic microbial mats and the underlying sediment of a sinkhole in Lake Huron (USA). We found that the diatoms rapidly accumulated NO3 - at the mat-water interface in the afternoon and 40% of the population migrated deep into the sediment, where they were exposed to dark and anoxic conditions for ~75% of the day. The vertical distribution of DNRA rates and diatom abundance maxima coincided, suggesting that DNRA was the main energy generating metabolism of the diatom population. We conclude that the illuminated redox-dynamic ecosystem selects for migratory diatoms that can store nitrate for respiration in the absence of light. A major implication of this study is that the dominance of DNRA over denitrification is not explained by kinetics or thermodynamics. Rather, the dynamic conditions select for migratory diatoms that perform DNRA and can outcompete sessile denitrifiers.
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Affiliation(s)
- Elisa Merz
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, Germany
| | - Gregory J Dick
- Geomicrobiology Lab, Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, Germany
| | - Sharon Grim
- Geomicrobiology Lab, Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas Hübener
- Department of Botany and Botanical Garden, University of Rostock, Institute of Biosciences, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, Germany
| | - Kirk Olsen
- Geomicrobiology Lab, Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Dack Stuart
- University of Michigan, Cooperative Institute for Great Lakes Research, Ann Arbor, Michigan, USA
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, Germany
| | - Hannah K Marchant
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, Germany
| | - Judith M Klatt
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, Germany.,Geomicrobiology Lab, Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
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12
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Chlamydomonas reinhardtii, an Algal Model in the Nitrogen Cycle. PLANTS 2020; 9:plants9070903. [PMID: 32708782 PMCID: PMC7412212 DOI: 10.3390/plants9070903] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
Abstract
Nitrogen (N) is an essential constituent of all living organisms and the main limiting macronutrient. Even when dinitrogen gas is the most abundant form of N, it can only be used by fixing bacteria but is inaccessible to most organisms, algae among them. Algae preferentially use ammonium (NH4+) and nitrate (NO3−) for growth, and the reactions for their conversion into amino acids (N assimilation) constitute an important part of the nitrogen cycle by primary producers. Recently, it was claimed that algae are also involved in denitrification, because of the production of nitric oxide (NO), a signal molecule, which is also a substrate of NO reductases to produce nitrous oxide (N2O), a potent greenhouse gas. This review is focused on the microalga Chlamydomonas reinhardtii as an algal model and its participation in different reactions of the N cycle. Emphasis will be paid to new actors, such as putative genes involved in NO and N2O production and their occurrence in other algae genomes. Furthermore, algae/bacteria mutualism will be considered in terms of expanding the N cycle to ammonification and N fixation, which are based on the exchange of carbon and nitrogen between the two organisms.
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13
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Stenow R, Olofsson M, Robertson EK, Kourtchenko O, Whitehouse MJ, Ploug H, Godhe A. Resting Stages of Skeletonema marinoi Assimilate Nitrogen From the Ambient Environment Under Dark, Anoxic Conditions. JOURNAL OF PHYCOLOGY 2020; 56:699-708. [PMID: 32012281 DOI: 10.1111/jpy.12975] [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] [Received: 08/26/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
The planktonic marine diatom Skeletonema marinoi forms resting stages, which can survive for decades buried in aphotic, anoxic sediments and resume growth when re-exposed to light, oxygen, and nutrients. The mechanisms by which they maintain cell viability during dormancy are poorly known. Here, we investigated cell-specific nitrogen (N) and carbon (C) assimilation and survival rate in resting stages of three S. marinoi strains. Resting stages were incubated with stable isotopes of dissolved inorganic N (DIN), in the form of 15 N-ammonium (NH4+ ) or -nitrate (NO3- ) and dissolved inorganic C (DIC) as 13 C-bicarbonate (HCO3- ) under dark and anoxic conditions for 2 months. Particulate C and N concentration remained close to the Redfield ratio (6.6) during the experiment, indicating viable diatoms. However, survival varied between <0.1% and 47.6% among the three different S. marinoi strains, and overall survival was higher when NO3- was available. One strain did not survive in the NH4+ treatment. Using secondary ion mass spectrometry (SIMS), we quantified assimilation of labeled DIC and DIN from the ambient environment within the resting stages. Dark fixation of DIC was insignificant across all strains. Significant assimilation of 15 N-NO3- and 15 N-NH4+ occurred in all S. marinoi strains at rates that would double the nitrogenous biomass over 77-380 years depending on strain and treatment. Hence, resting stages of S. marinoi assimilate N from the ambient environment at slow rates during darkness and anoxia. This activity may explain their well-documented long survival and swift resumption of vegetative growth after dormancy in dark and anoxic sediments.
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Affiliation(s)
- Rickard Stenow
- Department of Marine Sciences, University of Gothenburg, Box 461, SE 405 30, Gothenburg, Sweden
| | - Malin Olofsson
- Department of Marine Sciences, University of Gothenburg, Box 461, SE 405 30, Gothenburg, Sweden
| | - Elizabeth K Robertson
- Department of Marine Sciences, University of Gothenburg, Box 461, SE 405 30, Gothenburg, Sweden
| | - Olga Kourtchenko
- Department of Marine Sciences, University of Gothenburg, Box 461, SE 405 30, Gothenburg, Sweden
| | | | - Helle Ploug
- Department of Marine Sciences, University of Gothenburg, Box 461, SE 405 30, Gothenburg, Sweden
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Box 461, SE 405 30, Gothenburg, Sweden
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Plouviez M, Chambonnière P, Shilton A, Packer MA, Guieysse B. Nitrous oxide (N2O) emissions during real domestic wastewater treatment in an outdoor pilot-scale high rate algae pond. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101670] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Kennedy F, Martin A, Bowman JP, Wilson R, McMinn A. Dark metabolism: a molecular insight into how the Antarctic sea-ice diatom Fragilariopsis cylindrus survives long-term darkness. THE NEW PHYTOLOGIST 2019; 223:675-691. [PMID: 30985935 PMCID: PMC6617727 DOI: 10.1111/nph.15843] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/02/2019] [Indexed: 05/27/2023]
Abstract
Light underneath Antarctic sea-ice is below detectable limits for up to 4 months of the year. The ability of Antarctic sea-ice diatoms to survive this prolonged darkness relies on their metabolic capability. This study is the first to examine the proteome of a prominent sea-ice diatom in response to extended darkness, focusing on the protein-level mechanisms of dark survival. The Antarctic diatom Fragilariopsis cylindrus was grown under continuous light or darkness for 120 d. The whole cell proteome was quantitatively analysed by nano-LC-MS/MS to investigate metabolic changes that occur during sustained darkness and during recovery under illumination. Enzymes of metabolic pathways, particularly those involved in respiratory processes, tricarboxylic acid cycle, glycolysis, the Entner-Doudoroff pathway, the urea cycle and the mitochondrial electron transport chain became more abundant in the dark. Within the plastid, carbon fixation halted while the upper sections of the glycolysis, gluconeogenesis and pentose phosphate pathways became less active. We have discovered how F. cylindrus utilises an ancient alternative metabolic mechanism that enables its capacity for long-term dark survival. By sustaining essential metabolic processes in the dark, F. cylindrus retains the functionality of the photosynthetic apparatus, ensuring rapid recovery upon re-illumination.
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Affiliation(s)
- Fraser Kennedy
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobart7000TasmaniaAustralia
| | - Andrew Martin
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobart7000TasmaniaAustralia
| | - John P. Bowman
- Centre for Food Safety and InnovationTasmanian Institute of AgricultureHobart7000TasmaniaAustralia
| | - Richard Wilson
- Central Science LaboratoryUniversity of TasmaniaHobart7000TasmaniaAustralia
| | - Andrew McMinn
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobart7000TasmaniaAustralia
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16
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Gleason FH, Larkum AW, Raven JA, Manohar CS, Lilje O. Ecological implications of recently discovered and poorly studied sources of energy for the growth of true fungi especially in extreme environments. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.12.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Expression of novel nitrate reductase genes in the harmful alga, Chattonella subsalsa. Sci Rep 2018; 8:13417. [PMID: 30194416 PMCID: PMC6128913 DOI: 10.1038/s41598-018-31735-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 08/23/2018] [Indexed: 12/20/2022] Open
Abstract
Eukaryotic nitrate reductase (NR) catalyzes the first step in nitrate assimilation and is regulated transcriptionally in response to external cues and intracellular metabolic status. NRs are also regulated post-translationally in plants by phosphorylation and binding of 14-3-3 proteins at conserved serine residues. 14-3-3 binding motifs have not previously been identified in algal NRs. A novel NR (NR2-2/2HbN) with a 2/2 hemoglobin domain was recently described in the alga Chattonella subsalsa. Here, a second NR (NR3) in C. subsalsa is described with a 14-3-3 binding motif but lacking the Heme-Fe domain found in other NRs. Transcriptional regulation of both NRs was examined in C. subsalsa, revealing differential gene expression over a diel light cycle, but not under constant light. NR2 transcripts increased with a decrease in temperature, while NR3 remained unchanged. NR2 and NR3 transcript levels were not inhibited by growth on ammonium, suggesting constitutive expression of these genes. Results indicate that Chattonella responds to environmental conditions and intracellular metabolic status by differentially regulating NR transcription, with potential for post-translational regulation of NR3. A survey of algal NRs also revealed the presence of 14-3-3 binding motifs in other algal species, indicating the need for future research on regulation of algal NRs.
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Kamp A, Petro C, Røy H, Nielsen S, Carvalho P, Stief P, Schramm A. Intracellular nitrate in sediments of an oxygen-deficient marine basin is linked to pelagic diatoms. FEMS Microbiol Ecol 2018; 94:5040219. [PMID: 29931199 DOI: 10.1093/femsec/fiy122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/15/2018] [Indexed: 11/13/2022] Open
Abstract
Intracellular nitrate is an important electron acceptor in oxygen-deficient aquatic environments, either for the nitrate-storing microbes themselves, or for ambient microbial communities through nitrate leakage. This study links the spatial distribution of intracellular nitrate with the abundance and identity of nitrate-storing microbes in sediments of the Bornholm Basin, an environmental showcase for severe hypoxia. Intracellular nitrate (up to 270 nmol cm-3 sediment) was detected at all 18 stations along a 35-km transect through the basin and typically extended as deep as 1.6 cm into the sediment. Intracellular nitrate contents were particularly high at stations where chlorophyll contents suggested high settling rates of pelagic primary production. The depth distribution of intracellular nitrate matched that of the diatom-specific photopigment fucoxanthin in the upper 1.6 cm and calculations support that diatoms are the major nitrate-storing microbes in these sediments. In contrast, other known nitrate-storing microbes, such as sulfide-oxidizing bacteria and foraminifers, played only a minor role, if any. Strikingly, 18S rRNA gene sequencing revealed that the majority of the diatoms in the sediment were pelagic species. We conclude that intracellular nitrate stored by pelagic diatoms is transported to the seafloor by settling phytoplankton blooms, implying a so far overlooked 'biological nitrate pump'.
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Affiliation(s)
- Anja Kamp
- AIAS, Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark.,Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Caitlin Petro
- Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Hans Røy
- Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Susanne Nielsen
- Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Pedro Carvalho
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Peter Stief
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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Broman E, Sachpazidou V, Dopson M, Hylander S. Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments. Proc Biol Sci 2018; 284:rspb.2017.1617. [PMID: 28978732 DOI: 10.1098/rspb.2017.1617] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/04/2017] [Indexed: 01/05/2023] Open
Abstract
An important characteristic of marine sediments is the oxygen concentration that affects many central metabolic processes. There has been a widespread increase in hypoxia in coastal systems (referred to as 'dead zones') mainly caused by eutrophication. Hence, it is central to understand the metabolism and ecology of eukaryotic life in sediments during changing oxygen conditions. Therefore, we sampled coastal 'dead zone' Baltic Sea sediment during autumn and spring, and analysed the eukaryotic metatranscriptome from field samples and after incubation in the dark under oxic or anoxic conditions. Bacillariophyta (diatoms) dominated the eukaryotic metatranscriptome in spring and were also abundant during autumn. A large fraction of the diatom RNA reads was associated with the photosystems suggesting a constitutive expression in darkness. Microscope observation showed intact diatom cells and these would, if hatched, represent a significant part of the pelagic phytoplankton biomass. Oxygenation did not significantly change the relative proportion of diatoms nor resulted in any major shifts in metabolic 'signatures'. By contrast, diatoms rapidly responded when exposed to light suggesting that light is limiting diatom development in hypoxic sediments. Hence, it is suggested that diatoms in hypoxic sediments are on 'standby' to exploit the environment if they reach suitable habitats.
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Affiliation(s)
- Elias Broman
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, 39182 Kalmar, Sweden
| | - Varvara Sachpazidou
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, 39182 Kalmar, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, 39182 Kalmar, Sweden
| | - Samuel Hylander
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, 39182 Kalmar, Sweden
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20
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Marzocchi U, Thamdrup B, Stief P, Glud RN. Effect of settled diatom-aggregates on benthic nitrogen cycling. LIMNOLOGY AND OCEANOGRAPHY 2018; 63:431-444. [PMID: 29456269 PMCID: PMC5812115 DOI: 10.1002/lno.10641] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 06/08/2023]
Abstract
The marine sediment hosts a mosaic of microhabitats. Recently it has been demonstrated that the settlement of phycodetrital aggregates can induce local changes in the benthic O2 distribution due to confined enrichment of organic material and alteration of the diffusional transport. Here, we show how this microscale O2 shift substantially affects benthic nitrogen cycling. In sediment incubations, the settlement of diatom-aggregates markedly enhanced benthic O2 and NO3- consumption and stimulated NO2- and NH4+ production. Oxygen microprofiles revealed the rapid development of anoxic niches within and underneath the aggregates. During 120 h following the settling of the aggregates, denitrification of NO3- from the overlying water increased from 13.5 μmol m-2 h-1 to 24.3 μmol m-2 h-1, as quantified by 15N enrichment experiment. Simultaneously, N2 production from coupled nitrification-denitrification decreased from 33.4 μmol m-2 h-1 to 25.9 μmol m-2 h-1, probably due to temporary inhibition of the benthic nitrifying community. The two effects were of similar magnitude and left the total N2 production almost unaltered. At the aggregate surface, nitrification was, conversely, very efficient in oxidizing NH4+ liberated by mineralization of the aggregates. The produced NO3- was preferentially released into the overlying water and only a minor fraction contributed to denitrification activity. Overall, our data indicate that the abrupt change in O2 microdistribution caused by aggregates stimulates denitrification of NO3- from the overlying water, and loosens the coupling between benthic nitrification and denitrification both in time and space. The study contributes to expanding the conceptual and quantitative understanding of how nitrogen cycling is regulated in dynamic benthic environments.
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Affiliation(s)
- Ugo Marzocchi
- Department of Biology and Nordic Center for Earth Evolution (NordCEE)University of Southern Denmark, Odense MDenmark
- Department of AnalyticalEnvironmental and Geo‐Chemistry, Vrije Universiteit Brussel (VUB)BrusselsBelgium
- Center for Geomicrobiology and Section for Microbiology, Aarhus UniversityAarhusDenmark
| | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution (NordCEE)University of Southern Denmark, Odense MDenmark
| | - Peter Stief
- Department of Biology and Nordic Center for Earth Evolution (NordCEE)University of Southern Denmark, Odense MDenmark
| | - Ronnie N. Glud
- Department of Biology and Nordic Center for Earth Evolution (NordCEE)University of Southern Denmark, Odense MDenmark
- Scottish Association for Marine Science, ObanUnited Kingdom
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21
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22
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Plouviez M, Wheeler D, Shilton A, Packer MA, McLenachan PA, Sanz-Luque E, Ocaña-Calahorro F, Fernández E, Guieysse B. The biosynthesis of nitrous oxide in the green alga Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:45-56. [PMID: 28333392 DOI: 10.1111/tpj.13544] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 02/27/2017] [Accepted: 03/17/2017] [Indexed: 05/13/2023]
Abstract
Over the last decades, several studies have reported emissions of nitrous oxide (N2 O) from microalgal cultures and aquatic ecosystems characterized by a high level of algal activity (e.g. eutrophic lakes). As N2 O is a potent greenhouse gas and an ozone-depleting pollutant, these findings suggest that large-scale cultivation of microalgae (and possibly, natural eutrophic ecosystems) could have a significant environmental impact. Using the model unicellular microalga Chlamydomonas reinhardtii, this study was conducted to investigate the molecular basis of microalgal N2 O synthesis. We report that C. reinhardtii supplied with nitrite (NO2- ) under aerobic conditions can reduce NO2- into nitric oxide (NO) using either a mitochondrial cytochrome c oxidase (COX) or a dual enzymatic system of nitrate reductase (NR) and amidoxime-reducing component, and that NO is subsequently reduced into N2 O by the enzyme NO reductase (NOR). Based on experimental evidence and published literature, we hypothesize that when nitrate (NO3- ) is the main Nitrogen source and the intracellular concentration of NO2- is low (i.e. under physiological conditions), microalgal N2 O synthesis involves the reduction of NO3- to NO2- by NR followed by the reduction of NO2- to NO by the dual system involving NR. This microalgal N2 O pathway has broad implications for environmental science and algal biology because the pathway of NO3- assimilation is conserved among microalgae, and because its regulation may involve NO.
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Affiliation(s)
- Maxence Plouviez
- School of Engineering and Advanced Technology, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - David Wheeler
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Andy Shilton
- School of Engineering and Advanced Technology, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Michael A Packer
- Cawthron Institute, 98 Halifax Street, Nelson, 7010, New Zealand
| | - Patricia A McLenachan
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Emanuel Sanz-Luque
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Rabanales, Campus de excelencia internacional (CeiA3), Edif. Severo Ochoa, Córdoba, 14071, Spain
| | - Francisco Ocaña-Calahorro
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Rabanales, Campus de excelencia internacional (CeiA3), Edif. Severo Ochoa, Córdoba, 14071, Spain
| | - Emilio Fernández
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Rabanales, Campus de excelencia internacional (CeiA3), Edif. Severo Ochoa, Córdoba, 14071, Spain
| | - Benoit Guieysse
- School of Engineering and Advanced Technology, Massey University, Private Bag 11222, Palmerston North, New Zealand
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23
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Høgslund S, Cedhagen T, Bowser SS, Risgaard-Petersen N. Sinks and Sources of Intracellular Nitrate in Gromiids. Front Microbiol 2017; 8:617. [PMID: 28473806 PMCID: PMC5397464 DOI: 10.3389/fmicb.2017.00617] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/27/2017] [Indexed: 11/27/2022] Open
Abstract
A substantial nitrate pool is stored within living cells in various benthic marine environments. The fate of this bioavailable nitrogen differs according to the organisms managing the intracellular nitrate (ICN). While some light has been shed on the nitrate carried by diatoms and foraminiferans, no study has so far followed the nitrate kept by gromiids. Gromiids are large protists and their ICN concentration can exceed 1000x the ambient nitrate concentration. In the present study we investigated gromiids from diverse habitats and showed that they contained nitrate at concentrations ranging from 1 to 370 mM. We used 15N tracer techniques to investigate the source of this ICN, and found that it originated both from active nitrate uptake from the environment and from intracellular production, most likely through bacterial nitrification. Microsensor measurements showed that part of the ICN was denitrified to N2 when gromiids were exposed to anoxia. Denitrification seemed to be mediated by endobiotic bacteria because antibiotics inhibited denitrification activity. The active uptake of nitrate suggests that ICN plays a role in gromiid physiology and is not merely a consequence of the gromiid hosting a diverse bacterial community. Measurements of aerobic respiration rates and modeling of oxygen consumption by individual gromiid cells suggested that gromiids may occasionally turn anoxic by their own respiration activity and thus need strategies for coping with this self-inflicted anoxia.
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Affiliation(s)
- Signe Høgslund
- Department of Bioscience, Aarhus UniversityAarhus, Denmark
| | - Tomas Cedhagen
- Department of Bioscience, Aarhus UniversityAarhus, Denmark
| | - Samuel S Bowser
- Wadsworth Center, New York State Department of Health, AlbanyNY, USA
| | - Nils Risgaard-Petersen
- Department of Bioscience, Aarhus UniversityAarhus, Denmark.,Center for Geomicrobiology, Aarhus UniversityAarhus, Denmark
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24
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Kamp A, Stief P, Bristow LA, Thamdrup B, Glud RN. Intracellular Nitrate of Marine Diatoms as a Driver of Anaerobic Nitrogen Cycling in Sinking Aggregates. Front Microbiol 2016; 7:1669. [PMID: 27847498 PMCID: PMC5088207 DOI: 10.3389/fmicb.2016.01669] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/06/2016] [Indexed: 01/20/2023] Open
Abstract
Diatom-bacteria aggregates are key for the vertical transport of organic carbon in the ocean. Sinking aggregates also represent pelagic microniches with intensified microbial activity, oxygen depletion in the center, and anaerobic nitrogen cycling. Since some of the aggregate-forming diatom species store nitrate intracellularly, we explored the fate of intracellular nitrate and its availability for microbial metabolism within anoxic diatom-bacteria aggregates. The ubiquitous nitrate-storing diatom Skeletonema marinoi was studied as both axenic cultures and laboratory-produced diatom-bacteria aggregates. Stable 15N isotope incubations under dark and anoxic conditions revealed that axenic S. marinoi is able to reduce intracellular nitrate to ammonium that is immediately excreted by the cells. When exposed to a light:dark cycle and oxic conditions, S. marinoi stored nitrate intracellularly in concentrations >60 mmol L-1 both as free-living cells and associated to aggregates. Intracellular nitrate concentrations exceeded extracellular concentrations by three orders of magnitude. Intracellular nitrate was used up within 2-3 days after shifting diatom-bacteria aggregates to dark and anoxic conditions. Thirty-one percent of the diatom-derived nitrate was converted to nitrogen gas, indicating that a substantial fraction of the intracellular nitrate pool of S. marinoi becomes available to the aggregate-associated bacterial community. Only 5% of the intracellular nitrate was reduced to ammonium, while 59% was recovered as nitrite. Hence, aggregate-associated diatoms accumulate nitrate from the surrounding water and sustain complex nitrogen transformations, including loss of fixed nitrogen, in anoxic, pelagic microniches. Additionally, it may be expected that intracellular nitrate not converted before the aggregates have settled onto the seafloor could fuel benthic nitrogen transformations.
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Affiliation(s)
- Anja Kamp
- AIAS, Aarhus Institute of Advanced Studies, Aarhus UniversityAarhus, Denmark
| | - Peter Stief
- Department of Biology and Nordic Center for Earth Evolution, University of Southern DenmarkOdense, Denmark
| | - Laura A. Bristow
- Department of Biology and Nordic Center for Earth Evolution, University of Southern DenmarkOdense, Denmark
- Department of Biogeochemistry, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution, University of Southern DenmarkOdense, Denmark
| | - Ronnie N. Glud
- Department of Biology and Nordic Center for Earth Evolution, University of Southern DenmarkOdense, Denmark
- Department of Biogeochemistry and Earth Science, Scottish Association for Marine ScienceOban, UK
- Department of Bioscience, Arctic Research Centre, Aarhus UniversityAarhus, Denmark
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25
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Stief P, Kamp A, Thamdrup B, Glud RN. Anaerobic Nitrogen Turnover by Sinking Diatom Aggregates at Varying Ambient Oxygen Levels. Front Microbiol 2016; 7:98. [PMID: 26903977 PMCID: PMC4742529 DOI: 10.3389/fmicb.2016.00098] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/18/2016] [Indexed: 01/10/2023] Open
Abstract
In the world’s oceans, even relatively low oxygen levels inhibit anaerobic nitrogen cycling by free-living microbes. Sinking organic aggregates, however, might provide oxygen-depleted microbial hotspots in otherwise oxygenated surface waters. Here, we show that sinking diatom aggregates can host anaerobic nitrogen cycling at ambient oxygen levels well above the hypoxic threshold. Aggregates were produced from the ubiquitous diatom Skeletonema marinoi and the natural microbial community of seawater. Microsensor profiling through the center of sinking aggregates revealed internal anoxia at ambient 40% air saturation (∼100 μmol O2 L-1) and below. Accordingly, anaerobic nitrate turnover inside the aggregates was evident within this range of ambient oxygen levels. In incubations with 15N-labeled nitrate, individual Skeletonema aggregates produced NO2- (up to 10.7 nmol N h-1 per aggregate), N2 (up to 7.1 nmol N h-1), NH4+ (up to 2.0 nmol N h-1), and N2O (up to 0.2 nmol N h-1). Intriguingly, nitrate stored inside the diatom cells served as an additional, internal nitrate source for dinitrogen production, which may partially uncouple anaerobic nitrate turnover by diatom aggregates from direct ambient nitrate supply. Sinking diatom aggregates can contribute directly to fixed-nitrogen loss in low-oxygen environments in the ocean and vastly expand the ocean volume in which anaerobic nitrogen turnover is possible, despite relatively high ambient oxygen levels. Depending on the extent of intracellular nitrate consumption during the sinking process, diatom aggregates may also be involved in the long-distance export of nitrate to the deep ocean.
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Affiliation(s)
- Peter Stief
- Department of Biology and Nordic Center for Earth Evolution, University of Southern Denmark Odense, Denmark
| | - Anja Kamp
- AIAS, Aarhus Institute of Advanced Studies, Aarhus University Aarhus, Denmark
| | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution, University of Southern Denmark Odense, Denmark
| | - Ronnie N Glud
- Department of Biology and Nordic Center for Earth Evolution, University of Southern Denmark Odense, Denmark
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26
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Kamp A, Høgslund S, Risgaard-Petersen N, Stief P. Nitrate Storage and Dissimilatory Nitrate Reduction by Eukaryotic Microbes. Front Microbiol 2015; 6:1492. [PMID: 26734001 PMCID: PMC4686598 DOI: 10.3389/fmicb.2015.01492] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/10/2015] [Indexed: 11/13/2022] Open
Abstract
The microbial nitrogen cycle is one of the most complex and environmentally important element cycles on Earth and has long been thought to be mediated exclusively by prokaryotic microbes. Rather recently, it was discovered that certain eukaryotic microbes are able to store nitrate intracellularly and use it for dissimilatory nitrate reduction in the absence of oxygen. The paradigm shift that this entailed is ecologically significant because the eukaryotes in question comprise global players like diatoms, foraminifers, and fungi. This review article provides an unprecedented overview of nitrate storage and dissimilatory nitrate reduction by diverse marine eukaryotes placed into an eco-physiological context. The advantage of intracellular nitrate storage for anaerobic energy conservation in oxygen-depleted habitats is explained and the life style enabled by this metabolic trait is described. A first compilation of intracellular nitrate inventories in various marine sediments is presented, indicating that intracellular nitrate pools vastly exceed porewater nitrate pools. The relative contribution by foraminifers to total sedimentary denitrification is estimated for different marine settings, suggesting that eukaryotes may rival prokaryotes in terms of dissimilatory nitrate reduction. Finally, this review article sketches some evolutionary perspectives of eukaryotic nitrate metabolism and identifies open questions that need to be addressed in future investigations.
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Affiliation(s)
- Anja Kamp
- AIAS, Aarhus Institute of Advanced Studies Aarhus University Aarhus, Denmark
| | - Signe Høgslund
- Department of Bioscience, Aarhus University Aarhus, Denmark
| | | | - Peter Stief
- Department of Biology, Nordic Center for Earth Evolution, University of Southern Denmark Odense, Denmark
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Alcántara C, Muñoz R, Norvill Z, Plouviez M, Guieysse B. Nitrous oxide emissions from high rate algal ponds treating domestic wastewater. BIORESOURCE TECHNOLOGY 2015; 177:110-117. [PMID: 25481561 DOI: 10.1016/j.biortech.2014.10.134] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/24/2014] [Accepted: 10/27/2014] [Indexed: 06/04/2023]
Abstract
This study investigated the generation of N2O by microcosms withdrawn from 7-L high rate algal ponds (HRAPs) inoculated with Chlorella vulgaris and treating synthetic wastewater. Although HRAPs microcosms demonstrated the ability to generate algal-mediated N2O when nitrite was externally supplied under darkness in batch assays, negligible N2O emissions rates were consistently recorded in the absence of nitrite during 3.5-month monitoring under 'normal' operation. Thereafter, HRAP A and HRAP B were overloaded with nitrate and ammonium, respectively, in an attempt to stimulate N2O emissions via nitrite in situ accumulation. Significant N2O production (up to 5685±363 nmol N2O/g TSS h) was only recorded from HRAP B microcosms externally supplied with nitrite in darkness. Although confirmation under full-scale outdoors conditions is needed, this study provides the first evidence that the ability of microalgae to synthesize N2O does not affect the environmental performance of wastewater treatment in HRAPs.
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Affiliation(s)
- Cynthia Alcántara
- School of Engineering and Advanced Technology, Massey University, Private Bag 11222, Palmerston North, New Zealand; Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, 47011 Valladolid, Spain.
| | - Zane Norvill
- School of Engineering and Advanced Technology, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Maxence Plouviez
- School of Engineering and Advanced Technology, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Benoit Guieysse
- School of Engineering and Advanced Technology, Massey University, Private Bag 11222, Palmerston North, New Zealand
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Barra L, Chandrasekaran R, Corato F, Brunet C. The challenge of ecophysiological biodiversity for biotechnological applications of marine microalgae. Mar Drugs 2014; 12:1641-75. [PMID: 24663117 PMCID: PMC3967230 DOI: 10.3390/md12031641] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 01/31/2014] [Accepted: 02/12/2014] [Indexed: 01/26/2023] Open
Abstract
In this review, we aim to explore the potential of microalgal biodiversity and ecology for biotechnological use. A deeper exploration of the biodiversity richness and ecophysiological properties of microalgae is crucial for enhancing their use for applicative purposes. After describing the actual biotechnological use of microalgae, we consider the multiple faces of taxonomical, morphological, functional and ecophysiological biodiversity of these organisms, and investigate how these properties could better serve the biotechnological field. Lastly, we propose new approaches to enhancing microalgal growth, photosynthesis, and synthesis of valuable products used in biotechnological fields, mainly focusing on culture conditions, especially light manipulations and genetic modifications.
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Affiliation(s)
- Lucia Barra
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples 80121, Italy.
| | | | - Federico Corato
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples 80121, Italy.
| | - Christophe Brunet
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples 80121, Italy.
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Stief P, Fuchs-Ocklenburg S, Kamp A, Manohar CS, Houbraken J, Boekhout T, de Beer D, Stoeck T. Dissimilatory nitrate reduction by Aspergillus terreus isolated from the seasonal oxygen minimum zone in the Arabian Sea. BMC Microbiol 2014; 14:35. [PMID: 24517718 PMCID: PMC3928326 DOI: 10.1186/1471-2180-14-35] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/10/2014] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND A wealth of microbial eukaryotes is adapted to life in oxygen-deficient marine environments. Evidence is accumulating that some of these eukaryotes survive anoxia by employing dissimilatory nitrate reduction, a strategy that otherwise is widespread in prokaryotes. Here, we report on the anaerobic nitrate metabolism of the fungus Aspergillus terreus (isolate An-4) that was obtained from sediment in the seasonal oxygen minimum zone in the Arabian Sea, a globally important site of oceanic nitrogen loss and nitrous oxide emission. RESULTS Axenic incubations of An-4 in the presence and absence of oxygen and nitrate revealed that this fungal isolate is capable of dissimilatory nitrate reduction to ammonium under anoxic conditions. A ¹⁵N-labeling experiment proved that An-4 produced and excreted ammonium through nitrate reduction at a rate of up to 175 nmol ¹⁵NH₄⁺ g⁻¹ protein h⁻¹. The products of dissimilatory nitrate reduction were ammonium (83%), nitrous oxide (15.5%), and nitrite (1.5%), while dinitrogen production was not observed. The process led to substantial cellular ATP production and biomass growth and also occurred when ammonium was added to suppress nitrate assimilation, stressing the dissimilatory nature of nitrate reduction. Interestingly, An-4 used intracellular nitrate stores (up to 6-8 μmol NO₃⁻ g⁻¹ protein) for dissimilatory nitrate reduction. CONCLUSIONS Our findings expand the short list of microbial eukaryotes that store nitrate intracellularly and carry out dissimilatory nitrate reduction when oxygen is absent. In the currently spreading oxygen-deficient zones in the ocean, an as yet unexplored diversity of fungi may recycle nitrate to ammonium and nitrite, the substrates of the major nitrogen loss process anaerobic ammonium oxidation, and the potent greenhouse gas nitrous oxide.
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Affiliation(s)
- Peter Stief
- Max Planck Institute for Marine Microbiology, Microsensor Group, Bremen, Germany
- Department of Biology, University of Southern Denmark, NordCEE, Campusvej 55, 5230 Odense M, Denmark
| | - Silvia Fuchs-Ocklenburg
- Max Planck Institute for Marine Microbiology, Microsensor Group, Bremen, Germany
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Anja Kamp
- Max Planck Institute for Marine Microbiology, Microsensor Group, Bremen, Germany
- Jacobs University Bremen, Molecular Life Science Research Center, Bremen, Germany
| | | | - Jos Houbraken
- CBS-KNAW Fungal Diversity Centre, Utrecht, The Netherlands
| | - Teun Boekhout
- CBS-KNAW Fungal Diversity Centre, Utrecht, The Netherlands
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Microsensor Group, Bremen, Germany
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
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