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  • 1
    Unknown
    The Microbial Nitrogen Cycle (2015)
    Lausanne : Frontiers
    Details
    Keywords: nitrogen cycle ; microbial ecology ; nitrogen fixation ; denitrification ; Anammox ; nitrification ; microbiology
    Description / Table of Contents: Nitrogen is an essential element in biological systems, and one that often limits production in both aquatic and terrestrial systems. Due to its requirement in biological macromolecules, its acquisition and cycling have the potential to structure microbial communities, as well as to control productivity on the ecosystem scale. In addition, its versatile redox chemistry is the basis of complex biogeochemical transformations that control the inventory of fixed nitrogen, both in local environments and over geological time. Although many of the pathways in the microbial nitrogen cycle were described more than a century ago, additional fundamental pathways have been discovered only recently. These findings imply that we still have much to learn about the microbial nitrogen cycle, the organisms responsible for it, and their interactions in natural and human environments. Progress in nitrogen cycle research has been facilitated by recent rapid technological advances, especially in genomics and isotopic approaches. In this Research Topic, we reviewed the leading edge of nitrogen cycle research based on these approaches, as well as by exploring microbial processes in modern ecosystems.
    Pages: Online-Ressource (175 Seiten)
    ISBN: 9782889194124
    URL: https://doi.org/10.3389/978-2-88919-412-4
    Language: English
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    E-BOOK
  • 2
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    Nitrous oxide production kinetics from ammonia oxidation in the Eastern Tropical North Pacific in March/April 2018 (2021)
    PANGAEA
    Details
    Publication Date: 2023-07-22
    Description: In March/April 2018 during a cruise on R/V Sally Ride, SR1805, 15N-NH4+ incubations in 60mL glass serum bottles were performed to measure ammonium oxidation rates to nitrite and nitrous oxide in different depth at 3 different stations in the oxygen deficient zone (ODZ) of the Eastern Tropical North Pacific off the coast of Mexico. Water samples were collected from 30L Niskin bottles deployed with a conductivity-temperature-depth profiler (CTD, Seabird Electronics). The goal was to get a better understanding on the controls of nitrous oxide (N2O) production. The N2O production rate experiments were performed according to Bourbonnais et al. 2021 (https://doi.org/10.3389/fmars.2021.611937). Furthermore, ammonium (NH4+), nitrite (NO2-) and nitrate (NO3-) as well as N2O concentrations were determined using standard fluorometric (Holmes et al. 1999, https://doi.org/10.1139/f99-128), photometric (Strickland and Parsons 1972, hdl:10013/epic.46454.d001), chemiluminescent (Braman and Hendrix 1989, doi:10.1021/ac00199a007) and mass spectrometric techniques (McIlvin and Casciotti 2010, https://doi.org/10.4319/lom.2010.8.54), respectively. The N2O yield per nitrite produced was calculated. The archaeal ammonia monooxygenase gene subunit A (amoA) copy numbers/mL were determined using qPCR as described previously (Peng et al. 2015, https://doi.org/10.1002/2015GB005278).
    Keywords: 15N-tracer; 15N tracer incubations (Bourbonnais et al. 2021); Ammonium; Ammonium, labelled, fraction; Ammonium, oxidation rate; Ammonium, oxidation rate, standard error; ammonium oxidation; amoA gene, copy number; amoA gene, copy number, standard deviation; Bottle number; Calculated; Cast number; Chemiluminescence detection (Braman and Hendrix 1989); Comment; CTD, Sea-Bird; CTD/Rosette; CTD-RO; DATE/TIME; Density, sigma-theta (0); Depth, bottom/max; DEPTH, water; eastern tropical north pacific; Event label; Fluorometry (Holmes et al. 1999); greenhouse gas; Identification; LATITUDE; LONGITUDE; Mass spectrometry (McIlvin and Casciotti 2010); N2O production rates; Nitrate; Nitrite; nitrogen cycle; Nitrous oxide, dissolved; Nitrous oxide, hybrid; Nitrous oxide, hybrid, standard error; Nitrous oxide, standard deviation; Nitrous oxide, yield; Nitrous oxide, yield, standard error; Nitrous oxide production; Nitrous oxide production, standard error; North Pacific Ocean; ocean; Oxygen; Photometry (Strickland & Parsons, 1972); Radiation, photosynthetically active; Real-time quantitative polymerase chain reaction (qPCR); Salinity; Sally Ride; SR1805; SR1805_PS1_CTD16; SR1805_PS1_CTD5; SR1805_PS2_CTD32; SR1805_PS2_CTD45; SR1805_PS3_CTD71; SR1805_PS3_CTD84; Station label; STOX; Switchable trace oxygen sensor; Temperature, water; Treatment
    Type: Dataset
    Format: text/tab-separated-values, 796 data points
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    DATA PANGAEA
  • 3
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    Nitrous oxide production rates in the eastern tropical South Pacific during METEOR cruise M138 (2020)
    PANGAEA
    Details
    Publication Date: 2023-10-28
    Description: N2O production rates from ammonium, nitrite and nitrate and nitrate reduction rates and ammonium oxidation rates from the top 400 m water depth off the coast of Peru sampled from R/V Meteor during M138 in June 2017.
    Keywords: Ammonium; Ammonium, oxidation rate; Climate - Biogeochemistry Interactions in the Tropical Ocean; CTD/Rosette; CTD 013; CTD 018; CTD 036; CTD 044; CTD 063; CTD 069; CTD 076; CTD 085; CTD 099; CTD-RO; DATE/TIME; Density, sigma-theta (0); DEPTH, water; ELEVATION; Event label; LATITUDE; LONGITUDE; M138; M138_882-11; M138_883-15; M138_892-3; M138_894-4; M138_904-7; M138_906-7; M138_907-7; M138_912-1; M138_917-3; Meteor (1986); Nitrate; Nitrate, reduction rate; Nitrate and Nitrite; Nitrite; Nitrous oxide production; OMZ; Oxygen; Phosphate; Ratio; Salinity; Sample code/label; SFB754; Silicate; Standard deviation; Standard error; Temperature, water; Yield
    Type: Dataset
    Format: text/tab-separated-values, 474 data points
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    DATA PANGAEA
  • 4
    Electronic Resource
    Electronic Resource
    MOLECULAR APPROACHES TO MARINE MICROBIAL ECOLOGY AND THE MARINE NITROGEN CYCLE (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Earth and Planetary Sciences 33 (2005), S. 301-333 
    Details
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Microbes are recognized as important components of the Earth system, playing key roles in controlling the composition of the atmosphere and surface waters, forming the basis of the marine food web, and the cycling of chemicals in the ocean. A revolution in microbial ecology has occurred in the past 15Đ??20 years with the advent of rapid methods for discovering and sequencing the genes of uncultivated microbes from natural environments. Initially based on sequences from the 16S rRNA gene, this revolution made it possible to identify microorganisms without first cultivating them, to discover and characterize the immense previously unsuspected diversity of the microbial world, and to reconstruct the evolutionary relationships among microbes. Subsequent focus on functional genes, those that encode enzymes that catalyze biogeochemical transformations, and current work on larger DNA fragments and entire genomes make it possible to link microbial diversity to ecosystem function. These approaches have yielded insights into the regulation of microbial activity and proof of the microbial role in biogeochemical processes previously unknown. Questions raised by the molecular revolution, which are now the focus of microbial ecology research, include the significance of microbial diversity and redundancy to biogeochemical processes and ecosystem function.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.earth.33.092203.122514
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    Paper (German National Licenses)
    Fulltext
  • 5
    Electronic Resource
    Electronic Resource
    MOLECULAR APPROACHES TO MARINE MICROBIAL ECOLOGY AND THE MARINE NITROGEN CYCLE (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Earth and Planetary Sciences 33 (2005), S. 301-333 
    Details
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Microbes are recognized as important components of the Earth system, playing key roles in controlling the composition of the atmosphere and surface waters, forming the basis of the marine food web, and the cycling of chemicals in the ocean. A revolution in microbial ecology has occurred in the past 15Đ??20 years with the advent of rapid methods for discovering and sequencing the genes of uncultivated microbes from natural environments. Initially based on sequences from the 16S rRNA gene, this revolution made it possible to identify microorganisms without first cultivating them, to discover and characterize the immense previously unsuspected diversity of the microbial world, and to reconstruct the evolutionary relationships among microbes. Subsequent focus on functional genes, those that encode enzymes that catalyze biogeochemical transformations, and current work on larger DNA fragments and entire genomes make it possible to link microbial diversity to ecosystem function. These approaches have yielded insights into the regulation of microbial activity and proof of the microbial role in biogeochemical processes previously unknown. Questions raised by the molecular revolution, which are now the focus of microbial ecology research, include the significance of microbial diversity and redundancy to biogeochemical processes and ecosystem function.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.earth.33.092203.122514
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    Paper (German National Licenses)
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  • 6
    Electronic Resource
    Electronic Resource
    Molecular analysis of ammonia oxidation and denitrification in natural environments (2000)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology reviews 24 (2000), S. 0 
    Details
    ISSN: 1574-6976
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: This review summarizes aspects of the current knowledge about the ecology of ammonia-oxidizing and denitrifying bacteria. The development of molecular techniques has contributed enormously to the rapid recent progress in the field. Different techniques for doing so are discussed. The characterization of ammonia-oxidizing and -denitrifying bacteria by sequencing the genes encoding 16S rRNA and functional proteins opened the possibility of constructing specific probes. It is now possible to monitor the occurrence of a particular species of these bacteria in any habitat and to get an estimate of the relative abundance of different types, even if they are not culturable as yet. These data indicate that the composition of nitrifying and denitrifying communities is complex and apparently subject to large fluctuations, both in time and in space. More attempts are needed to enrich and isolate those bacteria which dominate the processes, and to characterize them by a combination of physiological, biochemical and molecular techniques. While PCR and probing with nucleotides or antibodies are primarily used to study the structure of nitrifying and denitrifying communities, studies of their function in natural habitats, which require quantification at the transcriptional level, are currently not possible.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6976.2000.tb00566.x
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  • 7
    Electronic Resource
    Electronic Resource
    Phylogenetic analysis of nitric oxide reductase gene homologues from aerobic ammonia-oxidizing bacteria (2005)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 52 (2005), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Nitric oxide (NO) and nitrous oxide (N2O) are climatically important trace gases that are produced by both nitrifying and denitrifying bacteria. In the denitrification pathway, N2O is produced from nitric oxide (NO) by the enzyme nitric oxide reductase (NOR). The ammonia-oxidizing bacterium Nitrosomonas europaea also possesses a functional nitric oxide reductase, which was shown recently to serve a unique function. In this study, sequences homologous to the large subunit of nitric oxide reductase (norB) were obtained from eight additional strains of ammonia-oxidizing bacteria, including Nitrosomonas and Nitrosococcus species (i.e., both β- and γ-Proteobacterial ammonia oxidizers), showing widespread occurrence of a norB homologue in ammonia-oxidizing bacteria. However, despite efforts to detect norB homologues from Nitrosospira strains, sequences have not yet been obtained. Phylogenetic analysis placed nitrifier norB homologues in a subcluster, distinct from denitrifier sequences. The similarities and differences of these sequences highlight the need to understand the variety of metabolisms represented within a “functional group” defined by the presence of a single homologous gene. These results expand the database of norB homologue sequences in nitrifying bacteria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2004.11.002
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  • 8
    Electronic Resource
    Electronic Resource
    Nitrite reductase genes in halobenzoate degrading denitrifying bacteria (2003)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 43 (2003), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Diversity of the functional genes encoding dissimilatory nitrite reductase was investigated for the first time in denitrifying halobenzoate degrading bacteria and in two 4-chlorobenzoate degrading denitrifying consortia. Nitrite reductase genes were PCR-amplified with degenerate primers (specific to the two different types of respiratory nitrite reductase, nirS and nirK), cloned and sequenced to determine which type of nitrite reductase was present in each isolate and consortium. Halobenzoate degrading isolates belonging to the genera Ochrobactrum, Ensifer and Mesorhizobium, as well as Pseudomonas mendocina CH91 were found to have nirK genes, which were closely related to the previously published nirK genes of Ochrobactrum anthropi, Achromobacter cycloclastes, Alcaligenes faecalis and Pseudomonas aureofaciens, respectively. The isolates assigned to the genera Acidovorax, Azoarcus and Thauera as well as all other species in the genera Thauera and Azoarcus contained nirS genes, which were closely related to the nirS genes from Pseudomonas stutzeri with some exceptions. In addition, only nirS genes were found in 4-chlorobenzoate degrading denitrifying consortia. Three different major terminal restriction fragments from the nirS genes were detected by terminal restriction fragment length polymorphism analysis of the consortia, and five different nirS genes were cloned from one consortium. Three nirS gene clones were closely related to nirS genes from Thauera chlorobenzoica, Azoarcus tolulyticus and Pseudomonas aeruginosa, respectively. The phylogeny of nir genes was not entirely congruent with the 16S rRNA phylogeny of the genera nor was it correlated with the ecological and geographical origins or isolation substrates used for isolation and enrichment of consortia.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2003.tb01075.x
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  • 9
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    Microbial community composition in sediments resists perturbation by nutrient enrichment (2011)
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in The ISME Journal 5 (2011): 1540–1548, doi:10.1038/ismej.2011.22.
    Description: Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply, despite demonstrable and diverse nutrient–induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation.
    Description: Funding for this research came from NSF(DEB-0717155 to JEH, DBI-0400819 to JLB). Support for the sequencing facility came from NIH and NSF (NIH/NIEHS-P50-ES012742-01 and NSF/OCE 0430724-J Stegeman PI to HGM and MLS, and WM Keck Foundation to MLS). Salary support provided from Princeton University Council on Science and Technology to JLB. Support for development of the functional gene microarray provided by NSF/OCE99-081482 to BBW. The Plum Island fertilization experiment was funded by NSF (DEB 0213767 and DEB 0816963).
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Format: application/pdf
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  • 10
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    Acidification alters the composition of ammonia‑oxidizing microbial assemblages in marine mesocosms (2013)
    Inter-Research
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © Inter-Research, 2013. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Marine Ecology Progress Series 492 (2013): 1-8, doi:10.3354/meps10526.
    Description: Increasing atmospheric CO2 concentrations are causing decreased pH over vast expanses of the ocean. This decreasing pH may alter biogeochemical cycling of carbon and nitrogen via the microbial process of nitrification, a key process that couples these cycles in the ocean, but which is often sensitive to acidic conditions. Recent reports have indicated a decrease in oceanic nitrification rates under experimentally lowered pH. How the composition and abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) assemblages respond to decreasing oceanic pH is unknown. We sampled microbes from 2 different acidification experiments and used a combination of qPCR and functional gene microarrays for the ammonia monooxygenase gene (amoA) to assess how acidification alters the structure of ammonia oxidizer assemblages. We show that despite widely different experimental conditions, acidification consistently altered the community composition of AOB by increasing the relative abundance of taxa related to the Nitrosomonas ureae clade. In one experiment, this increase was sufficient to cause an increase in the overall abundance of AOB. There were no systematic shifts in the community structure or abundance of AOA in either experiment. These different responses to acidification underscore the important role of microbial community structure in the resiliency of marine ecosystems.
    Description: NSF funding to B.B.W. supported the barrel experiments. Funding for the coral experiments came from NSF (GRF to M.H.; OCE-1041106), the Woods Hole Oceanographic Institution’s Ocean Life Institute, and the International Society for Reef Studies.
    Keywords: Ocean acidification ; Ammonia-oxidizing archaea ; Ammonia-oxidizing bacteria ; Nitrification
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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