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Chen C, Gong H, Wei Y, Xu T, Li J, Ding GC. Promoting agricultural waste-driven denitrification and nitrogen sequestration with nano-enabled strategy. BIORESOURCE TECHNOLOGY 2024; 401:130746. [PMID: 38679240 DOI: 10.1016/j.biortech.2024.130746] [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: 01/30/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Nanotechnology and biotechnology offer promising avenues for bolstering food security through the facilitation of soil nitrogen (N) sequestration and the reduction of nitrate leaching. Nonetheless, a comprehensive and mechanistic evaluation of their effectiveness and safety remains unclear. In this study, a soil remediation strategy employing nano-Fe3O4 and straw in N-contaminated soil was developed to elucidate N retention mechanisms via diverse metagenomics techniques. The findings revealed that subsoil amended with straw, particularly in conjunction with nano-Fe3O4, significantly increased subsoil N content (53.2%) and decreased nitrate concentration (74.6%) in leachate. Furthermore, the enrichment of functional genes associated with N-cycling, sulfate, nitrate, and iron uptake, along with chemotaxis, and responses to environmental stimuli or microbial collaboration, effectively mitigates nitrate leaching while enhancing soil N sequestration. This study introduces a pioneering approach utilizing nanomaterials in soil remediation, thereby offering the potential for the cultivation of safe vegetables in high N input greenhouse agriculture.
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Affiliation(s)
- Chen Chen
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; National Observation and Research Station for Yangtze Estuarine Wetland Ecosystems, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Haiqing Gong
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China
| | - Yuquan Wei
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Jiangsu Province 215128, China
| | - Ting Xu
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Jiangsu Province 215128, China
| | - Ji Li
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Jiangsu Province 215128, China
| | - Guo-Chun Ding
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Jiangsu Province 215128, China.
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2
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Wang X, Zain Ul Arifeen M, Hou S, Zheng Q. Depth-dependent microbial metagenomes sampled in the northeastern Indian Ocean. Sci Data 2024; 11:88. [PMID: 38238332 PMCID: PMC10796761 DOI: 10.1038/s41597-024-02939-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/09/2024] [Indexed: 01/22/2024] Open
Abstract
The northeastern Indian Ocean exhibits distinct hydrographic characteristics influenced by various local and remote forces. Variations in these driving factors may alter the physiochemical properties of seawater, such as dissolved oxygen levels, and affect the diversity and function of microbial communities. How the microbial communities change across water depths spanning a dissolved oxygen gradient has not been well understood. Here we employed both 16S rDNA amplicon and metagenomic sequencing approaches to study the microbial communities collected from different water depths along the E87 transect in the northeastern Indian Ocean. Samples were collected from the surface, Deep Chlorophyll Maximum (DCM), Oxygen Minimum Zone (OMZ), and bathypelagic layers. Proteobacteria were prevalent throughout the water columns, while Thermoproteota were found to be abundant in the aphotic layers. A total of 675 non-redundant metagenome-assembled genomes (MAGs) were constructed, spanning 21 bacterial and 5 archaeal phyla. The community structure and genomic information provided by this dataset offer valuable resources for the analysis of microbial biogeography and metabolism in the northeastern Indian Ocean.
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Affiliation(s)
- Xiaomeng Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen, 361102, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518000, China
| | - Muhammad Zain Ul Arifeen
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518000, China
| | - Shengwei Hou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China.
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518000, China.
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China.
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen, 361102, China.
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3
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Govindankutty Menon A, Davis CV, Nürnberg D, Nomaki H, Salonen I, Schmiedl G, Glock N. A deep-learning automated image recognition method for measuring pore patterns in closely related bolivinids and calibration for quantitative nitrate paleo-reconstructions. Sci Rep 2023; 13:19628. [PMID: 37949926 PMCID: PMC10638366 DOI: 10.1038/s41598-023-46605-y] [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: 06/16/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
Eutrophication is accelerating the recent expansion of oxygen-depleted coastal marine environments. Several bolivinid foraminifera are abundant in these oxygen-depleted settings, and take up nitrate through the pores in their shells for denitrification. This makes their pore density a possible nitrate proxy. This study documents three aspects related to the porosity of bolivinids. 1. A new automated image analysis technique to determine the number of pores in bolivinids is tested. 2. The pore patterns of Bolivina spissa from five different ocean settings are analysed. The relationship between porosity, pore density and mean pore size significantly differs between the studied locations. Their porosity is mainly controlled by the size of the pores at the Gulf of Guayaquil (Peru), but by the number of pores at other studied locations. This might be related to the presence of a different cryptic Bolivina species in the Gulf of Guayaquil. 3. The pore densities of closely related bolivinids in core-top samples are calibrated as a bottom-water nitrate proxy. Bolivina spissa and Bolivina subadvena showed the same correlation between pore density and bottom-water nitrate concentrations, while the pore density of Bolivina argentea and Bolivina subadvena accumeata is much higher.
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Affiliation(s)
- Anjaly Govindankutty Menon
- Department of Earth System Sciences, Institute for Geology, Universität Hamburg, Bundesstrasse 55, 20146, Hamburg, Germany.
| | - Catherine V Davis
- Department of Marine, Earth, and Atmospheric Sciences, North Carolina State University, 2800 Faucette Dr, Raleigh, NC, 27695, USA
| | - Dirk Nürnberg
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, Geb. 8c, Raum 106, 24148, Kiel, Germany
| | - Hidetaka Nomaki
- SUGAR, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Iines Salonen
- SUGAR, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
- Tvärminne Zoological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Hanko, Finland
| | - Gerhard Schmiedl
- Department of Earth System Sciences, Institute for Geology, Universität Hamburg, Bundesstrasse 55, 20146, Hamburg, Germany
- Center for Earth System Research and Sustainability, Institute for Geology, Universität Hamburg, Bundesstrasse 55, 20146, Hamburg, Germany
| | - Nicolaas Glock
- Department of Earth System Sciences, Institute for Geology, Universität Hamburg, Bundesstrasse 55, 20146, Hamburg, Germany
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4
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Rigonato J, Budinich M, Murillo AA, Brandão MC, Pierella Karlusich JJ, Soviadan YD, Gregory AC, Endo H, Kokoszka F, Vik D, Henry N, Frémont P, Labadie K, Zayed AA, Dimier C, Picheral M, Searson S, Poulain J, Kandels S, Pesant S, Karsenti E, Bork P, Bowler C, de Vargas C, Eveillard D, Gehlen M, Iudicone D, Lombard F, Ogata H, Stemmann L, Sullivan MB, Sunagawa S, Wincker P, Chaffron S, Jaillon O. Ocean-wide comparisons of mesopelagic planktonic community structures. ISME COMMUNICATIONS 2023; 3:83. [PMID: 37596349 PMCID: PMC10439195 DOI: 10.1038/s43705-023-00279-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 06/21/2023] [Accepted: 06/29/2023] [Indexed: 08/20/2023]
Abstract
For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean. Here, we conducted comparative analyses of trans-kingdom community assemblages thriving in the mesopelagic oxygen minimum zone (OMZ), mesopelagic oxic, and their epipelagic counterparts. We identified nine distinct types of intermediate water masses that correlate with variation in mesopelagic community composition. Furthermore, oxygen, NO3- and particle flux together appeared as the main drivers governing these communities. Novel taxonomic signatures emerged from OMZ while a global co-occurrence network analysis showed that about 70% of the abundance of mesopelagic plankton groups is organized into three community modules. One module gathers prokaryotes, pico-eukaryotes and Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from oxic regions, and the two other modules are enriched in OMZ prokaryotes and OMZ pico-eukaryotes, respectively. We hypothesize that OMZ conditions led to a diversification of ecological niches, and thus communities, due to selective pressure from limited resources. Our study further clarifies the interplay between environmental factors in the mesopelagic oxic and OMZ, and the compositional features of communities.
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Affiliation(s)
- Janaina Rigonato
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
| | - Marko Budinich
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680, Roscoff, France
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Alejandro A Murillo
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Manoela C Brandão
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Juan J Pierella Karlusich
- Institut de Biologie de l'ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Yawouvi Dodji Soviadan
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Ann C Gregory
- Department of Microbiology, The Ohio State University, Columbus, OH, 43214, USA
| | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Florian Kokoszka
- Institut de Biologie de l'ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Dean Vik
- Department of Microbiology, The Ohio State University, Columbus, OH, 43214, USA
| | - Nicolas Henry
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680, Roscoff, France
| | - Paul Frémont
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, OH, 43214, USA
| | - Céline Dimier
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Marc Picheral
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Sarah Searson
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
- Directors' Research European Molecular Biology Laboratory Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | - Eric Karsenti
- Institut de Biologie de l'ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
- Directors' Research European Molecular Biology Laboratory Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Institut de Biologie de l'ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680, Roscoff, France
| | - Damien Eveillard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Marion Gehlen
- Institut Pierre Simon Laplace, Laboratoire des Sciences du Climat et de l'Environnement, CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette cedex, France
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Lars Stemmann
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, 43214, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, 43214, USA
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
- Department of Biology; Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, 8093, Switzerland
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Samuel Chaffron
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Olivier Jaillon
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
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5
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Schweizer M, Jauffrais T, Choquel C, Méléder V, Quinchard S, Geslin E. Trophic strategies of intertidal foraminifera explored with single‐cell microbiome metabarcoding and morphological methods: What is on the menu? Ecol Evol 2022; 12:e9437. [PMCID: PMC9666909 DOI: 10.1002/ece3.9437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Magali Schweizer
- UMR 6112 LPG, Laboratoire de Planétologie et Géosciences, Univ Angers, Nantes Université, Le Mans Université CNRS Angers France
| | - Thierry Jauffrais
- UMR 6112 LPG, Laboratoire de Planétologie et Géosciences, Univ Angers, Nantes Université, Le Mans Université CNRS Angers France
- UMR 9220 ENTROPIE, Ifremer, IRD, Univ Nouvelle‐Calédonie, Univ La Réunion CNRS Noumea New Caledonia
| | - Constance Choquel
- UMR 6112 LPG, Laboratoire de Planétologie et Géosciences, Univ Angers, Nantes Université, Le Mans Université CNRS Angers France
- Department of Geology Lund University Lund Sweden
| | - Vona Méléder
- UR 2160, ISOMer, Institut des Substances et Organismes de la Mer Nantes Université Nantes France
| | - Sophie Quinchard
- UMR 6112 LPG, Laboratoire de Planétologie et Géosciences, Univ Angers, Nantes Université, Le Mans Université CNRS Angers France
| | - Emmanuelle Geslin
- UMR 6112 LPG, Laboratoire de Planétologie et Géosciences, Univ Angers, Nantes Université, Le Mans Université CNRS Angers France
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Chen Z, Dolfing J, Zhuang S, Wu Y. Periphytic biofilms-mediated microbial interactions and their impact on the nitrogen cycle in rice paddies. ECO-ENVIRONMENT & HEALTH (ONLINE) 2022; 1:172-180. [PMID: 38075597 PMCID: PMC10702904 DOI: 10.1016/j.eehl.2022.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 09/13/2022] [Accepted: 09/29/2022] [Indexed: 01/03/2024]
Abstract
Rice paddies are unique waterlogged wetlands artificially constructed for agricultural production. Periphytic biofilms (PBs) at the soil-water interface play an important role in rice paddies characterized by high nutrient input but low utilization efficiency. PBs are composed of microbial aggregates, including a wide variety of microorganisms (algae, bacteria, fungi, protozoa, and metazoa), extracellular polymeric substances and minerals (iron, aluminum, and calcium), which form an integrated food web and energy flux within a relatively stable micro-ecosystem. PBs are crucial to regulate and streamline the nitrogen cycle by neutralizing nitrogen losses and improving rice production since PBs can serve as both a sink by capturing surplus nitrogen and a source by slowly re-releasing this nitrogen for reutilization. Here the ecological advantages of PBs in regulating the nitrogen cycle in rice paddies are illustrated. We summarize the key functional importance of PBs, including the intricate and delicate community structure, microbial interactions among individual phylotypes, a wide diversity of self-produced organics, the active adaptation of PBs to constantly changing environments, and the intricate mechanisms by which PBs regulate the nitrogen cycle. We also identify the future challenges of microbial interspecific cooperation in PBs and their quantitative contributions to agricultural sustainability, optimizing nitrogen utilization and crop yields in rice paddies.
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Affiliation(s)
- Zhihao Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle Upon Tyne NE1 8QH, UK
| | - Shunyao Zhuang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China
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7
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Woehle C, Roy AS, Glock N, Michels J, Wein T, Weissenbach J, Romero D, Hiebenthal C, Gorb SN, Schönfeld J, Dagan T. Denitrification in foraminifera has an ancient origin and is complemented by associated bacteria. Proc Natl Acad Sci U S A 2022; 119:e2200198119. [PMID: 35704763 PMCID: PMC9231491 DOI: 10.1073/pnas.2200198119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/05/2022] [Indexed: 11/18/2022] Open
Abstract
Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown, and the missing denitrification pathway components are elusive. Analyzing transcriptomes and metagenomes of 10 foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteraceae, which harbor genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success in oxygen depleted habitats.
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Affiliation(s)
- Christian Woehle
- Institute of General Microbiology, Kiel University, Kiel 24118, Germany
| | | | - Nicolaas Glock
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24148, Germany
| | - Jan Michels
- Zoological Institute, Kiel University, Kiel 24118, Germany
| | - Tanita Wein
- Institute of General Microbiology, Kiel University, Kiel 24118, Germany
| | - Julia Weissenbach
- Institute of General Microbiology, Kiel University, Kiel 24118, Germany
| | - Dennis Romero
- Dirección General de Investigaciones Oceanográficas y Cambio Climático, Instituto del Mar del Perú, Callao 01, Peru 17
| | - Claas Hiebenthal
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24148, Germany
| | | | - Joachim Schönfeld
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24148, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel 24118, Germany
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8
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Rotterová J, Edgcomb VP, Čepička I, Beinart R. Anaerobic Ciliates as a Model Group for Studying Symbioses in Oxygen-depleted Environments. J Eukaryot Microbiol 2022; 69:e12912. [PMID: 35325496 DOI: 10.1111/jeu.12912] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anaerobiosis has independently evolved in multiple lineages of ciliates, allowing them to colonize a variety of anoxic and oxygen-depleted habitats. Anaerobic ciliates commonly form symbiotic relationships with various prokaryotes, including methanogenic archaea and members of several bacterial groups. The hypothesized functions of these ecto- and endosymbionts include the symbiont utilizing the ciliate's fermentative end-products to increase host's anaerobic metabolic efficiency, or the symbiont directly providing the host with energy by denitrification or photosynthesis. The host, in turn, may protect the symbiont from competition, the environment, and predation. Despite rapid advances in sampling, molecular, and microscopy methods, as well as the associated broadening of the known diversity of anaerobic ciliates, many aspects of these ciliate symbioses, including host-specificity and co-evolution, remain largely unexplored. Nevertheless, with the number of comparative genomic and transcriptomic analyses targeting anaerobic ciliates and their symbionts on the rise, insights into the nature of these symbioses and the evolution of the ciliate transition to obligate anaerobiosis continue to deepen. This review summarizes the current body of knowledge regarding the complex nature of symbioses in anaerobic ciliates, the diversity of these symbionts, their role in the evolution of ciliate anaerobiosis and their significance in ecosystem-level processes.
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Affiliation(s)
- Johana Rotterová
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Roxanne Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
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9
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Kleptoplast distribution, photosynthetic efficiency and sequestration mechanisms in intertidal benthic foraminifera. THE ISME JOURNAL 2022; 16:822-832. [PMID: 34635793 PMCID: PMC8857221 DOI: 10.1038/s41396-021-01128-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 11/19/2022]
Abstract
Foraminifera are ubiquitously distributed in marine habitats, playing a major role in marine sediment carbon sequestration and the nitrogen cycle. They exhibit a wide diversity of feeding and behavioural strategies (heterotrophy, autotrophy and mixotrophy), including species with the ability of sequestering intact functional chloroplasts from their microalgal food source (kleptoplastidy), resulting in a mixotrophic lifestyle. The mechanisms by which kleptoplasts are integrated and kept functional inside foraminiferal cytosol are poorly known. In our study, we investigated relationships between feeding strategies, kleptoplast spatial distribution and photosynthetic functionality in two shallow-water benthic foraminifera (Haynesina germanica and Elphidium williamsoni), both species feeding on benthic diatoms. We used a combination of observations of foraminiferal feeding behaviour, test morphology, cytological TEM-based observations and HPLC pigment analysis, with non-destructive, single-cell level imaging of kleptoplast spatial distribution and PSII quantum efficiency. The two species showed different feeding strategies, with H. germanica removing diatom content at the foraminifer's apertural region and E. williamsoni on the dorsal site. All E. williamsoni parameters showed that this species has higher autotrophic capacity albeit both feeding on benthic diatoms. This might represent two different stages in the evolutionary process of establishing a permanent symbiotic relationship, or may reflect different trophic strategies.
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10
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Gomaa F, Utter DR, Powers C, Beaudoin DJ, Edgcomb VP, Filipsson HL, Hansel CM, Wankel SD, Zhang Y, Bernhard JM. Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments. SCIENCE ADVANCES 2021; 7:7/22/eabf1586. [PMID: 34039603 PMCID: PMC8153729 DOI: 10.1126/sciadv.abf1586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 04/05/2021] [Indexed: 05/14/2023]
Abstract
Oceanic deoxygenation is increasingly affecting marine ecosystems; many taxa will be severely challenged, yet certain nominally aerobic foraminifera (rhizarian protists) thrive in oxygen-depleted to anoxic, sometimes sulfidic, sediments uninhabitable to most eukaryotes. Gene expression analyses of foraminifera common to severely hypoxic or anoxic sediments identified metabolic strategies used by this abundant taxon. In field-collected and laboratory-incubated samples, foraminifera expressed denitrification genes regardless of oxygen regime with a putative nitric oxide dismutase, a characteristic enzyme of oxygenic denitrification. A pyruvate:ferredoxin oxidoreductase was highly expressed, indicating the capability for anaerobic energy generation during exposure to hypoxia and anoxia. Near-complete expression of a diatom's plastid genome in one foraminiferal species suggests kleptoplasty or sequestration of functional plastids, conferring a metabolic advantage despite the host living far below the euphotic zone. Through a unique integration of functions largely unrecognized among "typical" eukaryotes, benthic foraminifera represent winning microeukaryotes in the face of ongoing oceanic deoxygenation.
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Affiliation(s)
- Fatma Gomaa
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Daniel R Utter
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher Powers
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - David J Beaudoin
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | | | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Scott D Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Joan M Bernhard
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
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11
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Graf JS, Schorn S, Kitzinger K, Ahmerkamp S, Woehle C, Huettel B, Schubert CJ, Kuypers MMM, Milucka J. Anaerobic endosymbiont generates energy for ciliate host by denitrification. Nature 2021; 591:445-450. [PMID: 33658719 PMCID: PMC7969357 DOI: 10.1038/s41586-021-03297-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/27/2021] [Indexed: 11/27/2022]
Abstract
Mitochondria are specialized eukaryotic organelles that have a dedicated function in oxygen respiration and energy production. They evolved about 2 billion years ago from a free-living bacterial ancestor (probably an alphaproteobacterium), in a process known as endosymbiosis1,2. Many unicellular eukaryotes have since adapted to life in anoxic habitats and their mitochondria have undergone further reductive evolution3. As a result, obligate anaerobic eukaryotes with mitochondrial remnants derive their energy mostly from fermentation4. Here we describe 'Candidatus Azoamicus ciliaticola', which is an obligate endosymbiont of an anaerobic ciliate and has a dedicated role in respiration and providing energy for its eukaryotic host. 'Candidatus A. ciliaticola' contains a highly reduced 0.29-Mb genome that encodes core genes for central information processing, the electron transport chain, a truncated tricarboxylic acid cycle, ATP generation and iron-sulfur cluster biosynthesis. The genome encodes a respiratory denitrification pathway instead of aerobic terminal oxidases, which enables its host to breathe nitrate instead of oxygen. 'Candidatus A. ciliaticola' and its ciliate host represent an example of a symbiosis that is based on the transfer of energy in the form of ATP, rather than nutrition. This discovery raises the possibility that eukaryotes with mitochondrial remnants may secondarily acquire energy-providing endosymbionts to complement or replace functions of their mitochondria.
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Affiliation(s)
- Jon S Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katharina Kitzinger
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Christian Woehle
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Carsten J Schubert
- Surface Waters - Research and Management, Eawag, Kastanienbaum, Switzerland
| | | | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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12
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Effects of temperature on the behaviour and metabolism of an intertidal foraminifera and consequences for benthic ecosystem functioning. Sci Rep 2021; 11:4013. [PMID: 33597653 PMCID: PMC7889916 DOI: 10.1038/s41598-021-83311-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/01/2021] [Indexed: 01/31/2023] Open
Abstract
Heatwaves have increased in intensity, duration and frequency over the last decades due to climate change. Intertidal species, living in a highly variable environment, are likely to be exposed to such heatwaves since they can be emerged for more than 6 h during a tidal cycle. Little is known, however, on how temperature affects species traits (e.g. locomotion and behaviour) of slow-moving organisms such as benthic foraminifera (single-celled protists), which abound in marine sediments. Here, we examine how temperature influences motion-behaviour and metabolic traits of the dominant temperate foraminifera Haynesina germanica by exposing individuals to usual (6, 12, 18, 24, 30 °C) and extreme (high; i.e. 32, 34, 36 °C) temperature regimes. Our results show that individuals reduced their activity by up to 80% under high temperature regimes whereas they remained active under the temperatures they usually experience in the field. When exposed to a hyper-thermic stress (i.e. 36 °C), all individuals remained burrowed and the photosynthetic activity of their sequestered chloroplasts significantly decreased. Recovery experiments subsequently revealed that individuals initially exposed to a high thermal regime partially recovered when the hyper-thermic stress ceased. H. germanica contribution to surface sediment reworking substantially diminished from 10 mm3 indiv-1 day-1 (usual temperature) to 0 mm3 indiv-1 day-1 when individuals were exposed to high temperature regimes (i.e. above 32 °C). Given their role in sediment reworking and organic matter remineralisation, our results suggest that heatwaves may have profound long-lasting effects on the functioning of intertidal muddy ecosystems and some key biogeochemical cycles.
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13
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Nomaki H, Chen C, Oda K, Tsuchiya M, Tame A, Uematsu K, Isobe N. Abundant Chitinous Structures in Chilostomella (Foraminifera, Rhizaria) and Their Potential Functions. J Eukaryot Microbiol 2021; 68:e12828. [PMID: 33128276 PMCID: PMC7894498 DOI: 10.1111/jeu.12828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/28/2020] [Accepted: 10/20/2020] [Indexed: 12/01/2022]
Abstract
Benthic foraminifera, members of Rhizaria, inhabit a broad range of marine environments and are particularly common in hypoxic sediments. The biology of benthic foraminifera is key to understanding benthic ecosystems and relevant biogeochemical cycles, especially in hypoxic environments. Chilostomella is a foraminiferal genus commonly found in hypoxic deep-sea sediments and has poorly understood ecological characteristics. For example, the carbon isotopic compositions of their lipids are substantially different from other co-occurring genera, probably reflecting unique features of its metabolism. Here, we investigated the cytoplasmic and ultrastructural features of Chilostomella ovoidea from bathyal sediments of Sagami Bay, Japan, based on serial semi-thin sections examined using an optical microscope followed by a three-dimensional reconstruction, combined with TEM observations of ultra-thin sections. Observations by TEM revealed the presence of abundant electron-dense structures dividing the cytoplasm. Based on histochemical staining, these structures are shown to be composed of chitin. Our 3D reconstruction revealed chitinous structures in the final seven chambers. These exhibited a plate-like morphology in the final chambers but became rolled up in earlier chambers (toward the proloculus). These chitinous, plate-like structures may function to partition the cytoplasm in a chamber to increase the surface/volume ratio and/or act as a reactive site for some metabolic functions.
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Affiliation(s)
- Hidetaka Nomaki
- SUGAR, X‐starJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)2‐15 Natsushima‐choYokosukaKanagawa237‐0061Japan
| | - Chong Chen
- SUGAR, X‐starJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)2‐15 Natsushima‐choYokosukaKanagawa237‐0061Japan
| | - Kaya Oda
- SUGAR, X‐starJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)2‐15 Natsushima‐choYokosukaKanagawa237‐0061Japan
| | - Masashi Tsuchiya
- Research Institute for Global Change (RIGC)Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaKanagawa
237‐0061Japan
| | - Akihiro Tame
- Marine Works Japan Ltd.3‐54‐1 Oppamahigashi‐choYokosukaKanagawa237‐0063Japan
| | - Katsuyuki Uematsu
- Marine Works Japan Ltd.3‐54‐1 Oppamahigashi‐choYokosukaKanagawa237‐0063Japan
| | - Noriyuki Isobe
- Research Institute for Marine Resources Utilization (MRU)Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaKanagawa237‐0061Japan
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14
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Bird C, LeKieffre C, Jauffrais T, Meibom A, Geslin E, Filipsson HL, Maire O, Russell AD, Fehrenbacher JS. Heterotrophic Foraminifera Capable of Inorganic Nitrogen Assimilation. Front Microbiol 2020; 11:604979. [PMID: 33343548 PMCID: PMC7744380 DOI: 10.3389/fmicb.2020.604979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/11/2020] [Indexed: 11/17/2022] Open
Abstract
Nitrogen availability often limits biological productivity in marine systems, where inorganic nitrogen, such as ammonium is assimilated into the food web by bacteria and photoautotrophic eukaryotes. Recently, ammonium assimilation was observed in kleptoplast-containing protists of the phylum foraminifera, possibly via the glutamine synthetase/glutamate synthase (GS/GOGAT) assimilation pathway imported with the kleptoplasts. However, it is not known if the ubiquitous and diverse heterotrophic protists have an innate ability for ammonium assimilation. Using stable isotope incubations (15N-ammonium and 13C-bicarbonate) and combining transmission electron microscopy (TEM) with quantitative nanoscale secondary ion mass spectrometry (NanoSIMS) imaging, we investigated the uptake and assimilation of dissolved inorganic ammonium by two heterotrophic foraminifera; a non-kleptoplastic benthic species, Ammonia sp., and a planktonic species, Globigerina bulloides. These species are heterotrophic and not capable of photosynthesis. Accordingly, they did not assimilate 13C-bicarbonate. However, both species assimilated dissolved 15N-ammonium and incorporated it into organelles of direct importance for ontogenetic growth and development of the cell. These observations demonstrate that at least some heterotrophic protists have an innate cellular mechanism for inorganic ammonium assimilation, highlighting a newly discovered pathway for dissolved inorganic nitrogen (DIN) assimilation within the marine microbial loop.
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Affiliation(s)
- Clare Bird
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom.,School of GeoSciences, Grant Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Charlotte LeKieffre
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,UMR CNRS 6112 LPG, Bio-Indicateurs Actuels et Fossiles, Université d'Angers, Angers, France
| | - Thierry Jauffrais
- Ifremer, IRD, Univ Nouvelle-Calédonie, Univ La Réunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Centre for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Emmanuelle Geslin
- UMR CNRS 6112 LPG, Bio-Indicateurs Actuels et Fossiles, Université d'Angers, Angers, France
| | | | - Olivier Maire
- Université de Bordeaux, EPOC, UMR 5805, Talence, France.,CNRS, EPOC, UMR 5805, Talence, France
| | - Ann D Russell
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, CA, United States
| | - Jennifer S Fehrenbacher
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
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15
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Anaerobic metabolism of Foraminifera thriving below the seafloor. ISME JOURNAL 2020; 14:2580-2594. [PMID: 32641728 PMCID: PMC7490399 DOI: 10.1038/s41396-020-0708-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/09/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023]
Abstract
Foraminifera are single-celled eukaryotes (protists) of large ecological importance, as well as environmental and paleoenvironmental indicators and biostratigraphic tools. In addition, they are capable of surviving in anoxic marine environments where they represent a major component of the benthic community. However, the cellular adaptations of Foraminifera to the anoxic environment remain poorly constrained. We sampled an oxic-anoxic transition zone in marine sediments from the Namibian shelf, where the genera Bolivina and Stainforthia dominated the Foraminifera community, and use metatranscriptomics to characterize Foraminifera metabolism across the different geochemical conditions. Relative Foraminifera gene expression in anoxic sediment increased an order of magnitude, which was confirmed in a 10-day incubation experiment where the development of anoxia coincided with a 20–40-fold increase in the relative abundance of Foraminifera protein encoding transcripts, attributed primarily to those involved in protein synthesis, intracellular protein trafficking, and modification of the cytoskeleton. This indicated that many Foraminifera were not only surviving but thriving, under the anoxic conditions. The anaerobic energy metabolism of these active Foraminifera was characterized by fermentation of sugars and amino acids, fumarate reduction, and potentially dissimilatory nitrate reduction. Moreover, the gene expression data indicate that under anoxia Foraminifera use the phosphogen creatine phosphate as an ATP store, allowing reserves of high-energy phosphate pool to be maintained for sudden demands of increased energy during anaerobic metabolism. This was co-expressed alongside genes involved in phagocytosis and clathrin-mediated endocytosis (CME). Foraminifera may use CME to utilize dissolved organic matter as a carbon and energy source, in addition to ingestion of prey cells via phagocytosis. These anaerobic metabolic mechanisms help to explain the ecological success of Foraminifera documented in the fossil record since the Cambrian period more than 500 million years ago.
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16
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Li Q, Lei Y, Morard R, Li T, Wang B. Diversity hotspot and unique community structure of foraminifera in the world's deepest marine blue hole - Sansha Yongle Blue Hole. Sci Rep 2020; 10:10257. [PMID: 32581270 PMCID: PMC7314809 DOI: 10.1038/s41598-020-67221-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/01/2020] [Indexed: 11/09/2022] Open
Abstract
Marine blue holes are precious geological heritages with high scientific research values. Their physical and chemical characteristics are unique because of the steep-walled structure and isolated water column which create isolated ecosystems in geographically restricted areas. The Sansha Yongle Blue Hole (SYBH) is the world's deepest marine blue hole. Here, we generated the first DNA metabarcoding dataset from SYBH sediment focusing on foraminifera, a group of protists that have colonized various marine environments. We collected sediment samples from SYBH along a depth gradient to characterize the foraminiferal diversity and compared them with the foraminiferal diversity of the costal Jiaozhou Bay (JZB) and the abyssal Northwest Pacific Ocean (NWP). We amplified the SSU rDNA of foraminifera and sequenced them with high-throughput sequencing. The results showed that the foraminiferal assemblages in SYBH were vertically structured in response to the abiotic gradients and diversity was higher than in JZB and NWP. This study illustrates the capacity of foraminifera to colonize hostile environments and shows that blue holes are natural laboratories to explore physiological innovation associated with anoxia.
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Affiliation(s)
- Qingxia Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanli Lei
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Raphaёl Morard
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359, Bremen, Germany
| | - Tiegang Li
- Key Laboratory of Marine Sedimentology and Environmental Geology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
- Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Baodong Wang
- Key Laboratory of Marine Sedimentology and Environmental Geology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
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17
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Gooday AJ, Schoenle A, Dolan JR, Arndt H. Protist diversity and function in the dark ocean - Challenging the paradigms of deep-sea ecology with special emphasis on foraminiferans and naked protists. Eur J Protistol 2020; 75:125721. [PMID: 32575029 DOI: 10.1016/j.ejop.2020.125721] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 11/27/2022]
Abstract
The dark ocean and the underlying deep seafloor together represent the largest environment on this planet, comprising about 80% of the oceanic volume and covering more than two-thirds of the Earth's surface, as well as hosting a major part of the total biosphere. Emerging evidence suggests that these vast pelagic and benthic habitats play a major role in ocean biogeochemistry and represent an "untapped reservoir" of high genetic and metabolic microbial diversity. Due to its huge volume, the water column of the dark ocean is the largest reservoir of organic carbon in the biosphere and likely plays a major role in the global carbon budget. The dark ocean and the seafloor beneath it are also home to a largely enigmatic food web comprising little-known and sometimes spectacular organisms, mainly prokaryotes and protists. This review considers the globally important role of pelagic and benthic protists across all protistan size classes in the deep-sea realm, with a focus on their taxonomy, diversity, and physiological properties, including their role in deep microbial food webs. We argue that, given the important contribution that protists must make to deep-sea biodiversity and ecosystem processes, they should not be overlooked in biological studies of the deep ocean.
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Affiliation(s)
- Andrew J Gooday
- National Oceanography Centre, University of Southampton Waterfront Campus, Southampton, UK; Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Alexandra Schoenle
- University of Cologne, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - John R Dolan
- Sorbonne Université, CNRS UMR 7093, Laboratoroire d'Océanographie de Villefranche-sur-Mer, Villefranche-sur-Mer, France
| | - Hartmut Arndt
- University of Cologne, Institute of Zoology, General Ecology, 50674 Cologne, Germany.
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18
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Zakem EJ, Mahadevan A, Lauderdale JM, Follows MJ. Stable aerobic and anaerobic coexistence in anoxic marine zones. THE ISME JOURNAL 2020; 14:288-301. [PMID: 31624350 PMCID: PMC6908664 DOI: 10.1038/s41396-019-0523-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/23/2019] [Accepted: 09/13/2019] [Indexed: 02/06/2023]
Abstract
Mechanistic description of the transition from aerobic to anaerobic metabolism is necessary for diagnostic and predictive modeling of fixed nitrogen loss in anoxic marine zones (AMZs). In a metabolic model where diverse oxygen- and nitrogen-cycling microbial metabolisms are described by underlying redox chemical reactions, we predict a transition from strictly aerobic to predominantly anaerobic regimes as the outcome of ecological interactions along an oxygen gradient, obviating the need for prescribed critical oxygen concentrations. Competing aerobic and anaerobic metabolisms can coexist in anoxic conditions whether these metabolisms represent obligate or facultative populations. In the coexistence regime, relative rates of aerobic and anaerobic activity are determined by the ratio of oxygen to electron donor supply. The model simulates key characteristics of AMZs, such as the accumulation of nitrite and the sustainability of anammox at higher oxygen concentrations than denitrification, and articulates how microbial biomass concentrations relate to associated water column transformation rates as a function of redox stoichiometry and energetics. Incorporating the metabolic model into an idealized two-dimensional ocean circulation results in a simulated AMZ, in which a secondary chlorophyll maximum emerges from oxygen-limited grazing, and where vertical mixing and dispersal in the oxycline also contribute to metabolic co-occurrence. The modeling approach is mechanistic yet computationally economical and suitable for global change applications.
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Affiliation(s)
- Emily J Zakem
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | | | - Jonathan M Lauderdale
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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19
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Enrichment of intracellular sulphur cycle -associated bacteria in intertidal benthic foraminifera revealed by 16S and aprA gene analysis. Sci Rep 2019; 9:11692. [PMID: 31406214 PMCID: PMC6690927 DOI: 10.1038/s41598-019-48166-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 07/30/2019] [Indexed: 12/21/2022] Open
Abstract
Benthic foraminifera are known to play an important role in marine carbon and nitrogen cycles. Here, we report an enrichment of sulphur cycle -associated bacteria inside intertidal benthic foraminifera (Ammonia sp. (T6), Haynesina sp. (S16) and Elphidium sp. (S5)), using a metabarcoding approach targeting the 16S rRNA and aprA -genes. The most abundant intracellular bacterial groups included the genus Sulfurovum and the order Desulfobacterales. The bacterial 16S OTUs are likely to originate from the sediment bacterial communities, as the taxa found inside the foraminifera were also present in the sediment. The fact that 16S rRNA and aprA -gene derived intracellular bacterial OTUs were species-specific and significantly different from the ambient sediment community implies that bacterivory is an unlikely scenario, as benthic foraminifera are known to digest bacteria only randomly. Furthermore, these foraminiferal species are known to prefer other food sources than bacteria. The detection of sulphur-cycle related bacterial genes in this study suggests a putative role for these bacteria in the metabolism of the foraminiferal host. Future investigation into environmental conditions under which transcription of S-cycle genes are activated would enable assessment of their role and the potential foraminiferal/endobiont contribution to the sulphur-cycle.
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