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Gao F, Li Y, Fan H, Luo D, Chapman SJ, Yao H. 15N-DNA stable isotope probing reveals niche differentiation of ammonia oxidizers in paddy soils. Appl Microbiol Biotechnol 2024; 108:342. [PMID: 38789552 PMCID: PMC11126484 DOI: 10.1007/s00253-024-13170-x] [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: 10/06/2023] [Revised: 03/14/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
Chemoautotrophic canonical ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) and complete ammonia oxidizers (comammox Nitrospira) are accountable for ammonia oxidation, which is a fundamental process of nitrification in terrestrial ecosystems. However, the relationship between autotrophic nitrification and the active nitrifying populations during 15N-urea incubation has not been totally clarified. The 15N-labeled DNA stable isotope probing (DNA-SIP) technique was utilized in order to study the response from the soil nitrification process and the active nitrifying populations, in both acidic and neutral paddy soils, to the application of urea. The presence of C2H2 almost completely inhibited NO3--N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15N-DNA-SIP technology could effectively distinguish active nitrifying populations in both soils. The active ammonia oxidation groups in both soils were significantly different, AOA (NS (Nitrososphaerales)-Alpha, NS-Gamma, NS-Beta, NS-Delta, NS-Zeta and NT (Ca. Nitrosotaleales)-Alpha), and AOB (Nitrosospira) were functionally active in the acidic paddy soil, whereas comammox Nitrospira clade A and Nitrosospira AOB were functionally active in the neutral paddy soil. This study highlights the effective discriminative effect of 15N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. KEY POINTS: • 15N-DNA-SIP technology could effectively distinguish active ammonia oxidizers. • Comammox Nitrospira clade A plays a lesser role than canonical ammonia oxidizers. • The active groups in the acidic and neutral paddy soils were significantly different.
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Affiliation(s)
- Fuyun Gao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.
| | - Haoxin Fan
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430073, People's Republic of China
| | - Dan Luo
- College of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, People's Republic of China
| | | | - Huaiying Yao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430073, People's Republic of China.
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2
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Wittenborn AK, Bauersachs T, Hassenrück C, Käding K, Wäge-Recchioni J, Jürgens K, Arz HW, Kaiser J. Nitrosopumilus as main source of isoprenoid glycerol dialkyl glycerol tetraether lipids in the central Baltic Sea. Front Microbiol 2023; 14:1216130. [PMID: 37840736 PMCID: PMC10575479 DOI: 10.3389/fmicb.2023.1216130] [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: 05/03/2023] [Accepted: 09/07/2023] [Indexed: 10/17/2023] Open
Abstract
Nitrososphaeria in the phylum Crenarchaeota, is a widespread archaeal class in the oceanic realm, playing an important role in the marine carbon and nitrogen cycle. Nitrososphaeria-derived membrane lipids, i.e., isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs), are commonly employed to reconstruct past water temperatures using the TetraEther indeX of 86 carbon atoms (TEX86). This index is of particular importance for the brackish Baltic Sea as to date it appears to be the only applicable organic temperature proxy. In this study, we investigated the distribution of intact and core GDGTs and their potential source organisms in the water column of three deep basins located in the central Baltic Sea to evaluate the application of TEX86. A lipidomic approach on suspended particulate matter was combined with the molecular techniques 16S rRNA gene amplicon sequencing and CARD-FISH. The archaeal community was dominated by Nitrosopumilus (~83-100% of the total archaeal sequences). As other detected taxa known to produce GDGTs each represented less than 2% of the total archaeal sequences, Nitrosopumilus is likely the most dominant GDGT producer in the central Baltic Sea. However, the occurrence of phosphohexose (PH), instead of hexose-phosphohexose (HPH) headgroups, suggested that Nitrosopumilus in the Baltic Sea may differ physiologically from representatives of marine settings and other marginal seas, such as the Black Sea. In the Baltic Sea, Nitrosopumilus is most abundant in the suboxic zone, where intact cells peak according to both CARD-FISH data and intact polar lipid concentrations. The presented data therefore suggest that TEX86 reflects subsurface rather than surface temperature in the central Baltic Sea.
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Affiliation(s)
| | | | - Christiane Hassenrück
- Biological Oceanography, Leibniz Institute for Baltic Sea Research – Warnemünde (IOW), Warnemünde, Germany
| | - Katja Käding
- Biological Oceanography, Leibniz Institute for Baltic Sea Research – Warnemünde (IOW), Warnemünde, Germany
| | - Janine Wäge-Recchioni
- Biological Oceanography, Leibniz Institute for Baltic Sea Research – Warnemünde (IOW), Warnemünde, Germany
| | - Klaus Jürgens
- Biological Oceanography, Leibniz Institute for Baltic Sea Research – Warnemünde (IOW), Warnemünde, Germany
| | - Helge Wolfgang Arz
- Marine Geology, Leibniz Institute for Baltic Sea Research – Warnemünde (IOW), Warnemünde, Germany
| | - Jérôme Kaiser
- Marine Geology, Leibniz Institute for Baltic Sea Research – Warnemünde (IOW), Warnemünde, Germany
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3
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Diao M, Balkema C, Suárez-Muñoz M, Huisman J, Muyzer G. Succession of bacteria and archaea involved in the nitrogen cycle of a seasonally stratified lake. FEMS Microbiol Lett 2023; 370:7043454. [PMID: 36796795 PMCID: PMC9990978 DOI: 10.1093/femsle/fnad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/07/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Human-driven changes affect nutrient inputs, oxygen solubility, and the hydrodynamics of lakes, which affect biogeochemical cycles mediated by microbial communities. However, information on the succession of microbes involved in nitrogen cycling in seasonally stratified lakes is still incomplete. Here, we investigated the succession of nitrogen-transforming microorganisms in Lake Vechten over a period of 19 months, combining 16S rRNA gene amplicon sequencing and quantification of functional genes. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) and anammox bacteria were abundant in the sediment during winter, accompanied by nitrate in the water column. Nitrogen-fixing bacteria and denitrifying bacteria emerged in the water column in spring when nitrate was gradually depleted. Denitrifying bacteria containing nirS genes were exclusively present in the anoxic hypolimnion. During summer stratification, abundances of AOA, AOB, and anammox bacteria decreased sharply in the sediment, and ammonium accumulated in hypolimnion. After lake mixing during fall turnover, abundances of AOA, AOB, and anammox bacteria increased and ammonium was oxidized to nitrate. Hence, nitrogen-transforming microorganisms in Lake Vechten displayed a pronounced seasonal succession, which was strongly determined by the seasonal stratification pattern. These results imply that changes in stratification and vertical mixing induced by global warming are likely to alter the nitrogen cycle of seasonally stratified lakes.
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Affiliation(s)
- Muhe Diao
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Cherel Balkema
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - María Suárez-Muñoz
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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4
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McClain CR, Bryant SR, Hanks G, Bowles MW. Extremophiles in Earth's Deep Seas: A View Toward Life in Exo-Oceans. ASTROBIOLOGY 2022; 22:1009-1028. [PMID: 35549348 DOI: 10.1089/ast.2021.0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Humanity's search for extraterrestrial life is a modern manifestation of the exploratory and curious nature that has led us through millennia of scientific discoveries. With the ongoing exploration of extraterrestrial bodies, the potential for discovery of extraterrestrial life has expanded. We may better inform this search through an understanding of how life persists and flourishes on Earth in a myriad of environmental extremes. A significant proportion of our knowledge of extremophiles on Earth comes from studies on deep ocean life. Here, we review and synthesize the range of environmental extremes observed in the deep sea, the life that persists in these extreme conditions, and the biological adaptations utilized by these remarkable life-forms. We also review confirmed and predicted extraterrestrial oceans in our solar system and propose deep-sea sites that may serve as planetary field analog environments. We show that the clever ingenuity of evolution under deep-sea conditions suggests that the plausibility of extraterrestrial life is much greater than previously thought.
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Affiliation(s)
- Craig R McClain
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - S River Bryant
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - Granger Hanks
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
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5
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Leberecht KM, Ritter SM, Lapp CJ, Klose L, Eschenröder J, Scholz C, Kühnel S, Stinnesbeck W, Kletzin A, Isenbeck-Schröter M, Gescher J. Microbially promoted calcite precipitation in the pelagic redoxcline: Elucidating the formation of the turbid layer. GEOBIOLOGY 2022; 20:498-517. [PMID: 35514106 DOI: 10.1111/gbi.12492] [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: 04/27/2021] [Revised: 02/24/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Large bell-shaped calcite formations called "Hells Bells" were discovered underwater in the stratified cenote El Zapote on the Yucatán Peninsula, Mexico. Together with these extraordinary speleothems, divers found a white, cloudy turbid layer into which some Hells Bells partially extend. Here, we address the central question if the formation of the turbid layer could be based on microbial activity, more specifically, on microbially induced calcite precipitation. Metagenomic and metatranscriptomic profiling of the microbial community in the turbid layer, which overlaps with the pelagic redoxcline in the cenote, revealed chemolithoautotrophic Hydrogenophilales and unclassified β-Proteobacteria as the metabolic key players. Bioinformatic and hydrogeochemical data suggest chemolithoautotrophic oxidation of sulfide to zero-valent sulfur catalyzed by denitrifying organisms due to oxygen deficiency. Incomplete sulfide oxidation via nitrate reduction and chemolithoautotrophy are both proton-consuming processes, which increase the pH in the redoxcline favoring authigenic calcite precipitation and may contribute to Hells Bells growth. The observed mechanism of microbially induced calcite precipitation is potentially applicable to many other stagnant sulfate-rich water bodies.
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Affiliation(s)
- Kerstin M Leberecht
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | - Simon M Ritter
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany
| | - Christian J Lapp
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | - Lukas Klose
- Department of Physics & Earth Sciences, Jacobs University Bremen, Bremen, Germany
| | | | - Christian Scholz
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany
| | - Sebastian Kühnel
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany
| | - Wolfgang Stinnesbeck
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany
- Heidelberg Center for the Environment (HCE), Heidelberg University, Heidelberg, Germany
| | - Arnulf Kletzin
- Department of Biology, Microbiology; Sulfur Biochemistry and Microbial Bioenergetics, Technical University of Darmstadt, Darmstadt, Germany
| | - Margot Isenbeck-Schröter
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany
- Heidelberg Center for the Environment (HCE), Heidelberg University, Heidelberg, Germany
| | - Johannes Gescher
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
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6
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Wu J, Hong Y, He X, Liu X, Ye J, Jiao L, Li Y, Wang Y, Ye F, Yang Y, Du J. Niche differentiation of ammonia-oxidizing archaea and related autotrophic carbon fixation potential in the water column of the South China Sea. iScience 2022; 25:104333. [PMID: 35602962 PMCID: PMC9118673 DOI: 10.1016/j.isci.2022.104333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/12/2022] [Accepted: 04/26/2022] [Indexed: 11/07/2022] Open
Abstract
The significant primary production by ammonia-oxidizing archaea (AOA) in the ocean was reported, but the carbon fixation process of AOA and its community composition along the water depth remain unclear. Here, we investigated the abundance, community composition, and potential carbon fixation of AOA in water columns of the South China Sea. Higher abundances of the amoA and accA genes of AOA were found below the euphotic zone. Similarly, higher carbon fixation potential of AOA, evaluated by the ratios of amoA to accA gene, was also observed below euphotic zone and the ratios increased with increasing water depth. The vertical niche differentiation of AOA was further evidenced, with the dominant genus shifting from Nitrosopelagicus in the epipelagic zone to uncultured genus in the meso- and bathypelagic zones. Our findings highlight the higher carbon fixation potential of AOA in deep water and the significance of AOA to the ocean carbon budget.
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Affiliation(s)
- Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Xiang He
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xiaohan Liu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jiaqi Ye
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Lijing Jiao
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yiben Li
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yu Wang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yunhua Yang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Juan Du
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
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7
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Kraft B, Jehmlich N, Larsen M, Bristow LA, Könneke M, Thamdrup B, Canfield DE. Oxygen and nitrogen production by an ammonia-oxidizing archaeon. Science 2022; 375:97-100. [PMID: 34990242 DOI: 10.1126/science.abe6733] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Ammonia-oxidizing archaea (AOA) are one of the most abundant groups of microbes in the world’s oceans and are key players in the nitrogen cycle. Their energy metabolism—the oxidation of ammonia to nitrite—requires oxygen. Nevertheless, AOA are abundant in environments where oxygen is undetectable. By carrying out incubations for which oxygen concentrations were resolved to the nanomolar range, we show that after oxygen depletion, Nitrosopumilus maritimus produces dinitrogen and oxygen, which is used for ammonia oxidation. The pathway is not completely resolved but likely has nitric oxide and nitrous oxide as key intermediates. N. maritimus joins a handful of organisms known to produce oxygen in the dark. On the basis of this ability, we reevaluate the role of N. maritimus in oxygen-depleted marine environments.
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Affiliation(s)
- Beate Kraft
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research UFZ GmbH, Leipzig, Germany
| | - Morten Larsen
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Laura A Bristow
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Martin Könneke
- Marine Archaea Group, Center for Marine Environmental Sciences (MARUM), and Department of Geosciences, University of Bremen, Bremen, Germany.,Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Bo Thamdrup
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Donald E Canfield
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark.,Key Laboratory of Petroleum Geochemistry, Research Institute of Petroleum Exploration and Development, China National Petroleum Corporation, Beijing 100083, China.,Danish Institute of Advanced Study, University of Southern Denmark, Odense, Denmark
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8
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Production and Excretion of Polyamines To Tolerate High Ammonia, a Case Study on Soil Ammonia-Oxidizing Archaeon " Candidatus Nitrosocosmicus agrestis". mSystems 2021; 6:6/1/e01003-20. [PMID: 33594004 PMCID: PMC8573960 DOI: 10.1128/msystems.01003-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ammonia tolerance is a universal characteristic among the ammonia-oxidizing bacteria (AOB); in contrast, the known species of ammonia-oxidizing archaea (AOA) have been regarded as ammonia sensitive, until the identification of the genus “Candidatus Nitrosocosmicus.” However, the mechanism of its ammonia tolerance has not been reported. In this study, the AOA species “Candidatus Nitrosocosmicus agrestis,” obtained from agricultural soil, was determined to be able to tolerate high concentrations of NH3 (>1,500 μM). In the genome of this strain, which was recovered from metagenomic data, a full set of genes for the pathways of polysaccharide metabolism, urea hydrolysis, arginine synthesis, and polyamine synthesis was identified. Among them, the genes encoding cytoplasmic carbonic anhydrase (CA) and a potential polyamine transporter (drug/metabolite exporter [DME]) were found to be unique to the genus “Ca. Nitrosocosmicus.” When “Ca. Nitrosocosmicus agrestis” was grown with high levels of ammonia, the genes that participate in CO2/HCO3− conversion, glutamate/glutamine syntheses, arginine synthesis, polyamine synthesis, and polyamine excretion were significantly upregulated, and the polyamines, including putrescine and spermidine, had significant levels of production. Based on genome analysis, gene expression quantification, and polyamine determination, we propose that the production and excretion of polyamines is probably one of the reasons for the ammonia tolerance of “Ca. Nitrosocosmicus agrestis,” and even of the genus “Ca. Nitrosocosmicus.” IMPORTANCE Ammonia tolerance of AOA is usually much lower than that of the AOB, which makes the AOB rather than AOA a predominant ammonia oxidizer in agricultural soils, contributing to global N2O emission. Recently, some AOA species from the genus “Ca. Nitrosocosmicus” were also found to have high ammonia tolerance. However, the reported mechanism for the ammonia tolerance is very rare and indeterminate for AOB and for AOA species. In this study, an ammonia-tolerant AOA strain of the species “Ca. Nitrosocosmicus agrestis” was identified and its potential mechanisms for ammonia tolerance were explored. This study will be of benefit for determining more of the ecological role of AOA in agricultural soils or other environments.
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Wu L, Chen X, Wei W, Liu Y, Wang D, Ni BJ. A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:9175-9190. [PMID: 32657581 DOI: 10.1021/acs.est.0c03948] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The continuous increase of nitrous oxide (N2O) in the atmosphere has become a global concern because of its property as a potent greenhouse gas. Given the important role of ammonia-oxidizing archaea (AOA) in ammonia oxidation and their involvement in N2O production, a clear understanding of the knowledge on archaeal N2O production is necessary for global N2O mitigation. Compared to bacterial N2O production by ammonia-oxidizing bacteria (AOB), AOA-driven N2O production pathways are less-well elucidated. In this Critical Review, we synthesized the currently proposed AOA-driven N2O production pathways in combination with enzymology distinction, analyzed the role of AOA species involved in N2O production pathways, discussed the relative contribution of AOA to N2O production in both natural and anthropogenic environments, summarized the factors affecting archaeal N2O yield, and compared the distinctions among approaches used to differentiate ammonia oxidizer-associated N2O production. We, then, put forward perspectives for archaeal N2O production and future challenges to further improve our understanding of the production pathways, putative enzymes involved and potential approaches for identification in order to potentially achieve effective N2O mitigations.
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Affiliation(s)
- Lan Wu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Xueming Chen
- College of Environment and Resources, Fuzhou University, Fujian 350116, PR China
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Yiwen Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Dongbo Wang
- Key Laboratory of Environmental Biology and Pollution Control, College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
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10
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Prosser JI, Hink L, Gubry-Rangin C, Nicol GW. Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies. GLOBAL CHANGE BIOLOGY 2020; 26:103-118. [PMID: 31638306 DOI: 10.1111/gcb.14877] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/30/2019] [Indexed: 05/02/2023]
Abstract
Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N2 O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia-based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle. Direct N2 O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N2 O production, vary within and between ammonia-oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N2 O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow-release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N2 O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N2 O emissions.
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Affiliation(s)
- James I Prosser
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Linda Hink
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
| | | | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Lyon, France
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11
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Caffrey JM, Bonaglia S, Conley DJ. Short exposure to oxygen and sulfide alter nitrification, denitrification, and DNRA activity in seasonally hypoxic estuarine sediments. FEMS Microbiol Lett 2019; 366:5266299. [PMID: 30596977 PMCID: PMC6343015 DOI: 10.1093/femsle/fny288] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/14/2018] [Indexed: 02/03/2023] Open
Abstract
Increased organic loading to sediments from eutrophication often results in hypoxia, reduced nitrification and increased production of hydrogen sulfide, altering the balance between nitrogen removal and retention. We examined the effect of short-term exposure to various oxygen and sulfide concentrations on sediment nitrification, denitrification and DNRA from a chronically hypoxic basin in Roskilde Fjord, Denmark. Surprisingly, nitrification rates were highest in the hypoxic and anoxic treatments (about 5 μmol cm−3 d−1) and the high sulfide treatment was not significantly different than the oxic treatment. Denitrification in the hypoxic treatment was highest at 1.4 μmol cm−3 d−1 and significantly higher than the high sulfide treatment. For DNRA, the rate in high sulfide treatment was 2 μmol cm−3 d−1. This was significantly higher than all oxygen treatments that were near zero. In this system, nitrifiers rapidly recovered from conditions typically considered inhibiting, while denitrifiers had a more muted response. DNRA bacteria appear to depend on sulfide for nitrate reduction. Anammox was insignificant. Thus, in estuaries and coastal systems that experience short-term variations in oxygen and sulfide, capabilities of microbial communities are more diverse and tolerant of suboptimal conditions than some paradigms suggest.
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Affiliation(s)
- Jane M Caffrey
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, 11000 University Parkway, Pensacola, FL 32514, USA
| | - Stefano Bonaglia
- Department of Geology, Lund University, Solvegatan 12, SE-223 62 Lund, Sweden
| | - Daniel J Conley
- Department of Geology, Lund University, Solvegatan 12, SE-223 62 Lund, Sweden
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12
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Köstner N, Jürgens K, Labrenz M, Herndl GJ, Winter C. Uneven host cell growth causes lysogenic virus induction in the Baltic Sea. PLoS One 2019; 14:e0220716. [PMID: 31386696 PMCID: PMC6684075 DOI: 10.1371/journal.pone.0220716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/22/2019] [Indexed: 12/04/2022] Open
Abstract
In the Baltic Sea redoxcline, lysogenic viruses infecting prokaryotes have rarely been detected using the commonly used inducing agent mitomycin C. However, it is well known that not all viruses are induceable by mitomycin C and growing evidence suggests that changes in trophic conditions may trigger the induction of lysogenic viruses. We hypothesized that using antibiotics to simulate a strong change in trophic conditions for antibiotica-resistant cells due to reduced competition for resources might lead to the induction of lysogenic viruses into the lytic cycle within these cells. This hypothesis was tested by incubating prokaryotes obtained throughout the Baltic Sea redoxcline in seawater with substantially reduced numbers of viruses. We used a mixture of the protein synthesis-inhibiting antibiotics streptomycin and erythromycin to induce the desired changes in trophic conditions for resistant cells and at the same time ensuring that no progeny viruses were formed in sensitive cells. No inducible lysogenic viruses could be detected in incubations amended with mitomycin C. Yet, the presence of streptomycin and erythromycin increased virus-induced mortality of prokaryotes by 56–930% compared to controls, resulting in the induction of lysogenic viruses equivalent to 2–14% of in situ prokaryotic abundance. The results indicate the existence of a previously unrecognized induction mechanism for lysogenic viruses in the Baltic Sea redoxcline, as the mode of action distinctly differs between the used antibiotics (no virus production within affected cells) and mitomycin C (lysogenic viruses are produced within affected cells). Obtaining accurate experimental data on levels of lysogeny in prokaryotic host cells remains challenging, as relying on mitomycin C alone may severely underestimate lysogeny.
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Affiliation(s)
- Nicole Köstner
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Klaus Jürgens
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research (IOW), Rostock-Warnemünde, Germany
| | - Matthias Labrenz
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research (IOW), Rostock-Warnemünde, Germany
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, AB Den Burg, The Netherlands
| | - Christian Winter
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- * E-mail:
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13
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Miettinen H, Bomberg M, Nyyssönen M, Reunamo A, Jørgensen KS, Vikman M. Oil degradation potential of microbial communities in water and sediment of Baltic Sea coastal area. PLoS One 2019; 14:e0218834. [PMID: 31265451 PMCID: PMC6605675 DOI: 10.1371/journal.pone.0218834] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/10/2019] [Indexed: 11/19/2022] Open
Abstract
Two long-term potentially oil exposed Baltic Sea coastal sites near old oil refineries and harbours were compared to nearby less exposed sites in terms of bacterial, archaeal and fungal microbiomes and oil degradation potential. The bacterial, archaeal and fungal diversities were similar in oil exposed and less exposed sampling sites based on bacterial and archaeal 16S rRNA gene and fungal 5.8S rRNA gene amplicon sequencing from both DNA and RNA fractions. The number of genes participating in alkane degradation (alkB) or PAH-ring hydroxylation (PAH–RHDα) were detected by qPCR in all water and sediment samples. These numbers correlated with the number of bacterial 16S rRNA gene copies in sediment samples but not with the concentration of petroleum hydrocarbons or PAHs. This indicates that both the clean and the more polluted sites at the Baltic Sea coastal areas have a potential for petroleum hydrocarbon degradation. The active community (based on RNA) of the coastal Baltic Sea water differed largely from the total community (based on DNA). The most noticeable difference was seen in the bacterial community in the water samples were the active community was dominated by Cyanobacteria and Proteobacteria whereas in total bacterial community Actinobacteria was the most abundant phylum. The abundance, richness and diversity of Fungi present in water and sediment samples was in general lower than that of Bacteria and Archaea. Furthermore, the sampling location influenced the fungal community composition, whereas the bacterial and archaeal communities were not influenced. This may indicate that the fungal species that are adapted to the Baltic Sea environments are few and that Fungi are potentially more vulnerable to or affected by the Baltic Sea conditions than Bacteria and Archaea.
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Affiliation(s)
- Hanna Miettinen
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, VTT, Finland
- * E-mail:
| | - Malin Bomberg
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, VTT, Finland
| | - Mari Nyyssönen
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, VTT, Finland
| | - Anna Reunamo
- Marine Research Centre, Finnish Environment Institute SYKE, Helsinki, Finland
| | | | - Minna Vikman
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, VTT, Finland
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14
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Song S, Wang P, Liu Y, Zhao D, Leng X, An S. Effects of Oenanthe javanica on Nitrogen Removal in Free-Water Surface Constructed Wetlands under Low-Temperature Conditions. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16081420. [PMID: 31010264 PMCID: PMC6518158 DOI: 10.3390/ijerph16081420] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/02/2019] [Accepted: 04/08/2019] [Indexed: 11/16/2022]
Abstract
To investigate the role and microorganism-related mechanisms of macrophytes and assess the feasibility of Oenanthe javanica (Blume) DC. in promoting nitrogen removal in free-water surface constructed wetlands (FWS-CWS) under low temperatures (<10 °C), pilot-scale FWS-CWS, planted with O. javanica, were set up and run for batch wastewater treatment in eastern China during winter. The presence of macrophytes observably improved the removal rates of ammonia nitrogen (65%-71%) and total nitrogen (41%-48%) (p < 0.05), with a sharp increase in chemical oxygen demand concentrations (about 3-4 times). Compared to the unplanted systems, the planted systems not only exhibited higher richness and diversity of microorganisms, but also significantly higher abundances of bacteria, ammonia monooxygenase gene (amoA), nitrous oxide reductase gene (nosZ), dissimilatory cd1-containing nitrite reductase gene (nirS), and dissimilatory copper-containing nitrite reductase gene (nirK) in the substrate. Meanwhile, the analysis of the microbial community composition further revealed significant differences. The results indicate that enhanced abundances of microorganisms, and the key functional genes involved with nitrogen metabolism in the planted systems played critical roles in nitrogen removal from wastewater in FWS-CWS. Furthermore, abundant carbon release from the wetland macrophytes could potentially aid nitrogen removal in FWS-CWS during winter.
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Affiliation(s)
- Siyuan Song
- Institute of Wetland Ecology, School of Life Science, Nanjing University, Nanjing 210046, China; (S.S.); (P.W.); (Y.L.); (X.L.); (S.A.)
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu 215500, China
| | - Penghe Wang
- Institute of Wetland Ecology, School of Life Science, Nanjing University, Nanjing 210046, China; (S.S.); (P.W.); (Y.L.); (X.L.); (S.A.)
- Shanghai Investigation, Design & Research Institute Co., Ltd. (SIDRI), Shanghai 200434, China
| | - Yongxia Liu
- Institute of Wetland Ecology, School of Life Science, Nanjing University, Nanjing 210046, China; (S.S.); (P.W.); (Y.L.); (X.L.); (S.A.)
| | - Dehua Zhao
- Institute of Wetland Ecology, School of Life Science, Nanjing University, Nanjing 210046, China; (S.S.); (P.W.); (Y.L.); (X.L.); (S.A.)
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu 215500, China
- Correspondence: ; Tel.: +86-25-89681309
| | - Xin Leng
- Institute of Wetland Ecology, School of Life Science, Nanjing University, Nanjing 210046, China; (S.S.); (P.W.); (Y.L.); (X.L.); (S.A.)
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu 215500, China
| | - Shuqing An
- Institute of Wetland Ecology, School of Life Science, Nanjing University, Nanjing 210046, China; (S.S.); (P.W.); (Y.L.); (X.L.); (S.A.)
- Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu 215500, China
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15
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Sollai M, Villanueva L, Hopmans EC, Keil RG, Sinninghe Damsté JS. Archaeal Sources of Intact Membrane Lipid Biomarkers in the Oxygen Deficient Zone of the Eastern Tropical South Pacific. Front Microbiol 2019; 10:765. [PMID: 31031734 PMCID: PMC6470261 DOI: 10.3389/fmicb.2019.00765] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/26/2019] [Indexed: 11/13/2022] Open
Abstract
Archaea are ubiquitous in the modern ocean where they are involved in the carbon and nitrogen biogeochemical cycles. However, the majority of Archaea remain uncultured. Archaeal specific membrane intact polar lipids (IPLs) are biomarkers of the presence and abundance of living cells. They comprise archaeol and glycerol dibiphytanyl glycerol tetraethers (GDGTs) attached to various polar headgroups. However, little is known of the IPLs of uncultured marine Archaea, complicating their use as biomarkers. Here, we analyzed suspended particulate matter (SPM) obtained in high depth resolution from a coastal and open ocean site in the eastern tropical South Pacific (ETSP) oxygen deficient zone (ODZ) with the aim of determining possible biological sources of archaeal IPL by comparing their composition by Ultra High Pressure Liquid Chromatography coupled to high resolution mass spectrometry with the archaeal diversity by 16S rRNA gene amplicon sequencing and their abundance by quantitative PCR. Thaumarchaeotal Marine Group I (MGI) closely related to Ca. Nitrosopelagicus and Nitrosopumilus dominated the oxic surface and upper ODZ water together with Marine Euryarchaeota Group II (MGII). High relative abundance of hexose phosphohexose- (HPH) crenarchaeol, the specific biomarker for living Thaumarchaeota, and HPH-GDGT-0, dihexose- (DH) GDGT-3 and -4 were detected in these water masses. Within the ODZ, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaea) of the Woesearchaeota DHVE-6 group and Marine Euryarchaeota Group III (MGIII) were present together with a higher proportion of archaeol-based IPLs, which were likely made by MGIII, since DPANN archaea are supposedly unable to synthesize their own IPLs and possibly have a symbiotic or parasitic partnership with MGIII. Finally, in deep suboxic/oxic waters a different MGI population occurred with HPH-GDGT-1, -2 and DH-GDGT-0 and -crenarchaeol, indicating that here MGI synthesize membranes with IPLs in a different relative abundance which could be attributed to the different detected population or to an environmental adaptation. Our study sheds light on the complex archaeal community of one of the most prominent ODZs and on the IPL biomarkers they potentially synthesize.
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Affiliation(s)
- Martina Sollai
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands
| | - Laura Villanueva
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands
| | - Ellen C Hopmans
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands
| | - Richard G Keil
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Jaap S Sinninghe Damsté
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands.,Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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16
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Abstract
Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group-the marine Thaumarchaeota-has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done.
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Affiliation(s)
- Alyson E Santoro
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, USA;
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17
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Chow J, Danso D, Ferrer M, Streit WR. The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli ΔbioH-complementing esterase EstN1. Sci Rep 2018; 8:13823. [PMID: 30218044 PMCID: PMC6138646 DOI: 10.1038/s41598-018-32059-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/28/2018] [Indexed: 12/15/2022] Open
Abstract
Biotin is an essential cofactor required for carboxylation and decarboxylation reactions in all domains of life. While biotin biosynthesis in most Bacteria and Eukarya is well studied, the complete pathway for this vitamer in Archaea is still not known. Detailed genome searches indicated the presence of possible bio gene clusters only in Methanococcales and Thaumarchaeota. Therefore, we analysed the functionality of the predicted genes bioA, bioB, bioD and bioF in the Thaumarchaeon Nitrososphaera gargensis Ga2.9 which are essential for the later steps of biotin synthesis. In complementation tests, the gene cluster-encoded N. gargensis bioABD genes except bioF restored growth of corresponding E. coli Rosetta-gami 2 (DE3) deletion mutants. To find out how biotin biosynthesis is initiated, we searched the genome for a possible bioH analogue encoding a pimeloyl-ACP-methylester carboxylesterase. The respective amino acid sequence of the ORF estN1 showed weak conserved domain similarity to this class of enzymes (e-value 3.70e-42). Remarkably, EstN1 is a promiscuous carboxylesterase that complements E. coli ΔbioH and Mesorhizobium loti ΔbioZ mutants for growth on biotin-free minimal medium. Additional 3D-structural models support the hypothesis that EstN1 is a BioH analogue. Thus, this is the first report providing experimental evidence that Archaea carry functional bio genes.
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Affiliation(s)
- Jennifer Chow
- Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | - Dominik Danso
- Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Wolfgang R Streit
- Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany.
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18
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Happel E, Bartl I, Voss M, Riemann L. Extensive nitrification and active ammonia oxidizers in two contrasting coastal systems of the Baltic Sea. Environ Microbiol 2018; 20:2913-2926. [PMID: 29921003 DOI: 10.1111/1462-2920.14293] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 04/30/2018] [Accepted: 05/16/2018] [Indexed: 11/27/2022]
Abstract
Nitrification is important in nitrogen (N) cycling of aquatic environments, but knowledge about its regulation and importance is sparse. Here we examined nitrification and ammonia oxidizers in the Baltic Sea. We investigated two sites with different catchment characteristics (agricultural and forest), the Bay of Gdánsk (south) and the Öre Estuary (north), and measured pelagic nitrification rates and abundance, composition and expression of ammonia monooxygenase (amoA) genes. Highest nitrification rates were found in the nutrient rich Bay of Gdańsk. Interestingly, abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were orders of magnitude lower than reported from other sites. Although AOA were most abundant at both sites, the highest expression levels were from AOB. Interestingly, few AOA and AOB taxa dominated amoA gene expression, with a Nitrosomarinus related phylotype showing widespread expression. AOA and AOB communities differed between sites and depths, respectively, with the composition in rivers being distinct. A storm event, causing an even depth distribution of nitrification and particles in the Bay of Gdańsk, indicated that the presence of particles stimulate nitrification. The study highlights coastal regions as dynamic sites of extensive pelagic nitrification, which may affect local food web dynamics and loss of N mediated by denitrification.
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Affiliation(s)
- Elisabeth Happel
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Ines Bartl
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research (IOW), Rostock, Germany
| | - Maren Voss
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research (IOW), Rostock, Germany
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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19
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Molina V, Dorador C, Fernández C, Bristow L, Eissler Y, Hengst M, Hernandez K, Olsen LM, Harrod C, Marchant F, Anguita C, Cornejo M. The activity of nitrifying microorganisms in a high-altitude Andean wetland. FEMS Microbiol Ecol 2018; 94:4969675. [DOI: 10.1093/femsec/fiy062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 04/09/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Verónica Molina
- Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha. Avenida Leopoldo Carvallo 270, Playa Ancha, Valparaíso, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta. Avenida Universidad de Antofagasta s/n, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beaucheff 851 (Piso 7)
| | - Camila Fernández
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650, Banyuls/mer, France
- Interdisciplinary Center for Aquaculture Research (INCAR), COPAS SUR-AUSTRAL Program, Barrio Universitario s/n, Universidad de Concepción, Concepción, Chile
| | - Laura Bristow
- Nordic Center for Earth Evolution (NordCEE), Department of Biology, University of Southern Denmark, Campusvej 55-5230, Odense, Denmark
| | - Yoanna Eissler
- Centro de Investigación y Gestión de Recursos Naturales, Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Playa Ancha, Valparaíso, Chile
| | - Martha Hengst
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beaucheff 851 (Piso 7)
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte. Av Angamos 0610 Antofagasta, Chile
| | - Klaudia Hernandez
- Centro de Investigacion Marina Quintay, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Avenida República 440, Santiago, Chile10
| | | | - Chris Harrod
- Fish and Stable Isotope Ecology Laboratory, Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Francisca Marchant
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta. Avenida Universidad de Antofagasta s/n, Antofagasta, Chile
| | - Cristobal Anguita
- Departamento de Ecologia y Biodiversidad, Facultad de Ecologia y Recursos Naturales, Universidad Andres Bello, Av. Republica 440, Santiago, Chile
| | - Marcela Cornejo
- Escuela de Ciencias del Mar e Instituto Milenio de Oceanografía , Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile, Altamirano 1480, Valparaíso
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20
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Gonzalez-Martinez A, Sihvonen M, Muñoz-Palazon B, Rodriguez-Sanchez A, Mikola A, Vahala R. Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi. Sci Rep 2018; 8:2208. [PMID: 29396546 PMCID: PMC5797233 DOI: 10.1038/s41598-018-20633-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/21/2018] [Indexed: 01/06/2023] Open
Abstract
Seven full-scale biological wastewater treatment systems located in the Polar Arctic Circle region in Finland were investigated to determine their Archaea, Bacteria and Fungi community structure, and their relationship with the operational conditions of the bioreactors by the means of quantitative PCR, massive parallel sequencing and multivariate redundancy analysis. The results showed dominance of Archaea and Bacteria members in the bioreactors. The activated sludge systems showed strong selection of Bacteria but not for Archaea and Fungi, as suggested by diversity analyses. Core OTUs in influent and bioreactors were classified as Methanobrevibacter, Methanosarcina, Terrestrial Group Thaumarchaeota and unclassified Euryarchaeota member for Archaea; Trichococcus, Leptotrichiaceae and Comamonadaceae family, and Methylorosula for Bacteria and Trichosporonaceae family for Fungi. All influents shared core OTUs in all domains, but in bioreactors this did not occur for Bacteria. Oligotype structure of core OTUs showed several ubiquitous Fungi oligotypes as dominant in sewage and bioreactors. Multivariate redundancy analyses showed that the majority of core OTUs were related to organic matter and nutrients removal. Also, there was evidence of competition among Archaea and Fungi core OTUs, while all Bacteria OTUs were positively correlated among them. The results obtained highlighted interesting features of extremely cold temperature bioreactors.
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Affiliation(s)
- Alejandro Gonzalez-Martinez
- Department of Built Environment, School of engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076, Espoo, Finland.
| | - Maija Sihvonen
- Department of Built Environment, School of engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076, Espoo, Finland
| | - Barbara Muñoz-Palazon
- Institute of Water Research, University of Granada, C/Ramón y Cajal, 4, 18071, Granada, Spain
| | | | - Anna Mikola
- Department of Built Environment, School of engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076, Espoo, Finland
| | - Riku Vahala
- Department of Built Environment, School of engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076, Espoo, Finland
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21
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Dang H, Chen CTA. Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment. Front Microbiol 2017; 8:1246. [PMID: 28769878 PMCID: PMC5509916 DOI: 10.3389/fmicb.2017.01246] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/20/2017] [Indexed: 11/15/2022] Open
Abstract
Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.
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Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Chen-Tung A Chen
- Department of Oceanography, National Sun Yat-sen UniversityKaohsiung, Taiwan
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22
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Rogge A, Vogts A, Voss M, Jürgens K, Jost G, Labrenz M. Success of chemolithoautotrophic SUP05 and Sulfurimonas GD17 cells in pelagic Baltic Sea redox zones is facilitated by their lifestyles as K- and r-strategists. Environ Microbiol 2017; 19:2495-2506. [PMID: 28464419 DOI: 10.1111/1462-2920.13783] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/25/2017] [Accepted: 04/25/2017] [Indexed: 11/27/2022]
Abstract
Chemolithoautotrophic sulfur-oxidizing and denitrifying Gamma- (particularly the SUP05 cluster) and Epsilonproteobacteria (predominantly Sulfurimonas subgroup GD17) are assumed to compete for substrates (electron donors and acceptors) in marine pelagic redox gradients. To elucidate their ecological niche separation we performed 34 S0 , 15 NO3- and H13 CO3- stable-isotope incubations with water samples from Baltic Sea suboxic, chemocline and sulfidic zones followed by combined phylogenetic staining and high-resolution secondary ion mass spectrometry of single cells. SUP05 cells were small-sized (0.06-0.09 µm3 ) and most abundant in low-sulfidic to suboxic zones, whereas Sulfurimonas GD17 cells were significantly larger (0.26-0.61 µm3 ) and most abundant at the chemocline and below. Together, SUP05 and GD17 cells accumulated up to 48% of the labelled substrates but calculation of cell volume-specific rates revealed that GD17 cells incorporated labelled substrates significantly faster throughout the redox zone, thereby potentially outcompeting SUP05 especially at high substrate concentrations. Thus, in synopsis with earlier described features of SUP05/GD17 we conclude that their spatially overlapping association in stratified sulfidic zones is facilitated by their different lifestyles: whereas SUP05 cells are streamlined, non-motile K-strategists adapted to low substrate concentrations, GD17 cells are motile r-strategists well adapted to fluctuating substrate and redox conditions.
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Affiliation(s)
- Andreas Rogge
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Angela Vogts
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Maren Voss
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Günter Jost
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Matthias Labrenz
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
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23
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Trimmer M, Chronopoulou PM, Maanoja ST, Upstill-Goddard RC, Kitidis V, Purdy KJ. Nitrous oxide as a function of oxygen and archaeal gene abundance in the North Pacific. Nat Commun 2016; 7:13451. [PMID: 27905393 PMCID: PMC5146275 DOI: 10.1038/ncomms13451] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 10/05/2016] [Indexed: 11/19/2022] Open
Abstract
Oceanic oxygen minimum zones are strong sources of the potent greenhouse gas N2O but its microbial source is unclear. We characterized an exponential response in N2O production to decreasing oxygen between 1 and 30 μmol O2 l−1 within and below the oxycline using 15NO2−, a relationship that held along a 550 km offshore transect in the North Pacific. Differences in the overall magnitude of N2O production were accounted for by archaeal functional gene abundance. A one-dimensional (1D) model, parameterized with our experimentally derived exponential terms, accurately reproduces N2O profiles in the top 350 m of water column and, together with a strong 45N2O signature indicated neither canonical nor nitrifier–denitrification production while statistical modelling supported production by archaea, possibly via hybrid N2O formation. Further, with just archaeal N2O production, we could balance high-resolution estimates of sea-to-air N2O exchange. Hence, a significant source of N2O, previously described as leakage from bacterial ammonium oxidation, is better described by low-oxygen archaeal production at the oxygen minimum zone's margins. Understanding the production processes behind oceanic sources of nitrous oxide (N2O), a potent greenhouse gas, is of critical importance. Here, the authors reveal an archaeal-mediated N2O production pathway in the North Pacific, which increases exponentially with decreasing oxygen.
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Affiliation(s)
- Mark Trimmer
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | | | - Susanna T Maanoja
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Robert C Upstill-Goddard
- School of Marine Science and Technology, Ridley Building, University of Newcastle, Newcastle upon, Tyne NE1 7RU, UK
| | - Vassilis Kitidis
- Plymouth Marine Laboratory, Prospect Place, West Hoe, Plymouth PL1 3DH, UK
| | - Kevin J Purdy
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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24
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Paranychianakis NV, Tsiknia M, Kalogerakis N. Pathways regulating the removal of nitrogen in planted and unplanted subsurface flow constructed wetlands. WATER RESEARCH 2016; 102:321-329. [PMID: 27379728 DOI: 10.1016/j.watres.2016.06.048] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
Single-stage constructed wetlands (CWs) are characterized by a low potential for N removal. Understanding the pathways regulating N cycling as well as their dependence on environmental variables might improve the potential of CWs for N removal and results in more accurate simulation tools. In this study we employed qPCR targeting marker functional genes (amoA, nirK, nirS, clade I and II nosZ) or microorganisms (anammox) regulating key pathways of N cycling to unravel their relative importance. Furthermore, the influence of plant species on treatment performance was studied. Our findings indicated nitrification-denitrification as the principal route of N removal in CWs, while anammox did not have a strong contribution. Evidence was also arisen that ammonia oxidizing archaea (AOA) contributed on NH3 oxidation. Overall, plant species had a weak effect on the abundance of N functional genes (amoA of AOA), but it strongly affected the performance of CWs in terms of N removal in the following order: unplanted < Phragmites communis < Typha latifolia. These findings suggest that plant species stimulate N removal by upregulating the rates that the responsible biochemical pathways operate, probably by increasing O2 supply. In addition, our study revealed differences in indicators linked to N2O emissions. The abundance of clade II nosZ genes remained low across the season scaling down a strong contribution in the reduction of the emitted N2O. The increasing ratios of nosZ/Σnir and nirS/nirK with the progress of season indicate a shift in the composition of denitrifiers towards strains with a lower genetic potential for N2O release. Similar trends were observed among the treatments but the mechanisms differed. The planted treatments stimulated an increase in the ΣnosZ/Σnir ratio, while the unplanted an increase in the nirS/nirK ratio.
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Affiliation(s)
- Nikolaos V Paranychianakis
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis, 73100, Chania, Greece.
| | - Myrto Tsiknia
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis, 73100, Chania, Greece
| | - Nicolas Kalogerakis
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis, 73100, Chania, Greece
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25
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Marchant HK, Mohr W, Kuypers MM. Recent advances in marine N-cycle studies using 15N labeling methods. Curr Opin Biotechnol 2016; 41:53-59. [PMID: 27218834 DOI: 10.1016/j.copbio.2016.04.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/01/2016] [Accepted: 04/18/2016] [Indexed: 01/01/2023]
Abstract
15N enriched compounds such as ammonium and nitrate, as well as 15-15N2 gas are invaluable tools in marine N-cycle research. 15N stable isotope approaches allow researchers to delve into the often complex world of N-transformations and trace microbially mediated processes such as nitrification, denitrification, anammox and N-fixation. While 15N stable isotope approaches are well established, experimental approaches which take advantage of them are constantly evolving. Here we summarize recent advances in methodology, including in the direct application of 15N stable isotopes themselves, improved experimental design and the use of 15N stable isotopes in single cell studies. Furthermore, we discuss how these advances have led to new insights into marine N-cycling, particularly in the fields of nitrification and N-fixation.
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Affiliation(s)
| | - Wiebke Mohr
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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26
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Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota. ISME JOURNAL 2016; 10:1836-45. [PMID: 26882267 DOI: 10.1038/ismej.2016.2] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 12/14/2015] [Accepted: 12/24/2015] [Indexed: 11/08/2022]
Abstract
Chemolithotrophic ammonia-oxidizing bacteria and Thaumarchaeota are central players in the global nitrogen cycle. Obligate ammonia chemolithotrophy has been characterized for bacteria; however, large gaps remain in the Thaumarchaeotal pathway. Using batch growth experiments and instantaneous microrespirometry measurements of resting biomass, we show that the terrestrial Thaumarchaeon Nitrososphaera viennensis EN76(T) exhibits tight control over production and consumption of nitric oxide (NO) during ammonia catabolism, unlike the ammonia-oxidizing bacterium Nitrosospira multiformis ATCC 25196(T). In particular, pulses of hydroxylamine into a microelectrode chamber as the sole substrate for N. viennensis resulted in iterative production and consumption of NO followed by conversion of hydroxylamine to nitrite. In support of these observations, oxidation of ammonia in growing cultures of N. viennensis, but not of N. multiformis, was inhibited by the NO-scavenger PTIO. When based on the marginal nitrous oxide (N2O) levels detected in cell-free media controls, the higher levels produced by N. multiformis were explained by enzyme activity, whereas N2O in N. viennensis cultures was attributed to abiotic reactions of released N-oxide intermediates with media components. Our results are conceptualized in a pathway for ammonia-dependent chemolithotrophy in Thaumarchaea, which identifies NO as an essential intermediate in the pathway and implements known biochemistry to be executed by a proposed but still elusive copper enzyme. Taken together, this work identifies differences in ammonia-dependent chemolithotrophy between bacteria and the Thaumarchaeota, advances a central catabolic role of NO only in the Thaumarchaeotal pathway and reveals stark differences in how the two microbial cohorts contribute to N2O emissions.
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27
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Berg C, Listmann L, Vandieken V, Vogts A, Jürgens K. Chemoautotrophic growth of ammonia-oxidizing Thaumarchaeota enriched from a pelagic redox gradient in the Baltic Sea. Front Microbiol 2015; 5:786. [PMID: 25642221 PMCID: PMC4295551 DOI: 10.3389/fmicb.2014.00786] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/21/2014] [Indexed: 11/15/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are an important component of the planktonic community in aquatic habitats, linking nitrogen and carbon cycles through nitrification and carbon fixation. Therefore, measurements of these processes in culture-based experiments can provide insights into their contributions to energy conservation and biomass production by specific AOA. In this study, by enriching AOA from a brackish, oxygen-depleted water-column in the Landsort Deep, central Baltic Sea, we were able to investigate ammonium oxidation, chemoautotrophy, and growth in seawater batch experiments. The highly enriched culture consisted of up to 97% archaea, with maximal archaeal numbers of 2.9 × 107 cells mL−1. Phylogenetic analysis of the 16S rRNA and ammonia monooxygenase subunit A (amoA) gene sequences revealed an affiliation with assemblages from low-salinity and freshwater habitats, with Candidatus Nitrosoarchaeum limnia as the closest relative. Growth correlated significantly with nitrite production, ammonium consumption, and CO2 fixation, which occurred at a ratio of 10 atoms N oxidized per 1 atom C fixed. According to the carbon balance, AOA biomass production can be entirely explained by chemoautotrophy. The cellular carbon content was estimated to be 9 fg C per cell. Single-cell-based 13C and 15N labeling experiments and analysis by nano-scale secondary ion mass spectrometry provided further evidence that cellular carbon was derived from bicarbonate and that ammonium was taken up by the cells. Our study therefore revealed that growth by an AOA belonging to the genus Nitrosoarchaeum can be sustained largely by chemoautotrophy.
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Affiliation(s)
- Carlo Berg
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW) Rostock, Germany
| | - Luisa Listmann
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW) Rostock, Germany
| | - Verona Vandieken
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW) Rostock, Germany ; Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg Oldenburg, Germany
| | - Angela Vogts
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW) Rostock, Germany
| | - Klaus Jürgens
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW) Rostock, Germany
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