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Wu M, Liu X, Engelberts JP, Tyson GW, McIlroy SJ, Guo J. Anaerobic oxidation of ammonium and short-chain gaseous alkanes coupled to nitrate reduction by a bacterial consortium. THE ISME JOURNAL 2024; 18:wrae063. [PMID: 38624180 PMCID: PMC11090206 DOI: 10.1093/ismejo/wrae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/01/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
The bacterial species "Candidatus Alkanivorans nitratireducens" was recently demonstrated to mediate nitrate-dependent anaerobic oxidation of short-chain gaseous alkanes (SCGAs). In previous bioreactor enrichment studies, the species appeared to reduce nitrate in two phases, switching from denitrification to dissimilatory nitrate reduction to ammonium (DNRA) in response to nitrite accumulation. The regulation of this switch or the nature of potential syntrophic partnerships with other microorganisms remains unclear. Here, we describe anaerobic multispecies cultures of bacteria that couple the oxidation of propane and butane to nitrate reduction and the oxidation of ammonium (anammox). Batch tests with 15N-isotope labelling and multi-omic analyses collectively supported a syntrophic partnership between "Ca. A. nitratireducens" and anammox bacteria, with the former species mediating nitrate-driven oxidation of SCGAs, supplying the latter with nitrite for the oxidation of ammonium. The elimination of nitrite accumulation by the anammox substantially increased SCGA and nitrate consumption rates, whereas it suppressed DNRA. Removing ammonium supply led to its eventual production, the accumulation of nitrite, and the upregulation of DNRA gene expression for the abundant "Ca. A. nitratireducens". Increasing the supply of SCGA had a similar effect in promoting DNRA. Our results suggest that "Ca. A. nitratireducens" switches to DNRA to alleviate oxidative stress caused by nitrite accumulation, giving further insight into adaptability and ecology of this microorganism. Our findings also have important implications for the understanding of the fate of nitrogen and SCGAs in anaerobic environments.
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Affiliation(s)
- Mengxiong Wu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St Lucia, QLD 4072, Australia
| | - Xiawei Liu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St Lucia, QLD 4072, Australia
| | - J Pamela Engelberts
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St Lucia, QLD 4072, Australia
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2
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Lin Z, Ma K, Yang Y. Nitrous Oxide Emission from Full-Scale Anammox-Driven Wastewater Treatment Systems. LIFE (BASEL, SWITZERLAND) 2022; 12:life12070971. [PMID: 35888061 PMCID: PMC9317218 DOI: 10.3390/life12070971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/16/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022]
Abstract
Wastewater treatment plants (WWTPs) are important contributors to global greenhouse gas (GHG) emissions, partly due to their huge emission of nitrous oxide (N2O), which has a global warming potential of 298 CO2 equivalents. Anaerobic ammonium-oxidizing (anammox) bacteria provide a shortcut in the nitrogen removal pathway by directly transforming ammonium and nitrite to nitrogen gas (N2). Due to its energy efficiency, the anammox-driven treatment has been applied worldwide for the removal of inorganic nitrogen from ammonium-rich wastewater. Although direct evidence of the metabolic production of N2O by anammox bacteria is lacking, the microorganisms coexisting in anammox-driven WWTPs could produce a considerable amount of N2O and hence affect the sustainability of wastewater treatment. Thus, N2O emission is still one of the downsides of anammox-driven wastewater treatment, and efforts are required to understand the mechanisms of N2O emission from anammox-driven WWTPs using different nitrogen removal strategies and develop effective mitigation strategies. Here, three main N2O production processes, namely, hydroxylamine oxidation, nitrifier denitrification, and heterotrophic denitrification, and the unique N2O consumption process termed nosZ-dominated N2O degradation, occurring in anammox-driven wastewater treatment systems, are summarized and discussed. The key factors influencing N2O emission and mitigation strategies are discussed in detail, and areas in which further research is urgently required are identified.
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A Reduced F 420-Dependent Nitrite Reductase in an Anaerobic Methanotrophic Archaeon. J Bacteriol 2022; 204:e0007822. [PMID: 35695516 PMCID: PMC9295563 DOI: 10.1128/jb.00078-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic methanotrophic archaea (ANME), which oxidize methane in marine sediments through syntrophic associations with sulfate-reducing bacteria, carry homologs of coenzyme F420-dependent sulfite reductase (Fsr) of Methanocaldococcus jannaschii, a hyperthermophilic methanogen from deep-sea hydrothermal vents. M. jannaschii Fsr (MjFsr) and ANME-Fsr belong to two phylogenetically distinct groups, FsrI and FsrII, respectively. MjFsrI reduces sulfite to sulfide with reduced F420 (F420H2), protecting methyl coenzyme M reductase (Mcr), an essential enzyme for methanogens, from sulfite inhibition. However, the function of FsrIIs in ANME, which also rely on Mcr and live in sulfidic environments, is unknown. We have determined the catalytic properties of FsrII from a member of ANME-2c. Since ANME remain to be isolated, we expressed ANME2c-FsrII in a closely related methanogen, Methanosarcina acetivorans. Purified recombinant FsrII contained siroheme, indicating that the methanogen, which lacks a native sulfite reductase, produced this coenzyme. Unexpectedly, FsrII could not reduce sulfite or thiosulfate with F420H2. Instead, it acted as an F420H2-dependent nitrite reductase (FNiR) with physiologically relevant Km values (nitrite, 5 μM; F420H2, 14 μM). From kinetic, thermodynamic, and structural analyses, we hypothesize that in FNiR, F420H2-derived electrons are delivered at the oxyanion reduction site at a redox potential that is suitable for reducing nitrite (E0' [standard potential], +440 mV) but not sulfite (E0', -116 mV). These findings and the known nitrite sensitivity of Mcr suggest that FNiR may protect nondenitrifying ANME from nitrite toxicity. Remarkably, by reorganizing the reductant processing system, Fsr transforms two analogous oxyanions in two distinct archaeal lineages with different physiologies and ecologies. IMPORTANCE Coenzyme F420-dependent sulfite reductase (Fsr) protects methanogenic archaea inhabiting deep-sea hydrothermal vents from the inactivation of methyl coenzyme M reductase (Mcr), one of their essential energy production enzymes. Anaerobic methanotrophic archaea (ANME) that oxidize methane and rely on Mcr, carry Fsr homologs that form a distinct clade. We show that a member of this clade from ANME-2c functions as F420-dependent nitrite reductase (FNiR) and lacks Fsr activity. This specialization arose from a distinct feature of the reductant processing system and not the substrate recognition element. We hypothesize FNiR may protect ANME Mcr from inactivation by nitrite. This is an example of functional specialization within a protein family that is induced by changes in electron transfer modules to fit an ecological need.
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Liu L, Lv AP, Narsing Rao MP, Ming YZ, Salam N, Li MM, Liu ZT, Zhang XT, Zhang JY, Xian WD, Jiao JY, Li WJ. Diversity and Distribution of Anaerobic Ammonium Oxidation Bacteria in Hot Springs of Conghua, China. Front Microbiol 2022; 12:739234. [PMID: 35145488 PMCID: PMC8822059 DOI: 10.3389/fmicb.2021.739234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Anaerobic ammonium oxidation (anammox) is an important process of the nitrogen cycle, and the anammox bacteria have been studied in a wide variety of environments. However, the distribution, diversity, and abundance of anammox bacteria in hot springs remain enigmatic. In this study, the anammox process was firstly investigated in hot springs of Conghua, China. Anammox-like bacterial sequences that closely affiliated to “Candidatus Brocadia,” “Candidatus Kuenenia,” “Candidatus Scalindua,” “Candidatus Anammoxoglobus,” and “Candidatus Jettenia” were detected. Several operational taxonomic units (OTUs) from this study shared low sequence identities to the 16S rRNA gene of the known anammox bacteria, suggesting that they might be representing putative novel anammox bacteria. A quantitative PCR analysis of anammox-specific 16S rRNA gene confirmed that the abundance of anammox bacteria ranged from 1.60 × 104 to 1.20 × 107 copies L–1. Nitrate was a key environmental factor defining the geographical distribution of the anammox bacterial community in the hot spring ecosystem. Dissolved inorganic carbon had a significant influence on anammox bacterial biodiversity. Our findings for the first time revealed that the diverse anammox bacteria, including putative novel anammox bacterial candidates, were present in Conghua hot spring, which extended the existence of anammox bacteria to the hot springs in China and expands our knowledge of the biogeography of anammox bacteria. This work filled up the research lacuna of anammox bacteria in Chinese hot spring habitat and would guide for enrichment strategies of anammox bacteria of Conghua hot springs.
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Affiliation(s)
- Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yu-Zhen Ming
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ze-Tao Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiao-Tong Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jing-Yi Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Jian-Yu Jiao,
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- *Correspondence: Wen-Jun Li,
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Akram M, Dietl A, Müller M, Barends TRM. Purification of the key enzyme complexes of the anammox pathway from DEMON sludge. Biopolymers 2021; 112:e23428. [PMID: 33798263 DOI: 10.1002/bip.23428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
Anaerobic Ammonium Oxidation ("anammox") is a bacterial process in which nitrite and ammonium are converted into nitrogen gas and water, yielding energy for the cell. Anammox is an important branch of the global biological nitrogen cycle, being responsible for up to 50% of the yearly nitrogen removal from the oceans. Strikingly, the anammox process uniquely relies on the extremely reactive and toxic compound hydrazine as a free intermediate. Given its global importance and biochemical novelty, there is considerable interest in the enzymes at the heart of the anammox pathway. Unfortunately, obtaining these enzymes in sufficiently large amounts for biochemical and structural studies is problematic, given the slow growth of pure cultures of anammox bacteria when high cell densities are required. However, the anammox process is being applied in wastewater treatment to remove nitrogenous waste in processes like DEamMONification (DEMON). In plants using such processes, which rely on a combination of aerobic ammonia-oxidizers and anammox organisms, kilogram amounts of anammox bacteria-containing sludge are readily available. Here, we report a protein isolation protocol starting from anammox cells present in DEMON sludge from a wastewater treatment plan that readily yields pure preparations of key anammox proteins in the tens of milligrams, including hydrazine synthase HZS and hydrazine dehydrogenase (HDH), as well as hydroxylamine oxidoreductase (HAO). HDH and HAO were active and of sufficient quality for biochemical studies and for HAO, the crystal structure could be determined. The method presented here provides a viable way to obtain materials for the study of proteins not only from the central anammox metabolism but also for the study of other exciting aspects of anammox bacteria, such as for example, their unusual ladderane lipids.
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Affiliation(s)
- Mohd Akram
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Andreas Dietl
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Melanie Müller
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thomas R M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
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6
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Unique Solid Phase Microextraction Sampler Reveals Distinctive Biogeochemical Profiles among Various Deep-Sea Hydrothermal Vents. Sci Rep 2020; 10:1360. [PMID: 31992838 PMCID: PMC6987176 DOI: 10.1038/s41598-020-58418-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 12/20/2019] [Indexed: 11/08/2022] Open
Abstract
Current methods for biochemical and biogeochemical analysis of the deep-sea hydrothermal vent ecosystems rely on water sample recovery, or in situ analysis using underwater instruments with limited range of analyte detection and limited sensitivity. Even in cases where large quantities of sample are recovered, labile dissolved organic compounds may not be detected due to time delays between sampling and preservation. Here, we present a novel approach for in situ extraction of organic compounds from hydrothermal vent fluids through a unique solid phase microextraction (SPME) sampler. These samplers were deployed to sample effluent of vents on sulphide chimneys, located on Axial Seamount in the North-East Pacific, in the Urashima field on the southern Mariana back-arc, and at the Hafa Adai site in the central Mariana back-arc. Among the compounds that were extracted, a wide range of unique organic compounds, including labile dissolved organic sulfur compounds, were detected through high-resolution LC-MS/MS, among which were biomarkers of anammox bacteria, fungi, and lower animals. This report is the first to show that SPME can contribute to a broader understanding of deep sea ecology and biogeochemical cycles in hydrothermal vent ecosystems.
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7
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Wang Y, Xu L, Wang S, Ye F, Zhu G. Global Distribution of Anaerobic Ammonia Oxidation (Anammox) Bacteria - Field Surveys in Wetland, Dryland, Groundwater Aquifer and Snow. Front Microbiol 2019; 10:2583. [PMID: 31798550 PMCID: PMC6861858 DOI: 10.3389/fmicb.2019.02583] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/24/2019] [Indexed: 11/26/2022] Open
Abstract
The discovery of anaerobic ammonia oxidation (anammox) expanded our knowledge on the microbial nitrogen cycle. Previous studies report that anammox bacteria are distributed in a wide range of habitats and plays significant roles in the global nitrogen cycle. However, most studies focus only on individual ecosystems or datasets from public databases. To date, our understanding of how anammox bacteria respond to environmental properties and are distributed in different habitats on a global scale, remain unclear. To explore the global distribution of anammox bacteria, samples were collected from different habitats at different locations globally, including wetlands, drylands, groundwater aquifers and snow from 10 countries across six continents. We then used high-throughput amplicon sequencing targeting the functional gene hydrazine synthase (HZS) and generated community profiles. Results showed that Candidatus Brocadia is detected as the dominant genus on a global scale, accounting for 80.0% to 99.9% of the retrieved sequences in different habitats. The Jettenia-like sequences were the second most abundant group, accounting for no more than 19.9% of the retrieved sequences in all sites. The samples in drylands, wetlands and groundwater aquifers showed similar community composition and diversity, with the snow samples being the most different. Deterministic processes seem stronger in regulating the community composition of anammox bacteria, which is supported by the higher proportion explained by local-scale factors. Groundwater aquifers showed high gene abundance and the most complex co-occurrence network among the four habitat types, suggesting that it might be the preferred habitat of anammox bacteria. There is little competition between anammox bacterial species based on co-occurrence analysis. Hence, we could infer that environmental factors such as anaerobic and stable conditions, instead of substrate limitations, may be vital factors determining the anammox bacteria community. These results provide a better understanding of the global distribution of anammox bacteria and the ecological factors that affect their community structuring in diverse habitats.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Guangzhou University, Guangzhou, China
| | - Liya Xu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Guangzhou University, Guangzhou, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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8
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Xia X, Li Z, Zhang S, Zhang L, Zhang L, Wang G. Occurrence of anammox on suspended sediment (SPS) in oxic river water: Effect of the SPS particle size. CHEMOSPHERE 2019; 235:40-48. [PMID: 31255764 DOI: 10.1016/j.chemosphere.2019.06.161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/05/2019] [Accepted: 06/21/2019] [Indexed: 06/09/2023]
Abstract
Anammox is a newly discovered nitrogen transformation process. However, its role in nitrogen removal in fresh water is far from understood. Here, we hypothesized that anammox could occur on suspended sediment in oxic river water. To test this hypothesis, simulation experiments with a nitrogen stable (15N) isotopic tracer technique were conducted to study the occurrence of anammox on suspended sediment (SPS) in oxic river water, and the effects of the SPS particle size, including <20 μm, 20-63 μm, 63-100 μm, 100-200 μm, and <200 μm (original SPS) size fractions, were investigated. The results showed that anammox occurred in oxic water with SPS due to the existence of low oxygen microsites around/on SPS, and the anammox rate was even higher than the denitrification rate. The anammox rate increased with the SPS concentration, and it was negatively correlated with the particle size and was positively correlated with the organic carbon content of SPS (p < 0.05). The 29N2 produced by anammox in a system containing 1.0 g L-1 SPS with a particle size below 20 μm was 0.27 mg-N/m3·d, which was 5.3 times higher than that produced with a particle size of 100-200 μm. The anammox rate was significantly positively correlated with the anammox bacterial abundance (p < 0.01), and Ca. Brocadia was the dominant species. This study suggests that the SPS in oxic water may be a 'hotspot' for the anammox process and that its role in nitrogen removal should be considered in future studies.
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Affiliation(s)
- Xinghui Xia
- School of Environment, Beijing Normal University / State Key Joint Laboratory of Environmental Simulation and Pollution Control / Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing, 100875, China.
| | - Zhihuang Li
- School of Environment, Beijing Normal University / State Key Joint Laboratory of Environmental Simulation and Pollution Control / Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing, 100875, China
| | - Sibo Zhang
- School of Environment, Beijing Normal University / State Key Joint Laboratory of Environmental Simulation and Pollution Control / Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing, 100875, China
| | - Liwei Zhang
- School of Environment, Beijing Normal University / State Key Joint Laboratory of Environmental Simulation and Pollution Control / Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing, 100875, China
| | - Ling Zhang
- School of Environment, Beijing Normal University / State Key Joint Laboratory of Environmental Simulation and Pollution Control / Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing, 100875, China
| | - Gongqin Wang
- School of Environment, Beijing Normal University / State Key Joint Laboratory of Environmental Simulation and Pollution Control / Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing, 100875, China
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9
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Aguzzi J, Chatzievangelou D, Marini S, Fanelli E, Danovaro R, Flögel S, Lebris N, Juanes F, De Leo FC, Del Rio J, Thomsen L, Costa C, Riccobene G, Tamburini C, Lefevre D, Gojak C, Poulain PM, Favali P, Griffa A, Purser A, Cline D, Edgington D, Navarro J, Stefanni S, D'Hondt S, Priede IG, Rountree R, Company JB. New High-Tech Flexible Networks for the Monitoring of Deep-Sea Ecosystems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:6616-6631. [PMID: 31074981 DOI: 10.1021/acs.est.9b00409] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Increasing interest in the acquisition of biotic and abiotic resources from within the deep sea (e.g., fisheries, oil-gas extraction, and mining) urgently imposes the development of novel monitoring technologies, beyond the traditional vessel-assisted, time-consuming, high-cost sampling surveys. The implementation of permanent networks of seabed and water-column-cabled (fixed) and docked mobile platforms is presently enforced, to cooperatively measure biological features and environmental (physicochemical) parameters. Video and acoustic (i.e., optoacoustic) imaging are becoming central approaches for studying benthic fauna (e.g., quantifying species presence, behavior, and trophic interactions) in a remote, continuous, and prolonged fashion. Imaging is also being complemented by in situ environmental-DNA sequencing technologies, allowing the traceability of a wide range of organisms (including prokaryotes) beyond the reach of optoacoustic tools. Here, we describe the different fixed and mobile platforms of those benthic and pelagic monitoring networks, proposing at the same time an innovative roadmap for the automated computing of hierarchical ecological information on deep-sea ecosystems (i.e., from single species' abundance and life traits to community composition, and overall biodiversity).
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Affiliation(s)
- Jacopo Aguzzi
- Instituto de Ciencias del Mar (ICM-CSIC) , Paseo Marítimo de la Barceloneta, 37-49 , 08012 Barcelona , Spain
| | | | - Simone Marini
- Institute of Marine Sciences , National Research Council of Italy (CNR) , 19036 La Spezia , Italy
| | - Emanuela Fanelli
- Department of Life and Environmental Sciences , Polytechnic University of Marche , 60121 Ancona , Italy
| | - Roberto Danovaro
- Department of Life and Environmental Sciences , Polytechnic University of Marche , 60121 Ancona , Italy
- Stazione Zoologica Anton Dohrn (SZN) , 80121 Naples , Italy
| | | | - Nadine Lebris
- Oceanological Observatory , CNRS LECOB, Sorbonne University , 66650 Banyuls-sur-mer , France
| | - Francis Juanes
- Department of Biology , University of Victoria , Victoria , British Columbia V8W 2Y2 , Canada
| | - Fabio C De Leo
- Department of Biology , University of Victoria , Victoria , British Columbia V8W 2Y2 , Canada
- Ocean Networks Canada (ONC) , University of Victoria , Victoria , British Columbia V8N 1V8 , Canada
| | - Joaquin Del Rio
- OBSEA, SARTI , Universitat Politècnica de Catalunya (UPC) , 08800 Barcelona , Spain
| | | | - Corrado Costa
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA-IT) , 00198 Monterotondo , Italy
| | - Giorgio Riccobene
- Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali del Sud , 95125 Catania , Italy
| | - Cristian Tamburini
- Institut Méditerranéen d'Océanoloie (MIO) , 13288 Cedex 09 Marseille , France
| | - Dominique Lefevre
- Institut Méditerranéen d'Océanoloie (MIO) , 13288 Cedex 09 Marseille , France
| | - Carl Gojak
- DT INSU , 83507 La Seyne-sur-Mer , France
| | - Pierre-Marie Poulain
- Istituto Nazionale di Oceanografia e Geofisica Sperimentale (OGS) , 34010 Trieste , Italy
| | - Paolo Favali
- Istituto Nazionale di Geofisica e Vulcanologia (INGV) , 00143 Rome , Italy
- European Multidisciplinary Seafloor and Water-Column Observatory European Research Infrastructure Consortium (EMSO ERIC) , 00143 Rome , Italy
| | - Annalisa Griffa
- Institute of Marine Sciences , National Research Council of Italy (CNR) , 19036 La Spezia , Italy
| | - Autun Purser
- Alfred Wegener Institute (AWI) . 27515 Bremerhaven , Germany
| | - Danelle Cline
- Monterey Bay Aquarium Research Institute (MBARI) , Moss Landing , California 95039 , United States
| | - Duane Edgington
- Monterey Bay Aquarium Research Institute (MBARI) , Moss Landing , California 95039 , United States
| | - Joan Navarro
- Instituto de Ciencias del Mar (ICM-CSIC) , Paseo Marítimo de la Barceloneta, 37-49 , 08012 Barcelona , Spain
| | | | - Steve D'Hondt
- Graduate School of Oceanography , University of Rhode Island , Narragansett , Rhode Island 02882 , United States
| | - Imants G Priede
- University of Aberdeen , Aberdeen AB24 3FX , United Kingdom
- Hellenic Centre for Marine Research , 71003 Heraklion Crete , Greece
| | - Rodney Rountree
- Department of Biology , University of Victoria , Victoria , British Columbia V8W 2Y2 , Canada
- The Fish Listener , 23 Joshua Lane , Waquoit , Massachusetts 02536 , United States
| | - Joan B Company
- Instituto de Ciencias del Mar (ICM-CSIC) , Paseo Marítimo de la Barceloneta, 37-49 , 08012 Barcelona , Spain
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10
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Zhou Z, Wei Q, Yang Y, Li M, Gu JD. Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples. Appl Microbiol Biotechnol 2018; 102:5859-5871. [PMID: 29802476 DOI: 10.1007/s00253-018-9078-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/05/2018] [Accepted: 05/07/2018] [Indexed: 01/21/2023]
Abstract
Research on anammox (anaerobic ammonium oxidizing) bacteria is important due to their biogeochemical and industrial application significance since the first discovery made over two decades ago. By coupling NH4+ and NO2- biochemically to form N2 gas, anammox bacteria contribute significantly to global marine and terrestrial nitrogen balance (responsible for 50, 9~40, and 4~37% of the nitrogen loss for marine, lakes, and paddy soil) and are also useful in energy-conserving nitrogen removal in wastewater treatment. PCR-based detection and quantification of anammox bacteria are an easy, essential, and widely accessible technique used ubiquitously for studying them in many environmental niches. In this article, we make a summary on practical applications of 16S rRNA and functional gene PCR primers, including hydrazine dehydrogenase (Hzo), nitrite reductase (NirS), hydrazine synthase (Hzs), and cytochrome c biogenesis proteins (Ccs) in detection of them. PCR primer performances in both practical applications and tests in silico are also presented for comparison. For detecting general and specific anammox bacterial groups, selection of appropriate PCR primers for different environmental samples and practical application guidance on choice of appropriate primer pairs for different purposes are also offered. This article provides practical information on selection and application of PCR technique in detection of anammox bacteria from the diverse environments to further promote convenient applications of this technique in research and other purposes.
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Affiliation(s)
- Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China
| | - Qiaoyan Wei
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China.
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR, People's Republic of China.
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11
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Gonzalez-Martinez A, Muñoz-Palazon B, Rodriguez-Sanchez A, Gonzalez-Lopez J. New concepts in anammox processes for wastewater nitrogen removal: recent advances and future prospects. FEMS Microbiol Lett 2018; 365:4847881. [DOI: 10.1093/femsle/fny031] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/07/2018] [Indexed: 01/26/2023] Open
Affiliation(s)
| | - Barbara Muñoz-Palazon
- Institute of Water Research, University of Granada, C/Ramon y Cajal, 4, 18071 Granada, Spain
| | | | - Jesus Gonzalez-Lopez
- Institute of Water Research, University of Granada, C/Ramon y Cajal, 4, 18071 Granada, Spain
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12
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Yu T, Li M, Niu M, Fan X, Liang W, Wang F. Difference of nitrogen-cycling microbes between shallow bay and deep-sea sediments in the South China Sea. Appl Microbiol Biotechnol 2017; 102:447-459. [DOI: 10.1007/s00253-017-8594-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 11/29/2022]
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13
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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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14
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Rasigraf O, Schmitt J, Jetten MSM, Lüke C. Metagenomic potential for and diversity of N-cycle driving microorganisms in the Bothnian Sea sediment. Microbiologyopen 2017; 6. [PMID: 28544522 PMCID: PMC5552932 DOI: 10.1002/mbo3.475] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 02/13/2017] [Accepted: 02/22/2017] [Indexed: 11/10/2022] Open
Abstract
The biological nitrogen cycle is driven by a plethora of reactions transforming nitrogen compounds between various redox states. Here, we investigated the metagenomic potential for nitrogen cycle of the in situ microbial community in an oligotrophic, brackish environment of the Bothnian Sea sediment. Total DNA from three sediment depths was isolated and sequenced. The characterization of the total community was performed based on 16S rRNA gene inventory using SILVA database as reference. The diversity of diagnostic functional genes coding for nitrate reductases (napA;narG), nitrite:nitrate oxidoreductase (nxrA), nitrite reductases (nirK;nirS;nrfA), nitric oxide reductase (nor), nitrous oxide reductase (nosZ), hydrazine synthase (hzsA), ammonia monooxygenase (amoA), hydroxylamine oxidoreductase (hao), and nitrogenase (nifH) was analyzed by blastx against curated reference databases. In addition, Polymerase chain reaction (PCR)‐based amplification was performed on the hzsA gene of anammox bacteria. Our results reveal high genomic potential for full denitrification to N2, but minor importance of anaerobic ammonium oxidation and dissimilatory nitrite reduction to ammonium. Genomic potential for aerobic ammonia oxidation was dominated by Thaumarchaeota. A higher diversity of anammox bacteria was detected in metagenomes than with PCR‐based technique. The results reveal the importance of various N‐cycle driving processes and highlight the advantage of metagenomics in detection of novel microbial key players.
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Affiliation(s)
- Olivia Rasigraf
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Julia Schmitt
- DVGW-Forschungsstelle TUHH, Hamburg University of Technology, Hamburg, Germany
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
| | - Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
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15
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Tan CH, Lee KWK, Burmølle M, Kjelleberg S, Rice SA. All together now: experimental multispecies biofilm model systems. Environ Microbiol 2017; 19:42-53. [DOI: 10.1111/1462-2920.13594] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Chuan Hao Tan
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
| | - Kai Wei Kelvin Lee
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
| | - Mette Burmølle
- Section of Microbiology, Department of BiologyUniversity of CopenhagenCopenhagen Denmark
| | - Staffan Kjelleberg
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
- The School of Biological SciencesNanyang Technological University Singapore
| | - Scott A. Rice
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
- The School of Biological SciencesNanyang Technological University Singapore
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16
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Xia X, Jia Z, Liu T, Zhang S, Zhang L. Coupled Nitrification-Denitrification Caused by Suspended Sediment (SPS) in Rivers: Importance of SPS Size and Composition. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:212-221. [PMID: 27966357 DOI: 10.1021/acs.est.6b03886] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Suspended sediment (SPS) is ubiquitous in rivers, and SPS with different particle sizes and compositions may affect coupled nitrification-denitrification (CND) occurring on SPS significantly. However, there is no related research report. In this work, 15N isotope tracer technique was adopted to explore the CND in systems containing SPS (8 g L-1 and 1 g L-1) collected from the Yellow River with various particle sizes, including <2, 2-20, 20-50, 50-100, and 100-200 μm. The results showed that the CND occurred on SPS and the CND rate was negatively related to particle size; both nitrification and denitrification rate constants increased with decreasing SPS particle size. For instance, SPS (8 g L-1) with a particle size below 2 μm had the highest 15N2 emission rate of 1.15 mg-N/(m3·d), which was 2.9 times that of 100-200 μm. This is because SPS with a smaller particle size had a larger specific surface area and a higher organic carbon content, which is beneficial for bacteria growth. Both the nitrifying and denitrifying bacteria population were positively correlated with CND rate (p < 0.05). Different from the 15N2 production, 15N2O emission rate did not decrease with increasing SPS particle size. For the system containing 8 g L-1 SPS, 15N2O emission rate reached the highest of 1.05 μg-N/(m3·d) in the 50-100 μm SPS system, which was 17.5 times that of 100-200 μm. Similar results could be found from the system with 1 g L-1 SPS. This is due to the fact that the oxygen concentration at the SPS-water interface increased with SPS particle size, and the oxygen conditions might be most suitable for the production of N2O in the 50-100 μm system. This study suggests that SPS size and composition play an important role in nitrogen cycle of river systems, especially for the production of N2O.
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Affiliation(s)
- Xinghui Xia
- School of Environment, Beijing Normal University , State Key Laboratory of Water Environment Simulation/Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing 100875, China
| | - Zhimei Jia
- School of Environment, Beijing Normal University , State Key Laboratory of Water Environment Simulation/Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing 100875, China
| | - Ting Liu
- School of Environment, Beijing Normal University , State Key Laboratory of Water Environment Simulation/Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing 100875, China
| | - Sibo Zhang
- School of Environment, Beijing Normal University , State Key Laboratory of Water Environment Simulation/Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing 100875, China
| | - Liwei Zhang
- School of Environment, Beijing Normal University , State Key Laboratory of Water Environment Simulation/Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing 100875, China
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17
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Lipsewers YA, Hopmans EC, Meysman FJR, Sinninghe Damsté JS, Villanueva L. Abundance and Diversity of Denitrifying and Anammox Bacteria in Seasonally Hypoxic and Sulfidic Sediments of the Saline Lake Grevelingen. Front Microbiol 2016; 7:1661. [PMID: 27812355 PMCID: PMC5071380 DOI: 10.3389/fmicb.2016.01661] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/05/2016] [Indexed: 11/13/2022] Open
Abstract
Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox, and sulfide-dependent denitrifying bacteria in the sediments of the seasonally hypoxic saline Lake Grevelingen, known to harbor an active microbial community involved in sulfur oxidation pathways. Depth distributions of 16S rRNA gene, nirS gene of denitrifying and anammox bacteria, aprA gene of sulfur-oxidizing and sulfate-reducing bacteria, and ladderane lipids of anammox bacteria were studied in sediments impacted by seasonally hypoxic bottom waters. Samples were collected down to 5 cm depth (1 cm resolution) at three different locations before (March) and during summer hypoxia (August). The abundance of denitrifying bacteria did not vary despite of differences in oxygen and sulfide availability in the sediments, whereas anammox bacteria were more abundant in the summer hypoxia but in those sediments with lower sulfide concentrations. The potential activity of denitrifying and anammox bacteria as well as of sulfur-oxidizing, including sulfide-dependent denitrifiers and sulfate-reducing bacteria, was potentially inhibited by the competition for nitrate and nitrite with cable and/or Beggiatoa-like bacteria in March and by the accumulation of sulfide in the summer hypoxia. The simultaneous presence and activity of organoheterotrophic denitrifying bacteria, sulfide-dependent denitrifiers, and anammox bacteria suggests a tight network of bacteria coupling carbon-, nitrogen-, and sulfur cycling in Lake Grevelingen sediments.
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Affiliation(s)
- Yvonne A Lipsewers
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University Den Burg, Netherlands
| | - Ellen C Hopmans
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University Den Burg, Netherlands
| | - Filip J R Meysman
- Department of Estuarine and Delta Systems, Royal Netherlands Institute for Sea Research, Utrecht University Den Burg, Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands; Faculty of Geosciences, Department of Earth Sciences, Utrecht UniversityUtrecht, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University Den Burg, Netherlands
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18
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Portail M, Olu K, Dubois SF, Escobar-Briones E, Gelinas Y, Menot L, Sarrazin J. Food-Web Complexity in Guaymas Basin Hydrothermal Vents and Cold Seeps. PLoS One 2016; 11:e0162263. [PMID: 27683216 PMCID: PMC5040445 DOI: 10.1371/journal.pone.0162263] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 08/20/2016] [Indexed: 11/29/2022] Open
Abstract
In the Guaymas Basin, the presence of cold seeps and hydrothermal vents in close proximity, similar sedimentary settings and comparable depths offers a unique opportunity to assess and compare the functioning of these deep-sea chemosynthetic ecosystems. The food webs of five seep and four vent assemblages were studied using stable carbon and nitrogen isotope analyses. Although the two ecosystems shared similar potential basal sources, their food webs differed: seeps relied predominantly on methanotrophy and thiotrophy via the Calvin-Benson-Bassham (CBB) cycle and vents on petroleum-derived organic matter and thiotrophy via the CBB and reductive tricarboxylic acid (rTCA) cycles. In contrast to symbiotic species, the heterotrophic fauna exhibited high trophic flexibility among assemblages, suggesting weak trophic links to the metabolic diversity of chemosynthetic primary producers. At both ecosystems, food webs did not appear to be organised through predator-prey links but rather through weak trophic relationships among co-occurring species. Examples of trophic or spatial niche differentiation highlighted the importance of species-sorting processes within chemosynthetic ecosystems. Variability in food web structure, addressed through Bayesian metrics, revealed consistent trends across ecosystems. Food-web complexity significantly decreased with increasing methane concentrations, a common proxy for the intensity of seep and vent fluid fluxes. Although high fluid-fluxes have the potential to enhance primary productivity, they generate environmental constraints that may limit microbial diversity, colonisation of consumers and the structuring role of competitive interactions, leading to an overall reduction of food-web complexity and an increase in trophic redundancy. Heterogeneity provided by foundation species was identified as an additional structuring factor. According to their biological activities, foundation species may have the potential to partly release the competitive pressure within communities of low fluid-flux habitats. Finally, ecosystem functioning in vents and seeps was highly similar despite environmental differences (e.g. physico-chemistry, dominant basal sources) suggesting that ecological niches are not specifically linked to the nature of fluids. This comparison of seep and vent functioning in the Guaymas basin thus provides further supports to the hypothesis of continuity among deep-sea chemosynthetic ecosystems.
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Affiliation(s)
- Marie Portail
- Laboratoire Environnement Profond, REM/EEP, Institut Carnot Ifremer EDROME, Centre de Bretagne, Plouzané, France
- * E-mail:
| | - Karine Olu
- Laboratoire Environnement Profond, REM/EEP, Institut Carnot Ifremer EDROME, Centre de Bretagne, Plouzané, France
| | - Stanislas F. Dubois
- Laboratoire Ecologie Benthique, DYNECO, Ifremer, Centre de Bretagne, Plouzané, France
| | - Elva Escobar-Briones
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City D.F., Mexico
| | - Yves Gelinas
- GEOTOP and Chemistry and Biochemistry Department, Concordia University, Montréal, Québec, Canada
| | - Lénaick Menot
- Laboratoire Environnement Profond, REM/EEP, Institut Carnot Ifremer EDROME, Centre de Bretagne, Plouzané, France
| | - Jozée Sarrazin
- Laboratoire Environnement Profond, REM/EEP, Institut Carnot Ifremer EDROME, Centre de Bretagne, Plouzané, France
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19
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Ribeiro H, Mucha AP, Azevedo I, Salgado P, Teixeira C, Almeida CMR, Joye SB, Magalhães C. Differential effects of crude oil on denitrification and anammox, and the impact on N2O production. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 216:391-399. [PMID: 27395442 DOI: 10.1016/j.envpol.2016.05.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 06/06/2023]
Abstract
Denitrification and anammox are key processes for reducing the external nitrogen loads delivered to coastal ecosystems, and these processes can be affected by pollutants. In this study, we investigated the effect of crude oil on denitrification and anammox. Controlled laboratory experiments were performed using sediment slurries from the Lima Estuary (NW Portugal). Anammox and denitrification rates were measured using (15)N-labeled NO3(-), and the production of (29)N2 and (30)N2 quantified by membrane inlet mass spectrometry. Results revealed that while denitrification rates were stimulated between 10 and 25 000 times after crude oil amendment, anammox activity was partially (between 2 and 5 times) or completely inhibited by the addition of crude oil when comparing to rates in unamended controls. Similar results were observed across four estuarine sediment types, despite their different physical-chemical characteristics. Moreover, N2O production was reduced by 2-36 times following crude oil addition. Further work is required to fully understand the mechanism(s) of the observed reduction in N2O production. This study represents one of the first contributions to the understanding of the impact of crude oil pollution on denitrification and anammox, with profound implications for the management of aquatic ecosystems regarding eutrophication (N-removal).
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Affiliation(s)
- Hugo Ribeiro
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal.
| | - Ana P Mucha
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Isabel Azevedo
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Paula Salgado
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas de Abel Salazar (ICBAS-UP), Universidade do Porto, Porto, Portugal
| | - Catarina Teixeira
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas de Abel Salazar (ICBAS-UP), Universidade do Porto, Porto, Portugal
| | - C Marisa R Almeida
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Catarina Magalhães
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
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20
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Oshiki M, Satoh H, Okabe S. Ecology and physiology of anaerobic ammonium oxidizing bacteria. Environ Microbiol 2016; 18:2784-96. [DOI: 10.1111/1462-2920.13134] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 11/08/2015] [Accepted: 11/13/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering National Institute of Technology Nagaoka College 888 Nishikatakaimachi Nagaoka Niigata 940‐0834 Japan
| | - Hisashi Satoh
- Division of Environmental Engineering Faculty of Engineering Hokkaido University North 13, West‐8 Sapporo Hokkaido 060‐8628 Japan
| | - Satoshi Okabe
- Division of Environmental Engineering Faculty of Engineering Hokkaido University North 13, West‐8 Sapporo Hokkaido 060‐8628 Japan
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21
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Teske A, Reysenbach AL. Editorial: Hydrothermal microbial ecosystems. Front Microbiol 2015; 6:884. [PMID: 26388842 PMCID: PMC4555087 DOI: 10.3389/fmicb.2015.00884] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/12/2015] [Indexed: 11/16/2022] Open
Affiliation(s)
- Andreas Teske
- Department of Marine Sciences, University of North Carolina Chapel Hill, NC, USA
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22
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Cao H, Zhang W, Wang Y, Qian PY. Microbial community changes along the active seepage site of one cold seep in the Red Sea. Front Microbiol 2015; 6:739. [PMID: 26284035 PMCID: PMC4523032 DOI: 10.3389/fmicb.2015.00739] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/06/2015] [Indexed: 01/11/2023] Open
Abstract
The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.
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Affiliation(s)
- Huiluo Cao
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong
| | - Weipeng Zhang
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong
| | - Yong Wang
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong ; Sanya Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences Sanya, China
| | - Pei-Yuan Qian
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong
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23
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Sonthiphand P, Hall MW, Neufeld JD. Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria. Front Microbiol 2014; 5:399. [PMID: 25147546 PMCID: PMC4123730 DOI: 10.3389/fmicb.2014.00399] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/15/2014] [Indexed: 02/01/2023] Open
Abstract
Anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce N2 gas. After being discovered in a wastewater treatment plant (WWTP), anammox bacteria were subsequently characterized in natural environments, including marine, estuary, freshwater, and terrestrial habitats. Although anammox bacteria play an important role in removing fixed N from both engineered and natural ecosystems, broad scale anammox bacterial distributions have not yet been summarized. The objectives of this study were to explore global distributions and diversity of anammox bacteria and to identify factors that influence their biogeography. Over 6000 anammox 16S rRNA gene sequences from the public database were analyzed in this current study. Data ordinations indicated that salinity was an important factor governing anammox bacterial distributions, with distinct populations inhabiting natural and engineered ecosystems. Gene phylogenies and rarefaction analysis demonstrated that freshwater environments and the marine water column harbored the highest and the lowest diversity of anammox bacteria, respectively. Co-occurrence network analysis indicated that Ca. Scalindua strongly connected with other Ca. Scalindua taxa, whereas Ca. Brocadia co-occurred with taxa from both known and unknown anammox genera. Our survey provides a better understanding of ecological factors affecting anammox bacterial distributions and provides a comprehensive baseline for understanding the relationships among anammox communities in global environments.
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Affiliation(s)
| | - Michael W Hall
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo Waterloo, ON, Canada
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Vigneron A, Cruaud P, Roussel EG, Pignet P, Caprais JC, Callac N, Ciobanu MC, Godfroy A, Cragg BA, Parkes JR, Van Nostrand JD, He Z, Zhou J, Toffin L. Phylogenetic and functional diversity of microbial communities associated with subsurface sediments of the Sonora Margin, Guaymas Basin. PLoS One 2014; 9:e104427. [PMID: 25099369 PMCID: PMC4123917 DOI: 10.1371/journal.pone.0104427] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/08/2014] [Indexed: 12/14/2022] Open
Abstract
Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments.
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Affiliation(s)
- Adrien Vigneron
- Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
| | - Perrine Cruaud
- Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
| | - Erwan G. Roussel
- School of Earth and Ocean Sciences, Cardiff University, Cardiff, United Kingdom
| | - Patricia Pignet
- Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
| | - Jean-Claude Caprais
- Ifremer, Laboratoire Etude des Environnements Profonds, UMR6197, ZI de la pointe du Diable, Plouzané, France
| | - Nolwenn Callac
- Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- Université de Brest, Domaines Océaniques IUEM, UMR6538, Place Nicolas Copernic, Plouzané, France
| | - Maria-Cristina Ciobanu
- Ifremer, Géosciences Marines, Laboratoire des Environnements Sédimentaires, ZI de la pointe du Diable, Plouzané, France
| | - Anne Godfroy
- Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
| | - Barry A. Cragg
- School of Earth and Ocean Sciences, Cardiff University, Cardiff, United Kingdom
| | - John R. Parkes
- School of Earth and Ocean Sciences, Cardiff University, Cardiff, United Kingdom
| | - Joy D. Van Nostrand
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Zhili He
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Laurent Toffin
- Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, ZI de la pointe du Diable, Plouzané, France
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Russ L, Speth DR, Jetten MSM, Op den Camp HJM, Kartal B. Interactions between anaerobic ammonium and sulfur-oxidizing bacteria in a laboratory scale model system. Environ Microbiol 2014; 16:3487-98. [DOI: 10.1111/1462-2920.12487] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 04/12/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Lina Russ
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen The Netherlands
| | - Daan R. Speth
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen The Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen The Netherlands
| | | | - Boran Kartal
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen The Netherlands
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26
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Bale NJ, Villanueva L, Fan H, Stal LJ, Hopmans EC, Schouten S, Sinninghe Damsté JS. Occurrence and activity of anammox bacteria in surface sediments of the southern North Sea. FEMS Microbiol Ecol 2014; 89:99-110. [DOI: 10.1111/1574-6941.12338] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 11/26/2022] Open
Affiliation(s)
- Nicole J. Bale
- Department of Marine Organic Biogeochemistry; NIOZ Royal Netherlands Institute for Sea Research; Den Burg the Netherlands
| | - Laura Villanueva
- Department of Marine Organic Biogeochemistry; NIOZ Royal Netherlands Institute for Sea Research; Den Burg the Netherlands
| | - Haoxin Fan
- Department of Marine Microbiology; NIOZ Royal Netherlands Institute for Sea Research; Yerseke the Netherlands
| | - Lucas J. Stal
- Department of Marine Microbiology; NIOZ Royal Netherlands Institute for Sea Research; Yerseke the Netherlands
| | - Ellen C. Hopmans
- Department of Marine Organic Biogeochemistry; NIOZ Royal Netherlands Institute for Sea Research; Den Burg the Netherlands
| | - Stefan Schouten
- Department of Marine Organic Biogeochemistry; NIOZ Royal Netherlands Institute for Sea Research; Den Burg the Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Organic Biogeochemistry; NIOZ Royal Netherlands Institute for Sea Research; Den Burg the Netherlands
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Song B, Buckner CT, Hembury DJ, Mills RA, Palmer MR. Impact of volcanic ash on anammox communities in deep sea sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:159-166. [PMID: 24596289 DOI: 10.1111/1758-2229.12137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 12/11/2013] [Indexed: 06/03/2023]
Abstract
Subaerial explosive volcanism contributes substantial amounts of material to the oceans, but little is known about the impact of volcanic ash on sedimentary microbial activity. We have studied anammox communities in deep sea sediments near the volcanically active island of Montserrat, Lesser Antilles. The rates of anammox and denitrification in the sediments were measured using (15)N isotope pairing incubation experiments, while 16S rRNA genes were used to examine anammox community structures. The higher anammox rates were measured in sediment containing the lower accumulation of volcanic ash in the surface sediments, while the lowest activities were found in sediments with the highest ash deposit. 16S rRNA gene analysis revealed the presence of 'Candidatus Scalindua spp.' in the sediments. The lowest diversity of anammox bacteria was observed in the sediments with the highest ash deposit. Overall, this study demonstrates that the deposition of volcanic material in deep sea sediments has negative impacts on activity and diversity of the anammox community. Since anammox may account for up to 79% of N2 production in marine ecosystems, periods of extensive explosive volcanism in Earth history may have had a hitherto unrecognized negative impact on the sedimentary nitrogen removal processes.
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Affiliation(s)
- Bongkeun Song
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, USA; Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
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28
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Winkel M, de Beer D, Lavik G, Peplies J, Mußmann M. Close association of active nitrifiers withBeggiatoamats covering deep-sea hydrothermal sediments. Environ Microbiol 2013; 16:1612-26. [DOI: 10.1111/1462-2920.12316] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 10/20/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Matthias Winkel
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 28359 Bremen Germany
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 28359 Bremen Germany
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 28359 Bremen Germany
| | - Jörg Peplies
- Ribocon GmbH; Fahrenheitstrasse 1 28359 Bremen Germany
| | - Marc Mußmann
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 28359 Bremen Germany
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29
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Callac N, Rommevaux-Jestin C, Rouxel O, Lesongeur F, Liorzou C, Bollinger C, Ferrant A, Godfroy A. Microbial colonization of basaltic glasses in hydrothermal organic-rich sediments at Guaymas Basin. Front Microbiol 2013; 4:250. [PMID: 23986754 PMCID: PMC3753459 DOI: 10.3389/fmicb.2013.00250] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 08/07/2013] [Indexed: 11/13/2022] Open
Abstract
Oceanic basalts host diverse microbial communities with various metabolisms involved in C, N, S, and Fe biogeochemical cycles which may contribute to mineral and glass alteration processes at, and below the seafloor. In order to study the microbial colonization on basaltic glasses and their potential biotic/abiotic weathering products, two colonization modules called AISICS ("Autonomous in situ Instrumented Colonization System") were deployed in hydrothermal deep-sea sediments at the Guaymas Basin for 8 days and 22 days. Each AISICS module contained 18 colonizers (including sterile controls) filled with basaltic glasses of contrasting composition. Chemical analyses of ambient fluids sampled through the colonizers showed a greater contribution of hydrothermal fluids (maximum temperature 57.6°C) for the module deployed during the longer time period. For each colonizer, the phylogenetic diversity and metabolic function of bacterial and archaeal communities were explored using a molecular approach by cloning and sequencing. Results showed large microbial diversity in all colonizers. The bacterial distribution was primarily linked to the deployment duration, as well as the depth for the short deployment time module. Some 16s rRNA sequences formed a new cluster of Epsilonproteobacteria. Within the Archaea the retrieved diversity could not be linked to either duration, depth or substrata. However, mcrA gene sequences belonging to the ANME-1 mcrA-guaymas cluster were found sometimes associated with their putative sulfate-reducers syntrophs depending on the colonizers. Although no specific glass alteration texture was identified, nano-crystals of barite and pyrite were observed in close association with organic matter, suggesting a possible biological mediation. This study gives new insights into the colonization steps of volcanic rock substrates and the capability of microbial communities to exploit new environmental conditions.
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Affiliation(s)
- Nolwenn Callac
- Laboratoire de Microbiologie des Environnements Extrêmes UMR 6197, Université de Bretagne Occidentale, UEB, IUEM Plouzané, France ; Laboratoire de Microbiologie des Environnements Extrêmes UMR 6197, Ifremer Plouzané, France ; Laboratoire de Microbiologie des Environnements Extrêmes UMR 6197, CNRS Plouzané, France ; Domaines Océaniques UMR6538, IUEM, Université de Bretagne Occidentale Plouzané, France
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