1
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von Kügelgen A, Cassidy CK, van Dorst S, Pagani LL, Batters C, Ford Z, Löwe J, Alva V, Stansfeld PJ, Bharat TAM. Membraneless channels sieve cations in ammonia-oxidizing marine archaea. Nature 2024; 630:230-236. [PMID: 38811725 PMCID: PMC11153153 DOI: 10.1038/s41586-024-07462-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/24/2024] [Indexed: 05/31/2024]
Abstract
Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle1,2. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle.
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Affiliation(s)
- Andriko von Kügelgen
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - C Keith Cassidy
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, USA
| | - Sofie van Dorst
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lennart L Pagani
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Christopher Batters
- Protein and Nucleic Acid Chemistry Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Zephyr Ford
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jan Löwe
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
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2
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Beeckman F, Annetta L, Corrochano-Monsalve M, Beeckman T, Motte H. Enhancing agroecosystem nitrogen management: microbial insights for improved nitrification inhibition. Trends Microbiol 2024; 32:590-601. [PMID: 37973432 DOI: 10.1016/j.tim.2023.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
Nitrification is a key microbial process in the nitrogen (N) cycle that converts ammonia to nitrate. Excessive nitrification, typically occurring in agroecosystems, has negative environmental impacts, including eutrophication and greenhouse gas emissions. Nitrification inhibitors (NIs) are widely used to manage N in agricultural systems by reducing nitrification rates and improving N use efficiency. However, the effectiveness of NIs can vary depending on the soil conditions, which, in turn, affect the microbial community and the balance between different functional groups of nitrifying microorganisms. Understanding the mechanisms underlying the effectiveness of NIs, and how this is affected by the soil microbial communities or abiotic factors, is crucial for promoting sustainable fertilizer practices. Therefore, this review examines the different types of NIs and how abiotic parameters can influence the nitrifying community, and, therefore, the efficacy of NIs. By discussing the latest research in this field, we provide insights that could facilitate the development of more targeted, efficient, or complementary NIs that improve the application of NIs for sustainable management practices in agroecosystems.
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Affiliation(s)
- Fabian Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Laure Annetta
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Mario Corrochano-Monsalve
- Departamento de Genética, Antropología Física y Fisiología Animal, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Leioa, Spain; Instituto Multidisciplinar Para el Estudio del Medio 'Ramon Margalef', Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Spain
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium.
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3
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Zhou Y, Yan A, Yang J, He W, Guo S, Li Y, Wu J, Dai Y, Pan X, Cui D, Pereira O, Teng W, Bi R, Chen S, Fan L, Wang P, Liao Y, Qin W, Sui SF, Zhu Y, Zhang C, Liu Z. Ultrastructural insights into cellular organization, energy storage and ribosomal dynamics of an ammonia-oxidizing archaeon from oligotrophic oceans. Front Microbiol 2024; 15:1367658. [PMID: 38737410 PMCID: PMC11082331 DOI: 10.3389/fmicb.2024.1367658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Introduction Nitrososphaeria, formerly known as Thaumarchaeota, constitute a diverse and widespread group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their importance in Earth's ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant unanswered question of how the machinery of these organisms underpins metabolic functions. Methods In this study, we combined spherical-chromatic-aberration-corrected cryo-electron tomography (cryo-ET), scanning transmission electron microscopy (STEM), and energy dispersive X-ray spectroscopy (EDS) to unveil the cellular organization and elemental composition of Nitrosopumilus maritimus SCM1, a representative member of marine Nitrososphaeria. Results and Discussion Our tomograms show the native ultrastructural morphology of SCM1 and one to several dense storage granules in the cytoplasm. STEM-EDS analysis identifies two types of storage granules: one type is possibly composed of polyphosphate and the other polyhydroxyalkanoate. With precise measurements using cryo-ET, we observed low quantity and density of ribosomes in SCM1 cells, which are in alignment with the documented slow growth of AOA in laboratory cultures. Collectively, these findings provide visual evidence supporting the resilience of AOA in the vast oligotrophic marine environment.
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Affiliation(s)
- Yangkai Zhou
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - An Yan
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jiawen Yang
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Shuai Guo
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yifan Li
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jing Wu
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yanchao Dai
- Shanghai NanoPort, Thermo Fisher Scientific Inc., Shanghai, China
| | - Xijiang Pan
- Shanghai NanoPort, Thermo Fisher Scientific Inc., Shanghai, China
| | - Dongyu Cui
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Olivier Pereira
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Institut AMU-WUT, Aix-Marseille Université and Wuhan University of Technology, Wuhan, Hubei, China
| | - Wenkai Teng
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Ran Bi
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Songze Chen
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lu Fan
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Peiyi Wang
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yan Liao
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, Australia
| | - Wei Qin
- School of Biological Sciences and Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Sen-Fang Sui
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuanqing Zhu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
- Advanced Institute for Ocean Research, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Zheng Liu
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
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4
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Guo X, Ong WM, Zhao HP, Lai CY. Enzyme-induced reactive oxygen species trigger oxidative degradation of sulfamethoxazole within a methanotrophic biofilm. WATER RESEARCH 2024; 253:121330. [PMID: 38387268 DOI: 10.1016/j.watres.2024.121330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/24/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024]
Abstract
Although microorganisms carrying copper-containing membrane-bound monooxygenase (CuMMOs), such as particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO), have been extensively documented for their capability to degrade organic micropollutants (OMPs), the underlying reactive mechanism remains elusive. In this study, we for the first time demonstrate biogenic reactive oxygen species (ROS) play important roles in the degradation of sulfamethoxazole (SMX), a representative OMP, within a methane-fed biofilm. Highly-efficient and consistent SMX biodegradation was achieved in a CH4-based membrane biofilm reactor (MBfR), manifesting a remarkable SMX removal rate of 1210.6 ± 39.0 μg·L-1·d-1. Enzyme inhibition and ROS clearance experiments confirmed the significant contribution of ROS, which were generated through the catalytic reaction of pMMO and AMO enzymes, in facilitating SMX degradation. Through a combination of density functional theory (DFT) calculations, electron paramagnetic resonance (EPR) analysis, and transformation product detection, we elucidated that the ROS primarily targeted the aniline group in the SMX molecule, inducing the formation of aromatic radicals and its progressive mineralization. In contrast, the isoxazole-ring was not susceptible to electrophilic ROS attacks, leading to accumulation of 3-amino-5-methylisoxazole (3A5MI). Furthermore, microbiological analysis suggested Methylosarcina (a methanotroph) and Candidatus Nitrosotenuis (an ammonia-oxidizing archaea) collaborated as the SMX degraders, who carried highly conserved and expressed CuMMOs (pMMO and AMO) for ROS generation, thereby triggering the oxidative degradation of SMX. This study deciphers SMX biodegradation through a fresh perspective of free radical chemistry, and concurrently providing a theoretical framework for the advancement of environmental biotechnologies aimed at OMP removal.
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Affiliation(s)
- Xu Guo
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058
| | - Weng Mun Ong
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058
| | - Chun-Yu Lai
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058.
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5
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Bollmann A, Sedlacek CJ, Sayavedra-Soto L, Norton JM. Metagenome-assembled genomes of two nitrifying microorganisms from the freshwater archaeal ammonia-oxidizing enrichment culture BO1. Microbiol Resour Announc 2024; 13:e0090023. [PMID: 38265223 PMCID: PMC10868196 DOI: 10.1128/mra.00900-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/10/2024] [Indexed: 01/25/2024] Open
Abstract
Two metagenome-assembled genomes (MAGs) were recovered from the ammonia-oxidizing enrichment culture BO1 obtained from the sediment of the freshwater reservoir Lake Burr Oak, Ohio, USA. High quality MAGs were assembled for the archaeal ammonia oxidizer Nitrosarchaeum sp. BO1 and the canonical nitrite oxidizer Nitrospira sp. BO1.
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Affiliation(s)
| | | | - Luis Sayavedra-Soto
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Jeanette M. Norton
- Department of Plants, Soil and Climate, Utah State University, Logan, Utah, USA
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6
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Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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7
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Bei Q, Reitz T, Schädler M, Hodgskiss LH, Peng J, Schnabel B, Buscot F, Eisenhauer N, Schleper C, Heintz-Buschart A. Metabolic potential of Nitrososphaera-associated clades. THE ISME JOURNAL 2024; 18:wrae086. [PMID: 38742714 PMCID: PMC11131427 DOI: 10.1093/ismejo/wrae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/13/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]
Abstract
Soil ammonia-oxidizing archaea (AOA) play a crucial role in converting ammonia to nitrite, thereby mobilizing reactive nitrogen species into their soluble form, with a significant impact on nitrogen losses from terrestrial soils. Yet, our knowledge regarding their diversity and functions remains limited. In this study, we reconstructed 97 high-quality AOA metagenome-assembled genomes (MAGs) from 180 soil samples collected in Central Germany during 2014-2019 summers. These MAGs were affiliated with the order Nitrososphaerales and clustered into four family-level clades (NS-α/γ/δ/ε). Among these MAGs, 75 belonged to the most abundant but least understood δ-clade. Within the δ-clade, the amoA genes in three MAGs from neutral soils showed a 99.5% similarity to the fosmid clone 54d9, which has served as representative of the δ-clade for the past two decades since even today no cultivated representatives are available. Seventy-two MAGs constituted a distinct δ sub-clade, and their abundance and expression activity were more than twice that of other MAGs in slightly acidic soils. Unlike the less abundant clades (α, γ, and ε), the δ-MAGs possessed multiple highly expressed intracellular and extracellular carbohydrate-active enzymes responsible for carbohydrate binding (CBM32) and degradation (GH5), along with highly expressed genes involved in ammonia oxidation. Together, these results suggest metabolic versatility of uncultured soil AOA and a potential mixotrophic or chemolithoheterotrophic lifestyle among 54d9-like AOA.
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Affiliation(s)
- Qicheng Bei
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States
| | - Thomas Reitz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Department of Community Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
| | - Logan H Hodgskiss
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
| | - Jingjing Peng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Beatrix Schnabel
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Christa Schleper
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
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8
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Kolovou M, Panagiotou D, Süße L, Loiseleur O, Williams S, Karpouzas DG, Papadopoulou ES. Assessing the activity of different plant-derived molecules and potential biological nitrification inhibitors on a range of soil ammonia- and nitrite-oxidizing strains. Appl Environ Microbiol 2023; 89:e0138023. [PMID: 37916825 PMCID: PMC10686072 DOI: 10.1128/aem.01380-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Synthetic nitrification inhibitors are routinely used with nitrogen fertilizers to reduce nitrogen losses from agroecosystems, despite having drawbacks like poor efficiency, cost, and entry into the food chain. Plant-derived BNIs constitute a more environmentally conducive alternative. Knowledge on the activity of BNIs to soil nitrifiers is largely based on bioassays with a single Nitrosomonas europaea strain which does not constitute a dominant member of the community of ammonia-oxidizing microorganisms (AOM) in soil. We determined the activity of several plant-derived molecules reported as having activity, including the recently discovered maize-isolated BNI, zeanone, and its natural analog, 2-methoxy-1,4-naphthoquinone, on a range of ecologically relevant AOM and one nitrite-oxidizing bacterial culture, expanding our knowledge on the intrinsic inhibition potential of BNIs toward AOM and highlighting the necessity for a deeper understanding of the effect of BNIs on the overall soil microbiome integrity before their further use in agricultural settings.
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Affiliation(s)
- Maria Kolovou
- Department of Environmental Sciences, Laboratory of Environmental Microbiology, University of Thessaly, Larissa, Greece
| | - Dimitra Panagiotou
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Lars Süße
- Syngenta Crop Protection AG, Basel, Switzerland
| | | | | | - Dimitrios G. Karpouzas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Evangelia S. Papadopoulou
- Department of Environmental Sciences, Laboratory of Environmental Microbiology, University of Thessaly, Larissa, Greece
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9
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Gwak JH, Awala SI, Kim SJ, Lee SH, Yang EJ, Park J, Jung J, Rhee SK. Transcriptomic Insights into Archaeal Nitrification in the Amundsen Sea Polynya, Antarctica. J Microbiol 2023; 61:967-980. [PMID: 38062325 DOI: 10.1007/s12275-023-00090-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/27/2023] [Accepted: 10/23/2023] [Indexed: 12/19/2023]
Abstract
Antarctic polynyas have the highest Southern Ocean summer primary productivity, and due to anthropogenic climate change, these areas have formed faster recently. Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant microorganisms in the ocean and play a primary role in the global nitrogen cycle. We utilized metagenomics and metatranscriptomics to gain insights into the physiology and metabolism of AOA in polar oceans, which are associated with ecosystem functioning. A polar-specific ecotype of AOA, from the "Candidatus Nitrosomarinus"-like group, was observed to be dominant in the Amundsen Sea Polynya (ASP), West Antarctica, during a succession of summer phytoplankton blooms. AOA had the highest transcriptional activity among prokaryotes during the bloom decline phase (DC). Metatranscriptomic analysis of key genes involved in ammonia oxidation, carbon fixation, transport, and cell division indicated that this polar AOA ecotype was actively involved in nitrification in the bloom DC in the ASP. This study revealed the physiological and metabolic traits of this key polar-type AOA in response to phytoplankton blooms in the ASP and provided insights into AOA functions in polar oceans.
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Affiliation(s)
- Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - So-Jeong Kim
- Geologic Environment Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Republic of Korea
| | - Sang-Hoon Lee
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Eun-Jin Yang
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jisoo Park
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jinyoung Jung
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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10
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Zhao J, Huang L, Chakrabarti S, Cooper J, Choi E, Ganan C, Tolchinsky B, Triplett EW, Daroub SH, Martens-Habbena W. Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil. THE ISME JOURNAL 2023; 17:1839-1850. [PMID: 37596409 PMCID: PMC10579303 DOI: 10.1038/s41396-023-01493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023]
Abstract
Soil represents the largest reservoir of Archaea on Earth. Present-day archaeal diversity in soils globally is dominated by members of the class Nitrososphaeria. The evolutionary radiation of this class is thought to reflect adaptations to a wide range of temperatures, pH, and other environmental conditions. However, the mechanisms that govern competition and coexistence among Nitrososphaeria lineages in soil remain poorly understood. Here we show that predominant soil Nitrososphaeria lineages compose a patchwork of gene inventory and expression profiles for ammonia, urea, and phosphate utilization. In contrast, carbon fixation, respiration, and ATP synthesis genes are conserved and expressed consistently among predominant phylotypes across 12 major evolutionary lineages commonly found in soil. In situ gene expression profiles closely resemble pure culture reference strains under optimal growth conditions. Together, these results reveal resource-based coexistence patterns among Nitrososphaeria lineages and suggest complementary ecophysiological niches associated with differential nutrient acquisition strategies among globally predominant archaeal lineages in soil.
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Affiliation(s)
- Jun Zhao
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Laibin Huang
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Seemanti Chakrabarti
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Jennifer Cooper
- Everglades Research and Education Center, Soil and Water Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - EunKyung Choi
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Carolina Ganan
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Bryn Tolchinsky
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Samira H Daroub
- Everglades Research and Education Center, Soil and Water Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA.
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11
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Wright CL, Lehtovirta-Morley LE. Nitrification and beyond: metabolic versatility of ammonia oxidising archaea. THE ISME JOURNAL 2023; 17:1358-1368. [PMID: 37452095 PMCID: PMC10432482 DOI: 10.1038/s41396-023-01467-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.
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Affiliation(s)
- Chloe L Wright
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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12
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Garritano AN, Majzoub ME, Ribeiro B, Damasceno T, Modolon F, Messias C, Vilela C, Duarte G, Hill L, Peixoto R, Thomas T. Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae. THE ISME JOURNAL 2023; 17:1517-1519. [PMID: 37258653 PMCID: PMC10432484 DOI: 10.1038/s41396-023-01439-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/02/2023]
Abstract
Sponges thrive in the deep, dark and nutrient-depleted ocean and may rely on microbial symbionts for carbon acquisition and energy generation. However, these symbiotic relationships remain largely unexplored. In this study, we analyze the microbiome of deep-sea sponges and show that ammonia-oxidizing archaea (AOA) of the family Nitrosopumilaceae make up at least 75% of the microbial communities of the sponges Aphrocallistes sp., Farrea sp. and Paratimea sp.. Given the known autotrophic metabolism of AOAs, this implies that these sponge holobionts can have the capacity for primary production in the deep-sea. We also show that specific AOA lineages are highly specific towards their hosts, hinting towards an unprecedent vertical transmission of these symbionts in deep-sea sponges. Our results show that the ecology and evolution of symbiotic relationships in deep-sea sponge is distinct from that of their shallow-water counterparts.
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Affiliation(s)
- Alessandro N Garritano
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, 2052, Australia
| | - Marwan E Majzoub
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, 2052, Australia
| | - Bárbara Ribeiro
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Taissa Damasceno
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Microbiologia Paulo de Goes, LEMM Laboratory, Rio de Janeiro, Brazil
| | - Fluvio Modolon
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Microbiologia Paulo de Goes, LEMM Laboratory, Rio de Janeiro, Brazil
| | - Camila Messias
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Microbiologia Paulo de Goes, LEMM Laboratory, Rio de Janeiro, Brazil
| | - Caren Vilela
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Microbiologia Paulo de Goes, LEMM Laboratory, Rio de Janeiro, Brazil
| | - Gustavo Duarte
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Microbiologia Paulo de Goes, LEMM Laboratory, Rio de Janeiro, Brazil
| | - Lilian Hill
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Microbiologia Paulo de Goes, LEMM Laboratory, Rio de Janeiro, Brazil
| | - Raquel Peixoto
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, 2052, Australia.
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13
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Oudova-Rivera B, Crombie AT, Murrell JC, Lehtovirta-Morley LE. Alcohols as inhibitors of ammonia oxidizing archaea and bacteria. FEMS Microbiol Lett 2023; 370:fnad093. [PMID: 37698885 PMCID: PMC11025371 DOI: 10.1093/femsle/fnad093] [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: 05/26/2023] [Revised: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 09/13/2023] Open
Abstract
Ammonia oxidizers are key players in the global nitrogen cycle and are responsible for the oxidation of ammonia to nitrite, which is further oxidized to nitrate by other microorganisms. Their activity can lead to adverse effects on some human-impacted environments, including water pollution through leaching of nitrate and emissions of the greenhouse gas nitrous oxide (N2O). Ammonia monooxygenase (AMO) is the key enzyme in microbial ammonia oxidation and shared by all groups of aerobic ammonia oxidizers. The AMO has not been purified in an active form, and much of what is known about its potential structure and function comes from studies on its interactions with inhibitors. The archaeal AMO is less well studied as ammonia oxidizing archaea were discovered much more recently than their bacterial counterparts. The inhibition of ammonia oxidation by aliphatic alcohols (C1-C8) using the model terrestrial ammonia oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus' C13 and the ammonia oxidizing bacterium Nitrosomonas europaea was examined in order to expand knowledge about the range of inhibitors of ammonia oxidizers. Methanol was the most potent specific inhibitor of the AMO in both ammonia oxidizers, with half-maximal inhibitory concentrations (IC50) of 0.19 and 0.31 mM, respectively. The inhibition was AMO-specific in 'Ca. N. franklandus' C13 in the presence of C1-C2 alcohols, and in N. europaea in the presence of C1-C3 alcohols. Higher chain-length alcohols caused non-specific inhibition and also inhibited hydroxylamine oxidation. Ethanol was tolerated by 'Ca. N. franklandus' C13 at a higher threshold concentration than other chain-length alcohols, with 80 mM ethanol being required for complete inhibition of ammonia oxidation.
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Affiliation(s)
- Barbora Oudova-Rivera
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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14
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Pessi IS, Rutanen A, Hultman J. Candidatus Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution. FEMS MICROBES 2022; 3:xtac019. [PMID: 37332501 PMCID: PMC10117904 DOI: 10.1093/femsmc/xtac019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 11/22/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle of polar soils. Here, we analyzed metagenomic data from tundra soils in Rásttigáisá, Norway, and recovered four metagenome-assembled genomes (MAGs) assigned to the genus 'UBA10452', an uncultured lineage of putative AOA in the order Nitrososphaerales ('terrestrial group I.1b'), phylum Thaumarchaeota. Analysis of other eight previously reported MAGs and publicly available amplicon sequencing data revealed that the UBA10452 lineage is predominantly found in acidic polar and alpine soils. In particular, UBA10452 MAGs were more abundant in highly oligotrophic environments such as mineral permafrost than in more nutrient-rich, vegetated tundra soils. UBA10452 MAGs harbour multiple copies of genes related to cold tolerance, particularly genes involved in DNA replication and repair. Based on the phylogenetic, biogeographic, and ecological characteristics of 12 UBA10452 MAGs, which include a high-quality MAG (90.8% complete, 3.9% redundant) with a nearly complete 16S rRNA gene, we propose a novel Candidatus genus, Ca. Nitrosopolaris, with four species representing clear biogeographic/habitat clusters.
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Affiliation(s)
- Igor S Pessi
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS),Yliopistonkatu 3, 00014 Helsinki, Finland
| | - Aino Rutanen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS),Yliopistonkatu 3, 00014 Helsinki, Finland
- Natural Resources Institute Finland (LUKE),Latokartanonkaari 9, 00790 Helsinki, Finland
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