In depth characterization of diazotroph activity across the Western Tropical South Pacific hot spot of N2 fixation

2018 ◽  
Author(s):  
Anonymous
Keyword(s):  
N2 Fixation ◽  
Hot Spot ◽  
South Pacific

scholarly journals In depth characterization of diazotroph activity across the Western Tropical South Pacific hot spot of N<sub>2</sub> fixation

2018 ◽  
Author(s):  
Sophie Bonnet ◽  
Mathieu Caffin ◽  
Hugo Berthelot ◽  
Olivier Grosso ◽  
Mar Benavides ◽  
...  
Keyword(s):  
N2 Fixation ◽  
Secondary Ion Mass Spectrometry ◽  
Hot Spot ◽  
Average Rate ◽  
South Pacific ◽  
Isotopic Analyses ◽  
Nitrogenase Genes ◽  
South Pacific Gyre ◽  
Secondary Ion

Abstract. Here we report quantification of N2 fixation rates over a ~ 4000 km transect in the western and central tropical South Pacific. Water samples were collected along a west to east transect from 160° E to 160° W, covering contrasting trophic regimes, from oligotrophy in the Melanesian archipelagoes (MA) waters to ultra-oligotrophy in the South Pacific Gyre (GY) waters. N2 fixation was detected at all 17 sampled stations with an average rate of 631 ± 286 µmol N m−2 d−1 (range 196–1153 µmol N m−2 d−1) in MA waters and of 85 ± 79 µmol N m−2 d−1 (range 18–172 µmol N m−2 d−1) in GY waters. Exceptionally high rates of N2 fixation in MA waters were favored by availability of both iron and phosphate and the observed warm sea surface temperatures (> 28 °C). Trichodesmium and UCYN-B cyanobacteria dominated the diazotroph community (> 80 %) and gene expression of nitrogenase genes (cDNA > 105 nifH copies L−1) in MA waters, and single-cell isotopic analyses performed by nanoscale secondary ion mass spectrometry at selected stations reveal that Trichodesmium was always the major contributor to N2 fixation in MA waters, accounting for 47.1 to 83.8 % of bulk N2 fixation.

scholarly journals In-depth characterization of diazotroph activity across the western tropical South Pacific hotspot of N<sub>2</sub> fixation (OUTPACE cruise)

2018 ◽  
Vol 15 (13) ◽  
pp. 4215-4232 ◽  
Author(s):  
Sophie Bonnet ◽  
Mathieu Caffin ◽  
Hugo Berthelot ◽  
Olivier Grosso ◽  
Mar Benavides ◽  
...  
Keyword(s):  
N2 Fixation ◽  
Secondary Ion Mass Spectrometry ◽  
Seawater Temperature ◽  
Nifh Gene ◽  
World Ocean ◽  
South Pacific ◽  
Isotopic Analyses ◽  
South Pacific Gyre

Abstract. Here we report N2 fixation rates from a ∼ 4000 km transect in the western and central tropical South Pacific, a particularly undersampled region in the world ocean. Water samples were collected in the euphotic layer along a west to east transect from 160∘ E to 160∘ W that covered contrasting trophic regimes, from oligotrophy in the Melanesian archipelago (MA) waters to ultra-oligotrophy in the South Pacific Gyre (GY) waters. N2 fixation was detected at all 17 sampled stations with an average depth-integrated rate of 631 ± 286 µmolNm-2d-1 (range 196–1153 µmolNm-2d-1) in MA waters and of 85 ± 79 µmolNm-2d-1 (range 18–172 µmolNm-2d-1) in GY waters. Two cyanobacteria, the larger colonial filamentous Trichodesmium and the smaller UCYN-B, dominated the enumerated diazotroph community (> 80 %) and gene expression of the nifH gene (cDNA > 105 nifH copies L−1) in MA waters. Single-cell isotopic analyses performed by nanoscale secondary ion mass spectrometry (nanoSIMS) at selected stations revealed that Trichodesmium was always the major contributor to N2 fixation in MA waters, accounting for 47.1–83.8 % of bulk N2 fixation. The most plausible environmental factors explaining such exceptionally high rates of N2 fixation in MA waters are discussed in detail, emphasizing the role of macro- and micro-nutrient (e.g., iron) availability, seawater temperature and currents.

scholarly journals Hot spot of N2 fixation in the western tropical South Pacific pleads for a spatial decoupling between N2 fixation and denitrification

2017 ◽  
Vol 114 (14) ◽  
pp. E2800-E2801 ◽  
Author(s):  
Sophie Bonnet ◽  
Mathieu Caffin ◽  
Hugo Berthelot ◽  
Thierry Moutin
Keyword(s):  
N2 Fixation ◽  
Hot Spot ◽  
South Pacific

scholarly journals Aphotic N<sub>2</sub> fixation along an oligotrophic to ultraoligotrophic transect in the western tropical South Pacific Ocean

2018 ◽  
Vol 15 (10) ◽  
pp. 3107-3119 ◽  
Author(s):  
Mar Benavides ◽  
Katyanne M. Shoemaker ◽  
Pia H. Moisander ◽  
Jutta Niggemann ◽  
Thorsten Dittmar ◽  
...  
Keyword(s):  
N2 Fixation ◽  
Water Mass ◽  
New Caledonia ◽  
Hot Spot ◽  
Nifh Gene ◽  
South Pacific ◽  
French Polynesia ◽  
Mode Water ◽  
Fixation Activity ◽  
Nitrogen Inputs

Abstract. The western tropical South Pacific (WTSP) Ocean has been recognized as a global hot spot of dinitrogen (N2) fixation. Here, as in other marine environments across the oceans, N2 fixation studies have focused on the sunlit layer. However, studies have confirmed the importance of aphotic N2 fixation activity, although until now only one had been performed in the WTSP. In order to increase our knowledge of aphotic N2 fixation in the WTSP, we measured N2 fixation rates and identified diazotrophic phylotypes in the mesopelagic layer along a transect spanning from New Caledonia to French Polynesia. Because non-cyanobacterial diazotrophs presumably need external dissolved organic matter (DOM) sources for their nutrition, we also identified DOM compounds using Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) with the aim of searching for relationships between the composition of DOM and non-cyanobacterial N2 fixation in the aphotic ocean. N2 fixation rates were low (average 0.63 ± 0.07 nmol N L−1 d−1) but consistently detected across all depths and stations, representing ∼ 6–88 % of photic N2 fixation. N2 fixation rates were not significantly correlated with DOM compounds. The analysis of nifH gene amplicons revealed a wide diversity of non-cyanobacterial diazotrophs, mostly matching clusters 1 and 3. Interestingly, a distinct phylotype from the major nifH subcluster 1G dominated at 650 dbar, coinciding with the oxygenated Subantarctic Mode Water (SAMW). This consistent pattern suggests that the distribution of aphotic diazotroph communities is to some extent controlled by water mass structure. While the data available are still too scarce to elucidate the distribution and controls of mesopelagic non-cyanobacterial diazotrophs in the WTSP, their prevalence in the mesopelagic layer and the consistent detection of active N2 fixation activity at all depths sampled during our study suggest that aphotic N2 fixation may contribute significantly to fixed nitrogen inputs in this area and/or areas downstream of water mass circulation.

scholarly journals Evidence for efficient regenerated production and dinitrogen fixation in nitrogen-deficient waters of the South Pacific Ocean: impact on new and export production estimates

2008 ◽  
Vol 5 (2) ◽  
pp. 323-338 ◽  
Author(s):  
P. Raimbault ◽  
N. Garcia
Keyword(s):  
Pacific Ocean ◽  
Nitrogen Uptake ◽  
N2 Fixation ◽  
Inorganic Nitrogen ◽  
South Pacific ◽  
Dinitrogen Fixation ◽  
The South ◽  
New Production ◽  
Marquesas Islands ◽  
South Pacific Ocean

Abstract. One of the major objectives of the BIOSOPE cruise, carried out on the R/V Atalante from October-November 2004 in the South Pacific Ocean, was to establish productivity rates along a zonal section traversing the oligotrophic South Pacific Gyre (SPG). These results were then compared to measurements obtained from the nutrient – replete waters in the Chilean upwelling and around the Marquesas Islands. A dual 13C/15N isotope technique was used to estimate the carbon fixation rates, inorganic nitrogen uptake (including dinitrogen fixation), ammonium (NH4) and nitrate (NO3) regeneration and release of dissolved organic nitrogen (DON). The SPG exhibited the lowest primary production rates (0.15 g C m−2 d−1), while rates were 7 to 20 times higher around the Marquesas Islands and in the Chilean upwelling, respectively. In the very low productive area of the SPG, most of the primary production was sustained by active regeneration processes that fuelled up to 95% of the biological nitrogen demand. Nitrification was active in the surface layer and often balanced the biological demand for nitrate, especially in the SPG. The percentage of nitrogen released as DON represented a large proportion of the inorganic nitrogen uptake (13–15% in average), reaching 26–41% in the SPG, where DON production played a major role in nitrogen cycling. Dinitrogen fixation was detectable over the whole study area; even in the Chilean upwelling, where rates as high as 3 nmoles l−1 d−1 were measured. In these nutrient-replete waters new production was very high (0.69±0.49 g C m−2 d−1) and essentially sustained by nitrate levels. In the SPG, dinitrogen fixation, although occurring at much lower daily rates (≈1–2 nmoles l−1 d−1), sustained up to 100% of the new production (0.008±0.007 g C m−2 d−1) which was two orders of magnitude lower than that measured in the upwelling. The annual N2-fixation of the South Pacific is estimated to 21×1012g, of which 1.34×1012g is for the SPG only. Even if our "snapshot" estimates of N2-fixation rates were lower than that expected from a recent ocean circulation model, these data confirm that the N-deficiency South Pacific Ocean would provide an ideal ecological niche for the proliferation of N2-fixers which are not yet identified.

scholarly journals Remote sensing of <i>Trichodesmium</i> spp. mats in the western tropical South Pacific

2018 ◽  
Vol 15 (16) ◽  
pp. 5203-5219 ◽  
Author(s):  
Guillaume Rousset ◽  
Florian De Boissieu ◽  
Christophe E. Menkes ◽  
Jérôme Lefèvre ◽  
Robert Frouin ◽  
...  
Keyword(s):  
Remote Sensing ◽  
Large Scale ◽  
New Caledonia ◽  
Hot Spot ◽  
Regional Scale ◽  
Atmospheric Correction ◽  
South Pacific ◽  
Aggregation Processes ◽  
Modis Imagery ◽  
Generate Surface

Abstract. Trichodesmium is the major nitrogen-fixing species in the western tropical South Pacific (WTSP) region, a hot spot of diazotrophy. Due to the paucity of in situ observations, remote-sensing methods for detecting Trichodesmium presence on a large scale have been investigated to assess the regional-to-global impact of this organism on primary production and carbon cycling. A number of algorithms have been developed to identify Trichodesmium surface blooms from space, but determining with confidence their accuracy has been difficult, chiefly because of the scarcity of sea-truth information at the time of satellite overpass. Here, we use a series of new cruises as well as airborne surveys over the WTSP to evaluate their ability to detect Trichodesmium surface blooms in the satellite imagery. The evaluation, performed on MODIS data at 250 m and 1 km resolution acquired over the region, shows limitations due to spatial resolution, clouds, and atmospheric correction. A new satellite-based algorithm is designed to alleviate some of these limitations, by exploiting optimally spectral features in the atmospherically corrected reflectance at 531, 645, 678, 748, and 869 nm. This algorithm outperforms former ones near clouds, limiting false positive detection and allowing regional-scale automation. Compared with observations, 80 % of the detected mats are within a 2 km range, demonstrating the good statistical skill of the new algorithm. Application to MODIS imagery acquired during the February-March 2015 OUTPACE campaign reveals the presence of surface blooms northwest and east of New Caledonia and near 20∘ S–172∘ W in qualitative agreement with measured nitrogen fixation rates. Improving Trichodesmium detection requires measuring ocean color at higher spectral and spatial (<250 m) resolution than MODIS, taking into account environment properties (e.g., wind, sea surface temperature), fluorescence, and spatial structure of filaments, and a better understanding of Trichodesmium dynamics, including aggregation processes to generate surface mats. Such sub-mesoscale aggregation processes for Trichodesmium are yet to be understood.

scholarly journals Redefining the Subsurface Biosphere: Characterization of Fungi Isolated From Energy-Limited Marine Deep Subsurface Sediment

2021 ◽  
Vol 2 ◽  
Author(s):  
Brandi Kiel Reese ◽  
Morgan S. Sobol ◽  
Marshall Wayne Bowles ◽  
Kai-Uwe Hinrichs
Keyword(s):  
Organic Carbon ◽  
Growth Parameters ◽  
Carbon Sources ◽  
South Pacific ◽  
Physical Growth ◽  
Energy Budgets ◽  
Deep Subsurface ◽  
Fungal Populations ◽  
South Pacific Gyre

The characterization of metabolically active fungal isolates within the deep marine subsurface will alter current ecosystem models and living biomass estimates that are limited to bacterial and archaeal populations. Although marine fungi have been studied for over fifty years, a detailed description of fungal populations within the deep subsurface is lacking. Fungi possess metabolic pathways capable of utilizing previously considered non-bioavailable energy reserves. Therefore, metabolically active fungi would occupy a unique niche within subsurface ecosystems, with the potential to provide an organic carbon source for heterotrophic prokaryotic populations from the transformation of non-bioavailable energy into substrates, as well as from the fungal necromass itself. These organic carbon sources are not currently being considered in subsurface energy budgets. Sediments from South Pacific Gyre subsurface, one of the most energy-limited environments on Earth, were collected during the Integrated Ocean Drilling Program Expedition 329. Anoxic and oxic sediment slurry enrichments using fresh sediment were used to isolate multiple fungal strains in media types that varied in organic carbon substrates and concentration. Metabolically active and dormant fungal populations were also determined from nucleic acids extracted from in situ cryopreserved South Pacific Gyre sediments. For further characterization of physical growth parameters, two isolates were chosen based on their representation of the whole South Pacific Gyre fungal community. Results from this study show that fungi have adapted to be metabolically active and key community members in South Pacific Gyre sediments and potentially within global biogeochemical cycles.

scholarly journals Identification and Characterization of a Novel clcn7 Variant Associated With Osteopetrosis

2020 ◽  
Author(s):  
Dmitrii S. Bug ◽  
Ildar M. Barkhatov ◽  
Yana V. Gudozhnikova ◽  
Artem V. Tishkov ◽  
Natalia V. Petukhova ◽  
...  
Keyword(s):  
Structure Analysis ◽  
Evolutionary History ◽  
Hot Spot ◽  
Phylogenetic Reconstruction ◽  
Novel Variant ◽  
Uncertain Significance ◽  
Precise Diagnosis ◽  
History Of ◽  
Identification And Characterization

Osteopetrosis is a group of rare inheritable disorders of the skeleton characterized by increased bone density. The disease is remarkably heterogeneous in clinical presentation and often misdiagnosed. Therefore, genetic testing and molecular pathogenicity analysis are essential for precise diagnosis and new targets for preventive pharmacotherapy. Mutations in the CLCN7 gene give rise to the complete spectrum of osteopetrosis phenotypes and are responsible for about 75% of cases of autosomal dominant osteopetrosis. In this study, we report the identification of a novel variant in the CLCN7 gene in a patient diagnosed with osteopetrosis and provide evidence for its significance (likely deleterious) based on extensive comparative genomics, protein sequence and structure analysis. A set of automated bioinformatics tools used to predict consequences of this variant identified it as deleterious or pathogenic. Structure analysis revealed that the variant is located at the same &ldquo;hot spot&rdquo; as the most common CLCN7 mutations causing osteopetrosis. Deep phylogenetic reconstruction showed that not only Leu614Arg, but any non-aliphatic substitutions in this position are evolutionarily intolerant, further supporting the deleterious nature of the variant. The present study provides further evidence that reconstructing a precise evolutionary history of a gene helps predicting phenotypical consequences of variants of uncertain significance.

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