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Pavlovska M, Prekrasna I, Dykyi E, Zotov A, Dzhulai A, Frolova A, Slobodnik J, Stoica E. Niche partitioning of bacterial communities along the stratified water column in the Black Sea. Microbiologyopen 2021; 10:e1195. [PMID: 34180601 PMCID: PMC8217838 DOI: 10.1002/mbo3.1195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 11/22/2022] Open
Abstract
The Black Sea is the largest semi‐closed permanently anoxic basin on our planet with long‐term stratification. The study aimed at describing the Black Sea microbial community taxonomic and functional composition within the range of depths spanning across oxic/anoxic interface, and to uncover the factors behind both their vertical and regional differentiation. 16S rRNA gene MiSeq sequencing was applied to get the data on microbial community taxonomy, and the PICRUSt pipeline was used to infer their functional profile. The normoxic zone was mainly inhabited by primary producers and heterotrophic prokaryotes (e.g., Flavobacteriaceae, Rhodobacteraceae, Synechococcaceae) whereas the euxinic zone—by heterotrophic and chemoautotrophic taxa (e.g., MSBL2, Piscirickettsiaceae, and Desulfarculaceae). Assimilatory sulfate reduction and oxygenic photosynthesis were prevailing within the normoxic zone, while the role of nitrification, dissimilatory sulfate reduction, and anoxygenic photosynthesis increased in the oxygen‐depleted water column part. Regional differentiation of microbial communities between the Ukrainian shelf and offshore zone was detected as well, yet it was significantly less pronounced than the vertical one. It is suggested that regional differentiation within a well‐oxygenated zone is driven by the difference in phytoplankton communities providing various substrates for the prokaryotes, whereas redox stratification is the main driving force behind microbial community vertical structure.
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Affiliation(s)
- Mariia Pavlovska
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,Ukrainian Scientific Center of Ecology of the Sea, Odesa, Ukraine.,National University of Life and Environmental Sciences of Ukraine, Kyiv, Ukraine
| | | | - Evgen Dykyi
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,Ukrainian Scientific Center of Ecology of the Sea, Odesa, Ukraine
| | - Andrii Zotov
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,State Institution Institute of Marine Biology of the NAS of Ukraine, Odesa, Ukraine
| | - Artem Dzhulai
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | | | - Elena Stoica
- National Institute for Marine Research and Development "Grigore Antipa", Constanta, Romania
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2
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Xiao Y, Yin X, Chen L, Wang J, Wang Y, Liu G, Hua Y, Wan X, Xiao N, Zhao J, Zhu D. Effects of illumination on nirS denitrifying and anammox bacteria in the rhizosphere of submerged macrophytes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 760:143420. [PMID: 33189380 DOI: 10.1016/j.scitotenv.2020.143420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/08/2020] [Accepted: 10/26/2020] [Indexed: 06/11/2023]
Abstract
Visibility in lakes can decrease due to increases in the amounts of suspended solids and algae, which inhibits the growth of submerged macrophytes. However, the understanding about whether illumination reduction affects the nitrogen-cycling microorganisms in the rhizosphere of submerged macrophytes, is limited. The abundance and biodiversity of nirS denitrifying and anammox bacteria in the rhizosphere of Potamogeton crispus were studied under 0% (natural light), 20%, 40%, and 60% shading treatments. The abundance of the nirS gene was highest under 60% shading treatment, while the anammox 16S rRNA gene was highest under 40% shading treatment. Moreover, the abundance of the two genes were lower under natural light than under shading conditions during most sampling periods. The quantitative ratio of the two gene (anammox 16S rRNA to nirS gene) abundance fluctuated wildly with the distance away from the roots, under natural light and 20% shading treatment. However, the ratio varied relatively little under 40% and 60% shading treatments. The diversity of nirS denitrifying bacteria was high in the rhizosphere, while the diversity of anammox bacteria was low, and Candidatus Brocadia fulgida was dominant. This study revealed that illumination reduction not only facilitated the growth of nirS denitrifying and anammox bacteria in the rhizosphere, but also weakened the competition between the two bacteria.
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Affiliation(s)
- Yang Xiao
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingjia Yin
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Lijuan Chen
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Jing Wang
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuchun Wang
- Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing 100038, China; State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Institute of Water Resources and China Hydropower Research, Beijing 100038, China.
| | - Guanglong Liu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yumei Hua
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoqiong Wan
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Naidong Xiao
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianwei Zhao
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Duanwei Zhu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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3
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Anoxic chlorophyll maximum enhances local organic matter remineralization and nitrogen loss in Lake Tanganyika. Nat Commun 2021; 12:830. [PMID: 33547297 PMCID: PMC7864930 DOI: 10.1038/s41467-021-21115-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 01/08/2021] [Indexed: 01/12/2023] Open
Abstract
In marine and freshwater oxygen-deficient zones, the remineralization of sinking organic matter from the photic zone is central to driving nitrogen loss. Deep blooms of photosynthetic bacteria, which form the suboxic/anoxic chlorophyll maximum (ACM), widespread in aquatic ecosystems, may also contribute to the local input of organic matter. Yet, the influence of the ACM on nitrogen and carbon cycling remains poorly understood. Using a suite of stable isotope tracer experiments, we examined the transformation of nitrogen and carbon under an ACM (comprising of Chlorobiaceae and Synechococcales) and a non-ACM scenario in the anoxic zone of Lake Tanganyika. We find that the ACM hosts a tight coupling of photo/litho-autotrophic and heterotrophic processes. In particular, the ACM was a hotspot of organic matter remineralization that controlled an important supply of ammonium driving a nitrification-anammox coupling, and thereby played a key role in regulating nitrogen loss in the oxygen-deficient zone. Enigmatic blooms of phytoplankton in aquatic oxygen-deficient zones could exacerbate depletion of nitrogen. Here the authors perform stable isotope experiments on the oxygen-deficient waters of Lake Tanganyika in Africa, finding that blooms drive down fixed nitrogen and could expand as a result of climate change.
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4
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Fuchsman CA, Stüeken EE. Using modern low-oxygen marine ecosystems to understand the nitrogen cycle of the Paleo- and Mesoproterozoic oceans. Environ Microbiol 2020; 23:2801-2822. [PMID: 32869502 DOI: 10.1111/1462-2920.15220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 11/29/2022]
Abstract
During the productive Paleoproterozoic (2.4-1.8 Ga) and less productive Mesoproterozoic (1.8-1.0 Ga), the ocean was suboxic to anoxic and multicellular organisms had not yet evolved. Here, we link geologic information about the Proterozoic ocean to microbial processes in modern low-oxygen systems. High iron concentrations and rates of Fe cycling in the Proterozoic are the largest differences from modern oxygen-deficient zones. In anoxic waters, which composed most of the Paleoproterozoic and ~40% of the Mesoproterozoic ocean, nitrogen cycling dominated. Rates of N2 production by denitrification and anammox were likely linked to sinking organic matter fluxes and in situ primary productivity under anoxic conditions. Additionally autotrophic denitrifiers could have used reduced iron or methane. 50% of the Mesoproterozoic ocean may have been suboxic, promoting nitrification and metal oxidation in the suboxic water and N2 O and N2 production by partial and complete denitrification in anoxic zones in organic aggregates. Sulfidic conditions may have composed ~10% of the Mesoproterozoic ocean focused along continental margins. Due to low nitrate concentrations in offshore regions, anammox bacteria likely dominated N2 production immediately above sulfidic zones, but in coastal regions, higher nitrate concentrations probably promoted complete S-oxidizing autotrophic denitrification at the sulfide interface.
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Affiliation(s)
- Clara A Fuchsman
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, 21613, USA
| | - Eva E Stüeken
- School of Earth & Environmental Sciences, University of St Andrews, St Andrews, KY16 9AL, Scotland, UK
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5
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Suter EA, Pachiadaki MG, Montes E, Edgcomb VP, Scranton MI, Taylor CD, Taylor GT. Diverse nitrogen cycling pathways across a marine oxygen gradient indicate nitrogen loss coupled to chemoautotrophic activity. Environ Microbiol 2020; 23:2747-2764. [PMID: 32761757 DOI: 10.1111/1462-2920.15187] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 08/01/2020] [Accepted: 08/02/2020] [Indexed: 11/28/2022]
Abstract
Genetic markers and geochemical assays of microbial nitrogen cycling processes, including autotrophic and heterotrophic denitrification, anammox, ammonia oxidation, and nitrite oxidation, were examined across the oxycline, suboxic, and anoxic zones of the Cariaco Basin, Venezuela. Ammonia and nitrite oxidation genes were expressed through the entire gradient. Transcripts associated with autotrophic and heterotrophic denitrifiers were mostly confined to the suboxic zone and below but were also present in particles in the oxycline. Anammox genes and transcripts were detected over a narrow depth range near the bottom of the suboxic zone and coincided with secondary NO2 - maxima and available NH4 + . Dissolved inorganic nitrogen (DIN) amendment incubations and comparisons between our sampling campaigns suggested that denitrifier activity may be closely coupled with NO3 - availability. Expression of denitrification genes at depths of high rates of chemoautotrophic carbon fixation and phylogenetic analyses of nitrogen cycling genes and transcripts indicated a diverse array of denitrifiers, including chemoautotrophs capable of using NO3 - to oxidize reduced sulfur species. Thus, results suggest that the Cariaco Basin nitrogen cycle is influenced by autotrophic carbon cycling in addition to organic matter oxidation and anammox.
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Affiliation(s)
- Elizabeth A Suter
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA.,Biology, Chemistry, and Environmental Studies Department, Center for Environmental Research and Coastal Oceans Monitoring, Molloy College, Rockville Centre, NY, USA.,Department of Biological Sciences, Wagner College, Staten Island, NY, USA
| | - Maria G Pachiadaki
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA.,Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Enrique Montes
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | | | - Mary I Scranton
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Craig D Taylor
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
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6
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Fuchsman CA, Palevsky HI, Widner B, Duffy M, Carlson MCG, Neibauer JA, Mulholland MR, Keil RG, Devol AH, Rocap G. Cyanobacteria and cyanophage contributions to carbon and nitrogen cycling in an oligotrophic oxygen-deficient zone. ISME JOURNAL 2019; 13:2714-2726. [PMID: 31249393 PMCID: PMC6794308 DOI: 10.1038/s41396-019-0452-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 04/20/2019] [Accepted: 05/26/2019] [Indexed: 12/03/2022]
Abstract
Up to half of marine N losses occur in oxygen-deficient zones (ODZs). Organic matter flux from productive surface waters is considered a primary control on N2 production. Here we investigate the offshore Eastern Tropical North Pacific (ETNP) where a secondary chlorophyll a maximum resides within the ODZ. Rates of primary production and carbon export from the mixed layer and productivity in the primary chlorophyll a maximum were consistent with oligotrophic waters. However, sediment trap carbon and nitrogen fluxes increased between 105 and 150 m, indicating organic matter production within the ODZ. Metagenomic and metaproteomic characterization indicated that the secondary chlorophyll a maximum was attributable to the cyanobacterium Prochlorococcus, and numerous photosynthesis and carbon fixation proteins were detected. The presence of chemoautotrophic ammonia-oxidizing archaea and the nitrite oxidizer Nitrospina and detection of nitrate oxidoreductase was consistent with cyanobacterial oxygen production within the ODZ. Cyanobacteria and cyanophage were also present on large (>30 μm) particles and in sediment trap material. Particle cyanophage-to-host ratio exceeded 50, suggesting that viruses help convert cyanobacteria into sinking organic matter. Nitrate reduction and anammox proteins were detected, congruent with previously reported N2 production. We suggest that autochthonous organic matter production within the ODZ contributes to N2 production in the offshore ETNP.
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Affiliation(s)
- Clara A Fuchsman
- School of Oceanography, University of Washington, Seattle, WA, USA. .,Horn Point Laboratory, University of Maryland, Cambridge, MD, USA.
| | - Hilary I Palevsky
- School of Oceanography, University of Washington, Seattle, WA, USA.,Geosciences Department, Wellesley College, Wellesley, MA, USA
| | - Brittany Widner
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.,Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University, Norfolk, VA, USA
| | - Megan Duffy
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Michael C G Carlson
- School of Oceanography, University of Washington, Seattle, WA, USA.,Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Margaret R Mulholland
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Richard G Keil
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Allan H Devol
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Gabrielle Rocap
- School of Oceanography, University of Washington, Seattle, WA, USA.
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7
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Chen R, Yao J, Ailijiang N, Liu R, Fang L, Chen Y. Abundance and diversity of nitrogen-removing microorganisms in the UASB-anammox reactor. PLoS One 2019; 14:e0215615. [PMID: 31009503 PMCID: PMC6476503 DOI: 10.1371/journal.pone.0215615] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 04/04/2019] [Indexed: 11/18/2022] Open
Abstract
Anaerobic ammonium oxidation is considered to be the most economical and low-energy biological nitrogen removal process. So far, anammox bacteria have not yet been purified from cultures. Some nitrogen-removing microorganisms cooperate to perform the anammox process. The objective of this research was to analyze the abundance and diversity of nitrogen-removing microorganisms in an anammox reactor started up with bulking sludge at room temperature. In this study, the ammonia-oxidizing archaea phylum Crenarchaeota was enriched from 9.2 to 53.0%. Nitrosomonas, Nitrosococcus, and Nitrosospira, which are ammonia-oxidizing bacteria, increased from 3.2, 1.7, and 0.1% to 12.8, 20.4, and 3.3%, respectively. Ca. Brocadia, Ca. Kuenenia, and Ca. Scalindua, which are anammox bacteria, were detected in the seeding sludge, accounting for 77.1, 11.5, and 10.6%. After cultivation, the dominant genus changed to Ca. Kuenenia, accounting for 82.0%. Nitrospirae, nitrite oxidation bacteria, decreased from 2.2 to 0.1%, while denitrifying genera decreased from 12.9 to 2.1%. The results of this study contribute to the understanding of nitrogen-removing microorganisms in an anammox reactor, thereby facilitating the improvement of such reactors. However, the physiological and metabolic functions of the ammonia-oxidizing archaea community in the anammox reactor need to be investigated in further studies.
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Affiliation(s)
- Rui Chen
- College of Resources and Environmental Science, Xinjiang University, Urumqi, China
| | - Junqin Yao
- College of Resources and Environmental Science, Xinjiang University, Urumqi, China
- * E-mail:
| | - Nuerla Ailijiang
- College of Resources and Environmental Science, Xinjiang University, Urumqi, China
| | - Ruisang Liu
- College of Resources and Environmental Science, Xinjiang University, Urumqi, China
| | - Lei Fang
- College of Resources and Environmental Science, Xinjiang University, Urumqi, China
| | - Yinguang Chen
- College of Resources and Environmental Science, Xinjiang University, Urumqi, China
- College of Environmental Science and Engineering, Tongji University, Shanghai, China
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8
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Capturing Compositional Variation in Denitrifying Communities: a Multiple-Primer Approach That Includes Epsilonproteobacteria. Appl Environ Microbiol 2017; 83:AEM.02753-16. [PMID: 28087525 DOI: 10.1128/aem.02753-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/03/2017] [Indexed: 11/20/2022] Open
Abstract
Denitrifying Epsilonproteobacteria may dominate nitrogen loss processes in marine habitats with intense redox gradients, but assessment of their importance is limited by the currently available primers for nitrite reductase genes. Nine new primers targeting the nirS gene of denitrifying Epsilonproteobacteria were designed and tested for use in sequencing and quantitative PCR on two microbial mat samples (vent 2 and vent 4) from the Calypso hydrothermal vent field, Bay of Plenty, New Zealand. Commonly used nirS and nirK primer sets nirS1F/nirS6R, cd3aF/R3cd, nirK1F/nirK5R, and F1aCu/R3Cu were also tested to determine what may be missed by the common single-primer approach to assessing denitrifier diversity. The relative importance of Epsilonproteobacteria in these samples was evaluated by 16S rRNA gene sequencing. Epsilonproteobacteria represented up to 75.6% of 16S rRNA libraries, but nirS genes from this group were not found with commonly used primers. Pairing of the new primer EPSnirS511F with either EPSnirS1100R or EPSnirS1105R recovered nirS sequences from members of the genera Sulfurimonas, Sulfurovum, and Nitratifractor. The new quantitative PCR primers EPSnirS103F/EPSnirS530R showed dominance of denitrifying Epsilonproteobacteria in vent 4 compared to vent 2, which had greater representation by "standard" denitrifiers measured with the cd3aF/R3cd primers. Limited results from commonly used nirK primers suggest biased amplification between primers. Future application of multiple nirS and nirK primers, including the new epsilonproteobacterial nirS primers, will improve the detection of denitrifier diversity and the capability to identify changes in dominant denitrifying communities.IMPORTANCE Estimating the potential for increasing nitrogen limitation in the changing global ocean is reliant on understanding the microbial community that removes nitrogen through the process of denitrification. This process is favored under oxygen limitation, which is a growing global-ocean phenomenon. Current methods use the nitrite reductase genes nirS and nirK to assess denitrifier diversity and abundance using primers that target only a few known denitrifiers and systematically exclude denitrifying Epsilonproteobacteria, a group known to dominate in reducing environments, such as hydrothermal vents and anoxic basins. As oxygen depletion expands in the oceans, it is important to study denitrifier community dynamics within those areas to predict future global ocean changes. This study explores the design and testing of new primers that target epsilonproteobacterial nirS and reveals the varied success of existing primers, leading to the recommendation of a multiple-primer approach to assessing denitrifier diversity.
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9
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Ward BB, Jensen MM. The microbial nitrogen cycle. Front Microbiol 2014; 5:553. [PMID: 25386170 PMCID: PMC4208395 DOI: 10.3389/fmicb.2014.00553] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/03/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Bess B Ward
- Geosciences, Princeton University Princeton, NJ, USA
| | - Marlene M Jensen
- Department of Environmental Engineering, Technical University of Denmark Lyngby, Denmark
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10
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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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11
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Han P, Huang YT, Lin JG, Gu JD. A comparison of two 16S rRNA gene-based PCR primer sets in unraveling anammox bacteria from different environmental samples. Appl Microbiol Biotechnol 2013; 97:10521-9. [PMID: 24177731 DOI: 10.1007/s00253-013-5305-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 09/27/2013] [Accepted: 09/30/2013] [Indexed: 10/26/2022]
Abstract
Two 16S rRNA gene-based PCR primer sets (Brod541F/Amx820R and A438f/A684r) for detecting anammox bacteria were compared using sediments from Mai Po wetlands (MP), the South China Sea (SCS), a freshwater reservoir (R2), and sludge granules from a wastewater treatment plant (A2). By comparing their ability in profiling anammox bacteria, the recovered diversity, community structure, and abundance of anammox bacteria among all these diverse samples indicated that A438f/A684r performed better than Brod541F/Amx820R in retrieving anammox bacteria from these different environmental samples. Five Scalindua subclusters (zhenghei-I, SCS-I, SCS-III, arabica, and brodae) dominated in SCS whereas two Scalindua subclusters (zhenghei-II and wagneri) and one cluster of Kuenenia dominated in MP. R2 showed a higher diversity of anammox bacteria with two new retrieved clusters (R2-New-1 and R2-New-2), which deserves further detailed study. The dominance of Brocadia in sample A2 was supported by both of the primer sets used. Results collectively indicate strongly niche-specific community structures of anammox bacteria in different environments, and A438f/A684r is highly recommended for screening anammox bacteria from various environments when dealing with a collection of samples with diverse physiochemical characteristics.
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Affiliation(s)
- Ping Han
- 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
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