Nitrogen Fixation in Denitrified Marine Waters

Nitrogen fixation is an essential process that biologically transforms atmospheric dinitrogen gas to ammonia, therefore compensating for nitrogen losses occurring via denitrification and anammox. Currently, inputs and losses of nitrogen to the ocean resulting from these processes are thought to be spatially separated: nitrogen fixation takes place primarily in open ocean environments (mainly through diazotrophic cyanobacteria), whereas nitrogen losses occur in oxygen-depleted intermediate waters and sediments (mostly via denitrifying and anammox bacteria). Here we report on rates of nitrogen fixation obtained during two oceanographic cruises in 2005 and 2007 in the eastern tropical South Pacific (ETSP), a region characterized by the presence of coastal upwelling and a major permanent oxygen minimum zone (OMZ). Our results show significant rates of nitrogen fixation in the water column; however, integrated rates from the surface down to 120 m varied by ∼30 fold between cruises (7.5±4.6 versus 190±82.3 µmol m−2 d−1). Moreover, rates were measured down to 400 m depth in 2007, indicating that the contribution to the integrated rates of the subsurface oxygen-deficient layer was ∼5 times higher (574±294 µmol m−2 d−1) than the oxic euphotic layer (48±68 µmol m−2 d−1). Concurrent molecular measurements detected the dinitrogenase reductase gene nifH in surface and subsurface waters. Phylogenetic analysis of the nifH sequences showed the presence of a diverse diazotrophic community at the time of the highest measured nitrogen fixation rates. Our results thus demonstrate the occurrence of nitrogen fixation in nutrient-rich coastal upwelling systems and, importantly, within the underlying OMZ. They also suggest that nitrogen fixation is a widespread process that can sporadically provide a supplementary source of fixed nitrogen in these regions

Enactive management: a nurturing technology enabling fresh decision making to cope with conflict situations

The focus of this paper is observation, self-observation, and enactive management of organizational conflict situations whereby a community, an organization, or a human being has the possibility of recognizing their resources and generating changes in their practices if they so desire, and making fresh decisions, in the sense that different ontological dimensions are involved. We show how considering Body1- Language- Emotions- History- Eros- Silence can configure a nurturing technology call CLEHES. This tool has been applied for diverse people, groups, communities, and organizations that need and wish to develop their own skills to inquire conflict practice resolutions, in order to learn as a human decision support system. Conflict situations are understood as interactions, a breakdown in-between CLEHES from the individual or social standpoints. This tool allows observing the boundaries of conflict situations and building an observer system with the ability to manage, solve, or attenuate the situation, enabling fresh decision-making attending to the context in which the organization moves. This learning process happens in a constructed place called an Enactive Laboratory where strategies are developed to cope with the domains and context in the perceived individual and human activities systems. We present a case study focusing on a Learning Family Mediators System

An ontological and enactive tool for education in management of coexistence

Higher Education and the management of coexistence is an issue that is beginning to be included in the training of students and in teaching based on the demands made to teachers by the civil society and by the State in the last decade. The Ministry of Education of Chile formulates a National School Coexistence Policy that is being applied since 2002 in the country’s schools. It provides a conceptual and ethical framework to understand and act school coexistence from a rights and gender approach. It requires schools and universities to deal actively with this issue by placing teachers and professors as Promotors of Coexistence, i.e., it stresses their responsibility (beyond the disciplinary setting) in creating the conditions for training in citizenship, personal and social ethics, socio-emotional development, and social skills, among others. This obligation requires the teachers to question how they are acting, in their own coexistence and rupture spaces, to incorporate distinctions that allow them to act in the future from a pedagogical and generative perspective as established by the new State demands.Facultad de Psicologí

Oxygen at Nanomolar Levels Reversibly Suppresses Process Rates and Gene Expression in Anammox and Denitrification in the Oxygen Minimum Zone off Northern Chile

A major percentage (20 to 40%) of global marine fixed-nitrogen loss occurs in oxygen minimum zones (OMZs). Concentrations of O[subscript 2] and the sensitivity of the anaerobic N[subscript 2]-producing processes of anammox and denitrification determine where this loss occurs. We studied experimentally how O[subscript 2] at nanomolar levels affects anammox and denitrification rates and the transcription of nitrogen cycle genes in the anoxic OMZ off Chile. Rates of anammox and denitrification were reversibly suppressed, most likely at the enzyme level. Fifty percent inhibition of N[subscript 2] and N[subscript 2]O production by denitrification was achieved at 205 and 297 nM O[subscript 2], respectively, whereas anammox was 50% inhibited at 886 nM O2. Coupled metatranscriptomic analysis revealed that transcripts encoding nitrous oxide reductase (nosZ), nitrite reductase (nirS), and nitric oxide reductase (norB) decreased in relative abundance above 200 nM O[subscript 2]. This O[subscript 2] concentration did not suppress the transcription of other dissimilatory nitrogen cycle genes, including nitrate reductase (narG), hydrazine oxidoreductase (hzo), and nitrite reductase (nirK). However, taxonomic characterization of transcripts suggested inhibition of narG transcription in gammaproteobacteria, whereas the transcription of anammox narG, whose gene product is likely used to oxidatively replenish electrons for carbon fixation, was not inhibited. The taxonomic composition of transcripts differed among denitrification enzymes, suggesting that distinct groups of microorganisms mediate different steps of denitrification. Sulfide addition (1 µM) did not affect anammox or O[subscript 2] inhibition kinetics but strongly stimulated N[subscript 2]O production by denitrification. These results identify new O[subscript 2] thresholds for delimiting marine nitrogen loss and highlight the utility of integrating biogeochemical and metatranscriptomic analyses.Gordon and Betty Moore FoundationAgouron InstituteDanish National Research Foundation (Grant DNRF53

Bio-Optical Sensors on Argo Floats

The general objective of the IOCCG BIO-Argo working group is to elaborate recommendations for establishing a framework for the future development of a cost-effective, bio-optical float network corresponding to the needs and expectations of the scientific community. In this context, our recommendations will necessarily be broad; they range from the identification of key bio-optical measurements to be implemented on floats, to the real-time management of the data flux resulting from the deployment of a "fleet of floats". Each chapter of this report is dedicated to an essential brick leading towards the goal of implementing a bio-optical profiling float network. The following topics are discussed in the Chapters listed below: - Chapter 2 reviews the scientific objectives that could be tackled through the development of such networks, by allowing some of the gaps in the present spatio-temporal resolution of bio-optical variables to be progressively filled. - Chapter 3 identifies the optical and bio-optical properties that are now amenable to remote and autonomous measurement through the use of optical sensors mounted on floats. - Chapter 4 addresses the question of sensor requirements, in particular with respect to measurements performed from floats. - Chapter 5 proposes and argues for the development of dedicated float missions corresponding to specific scientific objectives and relying on specific optical sensor suites, as well as on specific modes of float operation. - Chapter 6 identifies technological issues that need to be addressed for the various bio-optical float missions to become even more cost-effective. - Chapter 7 covers all aspects of data treatment ranging from the development of various quality control procedures (from real-time to delayed mode) to the architecture required for favoring easy access to data. - Chapter 8 reviews the necessary steps and experience required before the operational implementation of different types of float networks can become a reality.JRC.H.5-Land Resources Managemen

Autonomous observations of in vivo fluorescence and particle backscattering in an oceanic oxygen minimum zone

The eastern South Pacific (ESP) oxygen minimum zone (OMZ) is a permanent hydrographic feature located directly off the coasts of northern Chile and Peru. The ESP OMZ reaches from coastal waters out to thousands of kilometers offshore, and can extend from the near surface to depths greater than 700 m. Oxygen minimum zones support unique microbial assemblages and play an important role in marine elemental cycles. We present results from two autonomous profiling floats that provide nine months of time-series data on temperature, salinity, dissolved oxygen, chlorophyll a, and particulate backscattering in the ESP OMZ. We observed consistently elevated backscattering signals within low-oxygen waters, which appear to be the result of enhanced microbial biomass in the OMZ intermediate waters. We also observed secondary chlorophyll a fluorescence maxima within low-oxygen waters when the upper limit of the OMZ penetrated the base of the photic zone. We suggest that autonomous profiling floats are useful tools for monitoring physical dynamics of OMZs and the microbial response to perturbations in these areas.This paper was published in Optics Express and is made available as an electronic reprint with the permission of OSA. The paper can be found at the following URL on the OSA website: http://www.opticsinfobase.org/oe/home.cfm. Systematic or multiple reproduction or distribution to multiple locations via electronic or other means is prohibited and is subject to penalties under law

Nitrogen Assimilation in Picocyanobacteria Inhabiting the Oxygen-Deficient Waters of the Eastern Tropical North and South Pacific

Prochlorococcus and Synechococcus are the most abundant free-living photosynthetic microorganisms in the ocean. Uncultivated lineages of these picocyanobacteria also thrive in the dimly illuminated upper part of oxygen-deficient zones (ODZs), where an important portion of ocean nitrogen (N) loss takes place via denitrification and anaerobic ammonium oxidation. Recent metagenomic studies revealed that ODZ Prochlorococcus have the genetic potential for using different N forms, including nitrate and nitrite, uncommon N sources for Prochlorococcus, but common for Synechococcus. To determine which N sources ODZ picocyanobacteria are actually using in nature, the cellular 15N natural abundance (δ15N) and assimilation rates of different N compounds were determined using cell sorting by flow cytometry and mass spectrometry. The natural δ15N of the ODZ Prochlorococcus varied from −4.0‰ to 13.0‰ (n = 9), with 50% of the values in the range of −2.1–2.6‰. While the highest values suggest nitrate use, most observations indicate the use of nitrite, ammonium, or a mixture of N sources. Meanwhile, incubation experiments revealed potential assimilation rates of ammonium and urea in the same order of magnitude as that expected for total N in several environments including ODZs, whereas rates of nitrite and nitrate assimilation were very low. Our results thus indicate that reduced forms of N and nitrite are the dominant sources for ODZ picocyanobacteria, although nitrate might be important on some occasions. ODZ picocyanobacteria might thus represent potential competitors with anammox bacteria for ammonium and nitrite, with ammonia-oxidizing archaea for ammonium, and with nitrite-oxidizing bacteria for nitrite

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gazitua, M. C., Vik, D. R., Roux, S., Gregory, A. C., Bolduc, B., Widner, B., Mulholland, M. R., Hallam, S. J., Ulloa, O., & Sullivan, M. B. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. Isme Journal, (2020), doi:10.1038/s41396-020-00825-6.Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.We thank Sullivan Lab members and Heather Maughan for comments on the paper, Bess Ward for her contribution in the N-cycle context of our story, Kurt Hanselmann for his assistance in the calculations of the Gibbs-free energies, and the scientific party and crew of the R/V Atlantis (grant OCE-1356056 to MRM) for the sampling opportunity and support at sea. This work was funded in part by awards from the Agouron Institute to OU and MBS, a Gordon and Betty Moore Foundation Investigator Award (#3790) and NSF Biological Oceanography Awards (#1536989 and #1829831) to MBS, and the Millennium Science Initiative (grant ICN12_019-IMO) to OU. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231

Potential Virus-Mediated Nitrogen Cycling in Oxygen-Depleted Oceanic Waters

Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models