scholarly journals Comment on “Diversity and distribution of Nitrogen Fixation Genes in the Oxygen Minimum Zones of the World Oceans” by Amal Jayakumar and Bess B. Ward

2020 ◽  
Keyword(s):  
Nitrogen Fixation ◽  
Oxygen Minimum Zones ◽  
The World ◽  
Oxygen Minimum ◽  
Nitrogen Fixation Genes

scholarly journals Diversity and distribution of Nitrogen Fixation Genes in the Oxygen Minimum Zones of the World Oceans

2020 ◽  
Author(s):  
Amal Jayakumar ◽  
Bess B. Ward
Keyword(s):  
Nitrogen Fixation ◽  
Surface Waters ◽  
World Ocean ◽  
Operational Taxonomic Unit ◽  
N Fixation ◽  
Oxygen Minimum Zones ◽  
Abundant Otus ◽  
The World ◽  
Nifh Genes ◽  
Oxygen Minimum

Abstract. Diversity and community composition of nitrogen fixing microbes in the three main oxygen minimum zones (OMZs) of the world ocean were investigated using operational taxonomic unit (OTU) analysis of nifH clone libraries. Representatives of the all four main clusters of nifH genes were detected. Cluster I sequences were most diverse in the surface waters and the most abundant OTUs were affiliated with Alpha- and Gammaproteobacteria. Cluster II, III, IV assemblages were most diverse at oxygen depleted depths and none of the sequences were closely related to sequences from cultivated organisms. The OTUs were biogeographically distinct for the most part – there was little overlap among regions, between depths or between cDNA and DNA. Only a few cyanobacterial sequences were detected. The prevalence and diversity of microbes that harbour nifH genes in the OMZ regions, where low rates of N fixation are reported, remains an enigma.

scholarly journals Diversity and distribution of nitrogen fixation genes in the oxygen minimum zones of the world oceans

2020 ◽  
Vol 17 (23) ◽  
pp. 5953-5966
Author(s):  
Amal Jayakumar ◽  
Bess B. Ward
Keyword(s):  
Community Composition ◽  
Surface Waters ◽  
World Ocean ◽  
Operational Taxonomic Unit ◽  
N Fixation ◽  
Oxygen Minimum Zones ◽  
Abundant Otus ◽  
The World ◽  
Nifh Genes ◽  
Oxygen Minimum

Abstract. Diversity and community composition of nitrogen (N) fixing microbes in the three main oxygen minimum zones (OMZs) of the world ocean were investigated using operational taxonomic unit (OTU) analysis of nifH clone libraries. Representatives of three of the four main clusters of nifH genes were detected. Cluster I sequences were most diverse in the surface waters, and the most abundant OTUs were affiliated with Alpha- and Gammaproteobacteria. Cluster II, III, and IV assemblages were most diverse at oxygen-depleted depths, and none of the sequences were closely related to sequences from cultivated organisms. The OTUs were biogeographically distinct for the most part – there was little overlap among regions, between depths, or between cDNA and DNA. In this study of all three OMZ regions, as well as from the few other published reports from individual OMZ sites, the dominance of a few OTUs was commonly observed. This pattern suggests the dynamic response of the components of the overall diverse assemblage to variable environmental conditions. Community composition in most samples was not clearly explained by environmental factors, but the most abundant OTUs were differentially correlated with the obvious variables, temperature, salinity, oxygen, and nitrite concentrations. Only a few cyanobacterial sequences were detected. The prevalence and diversity of microbes that harbor nifH genes in the OMZ regions, where low rates of N fixation are reported, remains an enigma.

scholarly journals In situ quantification of ultra‐low O 2 concentrations in oxygen minimum zones: Application of novel optodes

2016 ◽  
Vol 14 (12) ◽  
pp. 784-800 ◽  
Author(s):  
Morten Larsen ◽  
Philipp Lehner ◽  
Sergey M. Borisov ◽  
Ingo Klimant ◽  
Jan P. Fischer ◽  
...  
Keyword(s):  
Oxygen Minimum Zones ◽  
Oxygen Minimum

Expression of the nodulation and nitrogen fixation genes in Rhizobium meliloti during development

Genome ◽  
1989 ◽  
Vol 31 (1) ◽  
pp. 354-360 ◽  
Author(s):  
San Chiun Shen ◽  
Shui Ping Wang ◽  
Guan Qiao Yu ◽  
Jia Bi Zhu
Keyword(s):  
Nitrogen Fixation ◽  
Rhizobium Meliloti ◽  
Abnormal Development ◽  
Wild Type ◽  
Free Living ◽  
Nod Genes ◽  
Nodule Initiation ◽  
Fix Genes ◽  
Nitrogen Fixation Genes

Genes that specify nodulation (nod genes) are only active in the free-living rhizobia or in the nodule initiation state of rhizobia. As soon as the repression of nod genes occurs in the bacteroids of the nodule, nifA is induced, while ntrC is inactivated and thus the nifA-mediated nif/fix genes are turned on. Limitation of available oxygen brings about the induction of nifA, which reflects the actual status of nif/fix gene activities in symbiotic state of rhizobia. Oxygen thus appears to be a major symbiotic signal to the expression of bacteroid nif/fix genes. Mutation of nifA or shortage of nifA product in wild-type rhizobia caused by the inhibition of multicopy nifH/fixA promoters leads to an abnormal development of nodules and premature degradation of bacteroids in nodules.Key words: nitrogen fixation, nodulation, nif/fix regulation, nifA mutant.

scholarly journals Expanded oxygen minimum zones during the late Paleocene-early Eocene: Hints from multiproxy comparison and ocean modeling

2016 ◽  
Vol 31 (12) ◽  
pp. 1532-1546 ◽  
Author(s):  
X. Zhou ◽  
E. Thomas ◽  
A. M. E. Winguth ◽  
A. Ridgwell ◽  
H. Scher ◽  
...  
Keyword(s):  
Ocean Modeling ◽  
Early Eocene ◽  
Oxygen Minimum Zones ◽  
Late Paleocene ◽  
Oxygen Minimum

scholarly journals Biological nitrogen fixation in the oxygen-minimum region of the eastern tropical North Pacific ocean

2017 ◽  
Vol 11 (10) ◽  
pp. 2356-2367 ◽  
Author(s):  
Amal Jayakumar ◽  
Bonnie X Chang ◽  
Brittany Widner ◽  
Peter Bernhardt ◽  
Margaret R Mulholland ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Pacific Ocean ◽  
North Pacific ◽  
Biological Nitrogen Fixation ◽  
North Pacific Ocean ◽  
Biological Nitrogen ◽  
Oxygen Minimum

scholarly journals Following the N<sub>2</sub>O consumption at the Oxygen Minimum Zone in the eastern South Pacific

2012 ◽  
Vol 9 (3) ◽  
pp. 2691-2707 ◽  
Author(s):  
M. Cornejo ◽  
L. Farías
Keyword(s):  
Primary Productivity ◽  
High Reliability ◽  
World Ocean ◽  
South Pacific ◽  
Future Scenarios ◽  
N2o Production ◽  
The World ◽  
Minimum Zone ◽  
Latitudinal Range ◽  
Oxygen Minimum

Abstract. Oxygen deficient zones (OMZs), such as those found in the eastern South Pacific (ESP), are the most important N2O sources in the world ocean relative to their volume. N2O production is related to low O2 concentrations and high primary productivity. However, when O2 is sufficiently low, canonical denitrification takes place and N2O consumption can be expected. N2O distribution in the ESP was analyzed over a wide latitudinal range (from 5° to 30° S and 71°–76° to ~84° W) based on ~890 N2O measurements. The intense consumption of N2O appears to be related to secondary NO2− accumulation, the best indicator of very low O2 levels. Using relationships that depend on threshold levels of O2 (<8 μM) and nitrite (>0.75 μM), we reproduced the apparent N2O production (ΔN2O) with high reliability (r2=0.73 p=0.01). Our results contribute to quantify the ratio of N2O production/consumption that is being cycling in O2 deficient water of N2O and may improve the prediction of N2O behavior under future scenarios of the OMZ expansion.

scholarly journals Toward a global calibration for quantifying past oxygenation in oxygen minimum zones using benthic Foraminifera

2021 ◽  
Author(s):  
Martin Tetard ◽  
Laetitia Licari ◽  
Kazuyo Tachikawa ◽  
Ekaterina Ovsepyan ◽  
Luc Beaufort
Keyword(s):  
North Pacific ◽  
Transfer Functions ◽  
Late Quaternary ◽  
Global Climate ◽  
Single Species ◽  
Pore Waters ◽  
Oxygen Minimum Zones ◽  
Global Calibration ◽  
Circularity Index ◽  
Oxygen Minimum

Abstract. Oxygen Minimum Zones (OMZs) are oceanic areas largely depleted in dissolved oxygen, nowadays considered in expansion in the face of global warming. Their ecological and economic consequences are being debated. The investigation of past OMZ conditions allows us to better understand biological and physical mechanisms responsible for their variability with regards to climate change, carbon pump and carbonate system. To investigate the relationship between OMZ expansion and global climate changes during the late Quaternary, quantitative oxygen reconstructions are needed, but are still in their early development. Here, past bottom water oxygenation (BWO) was quantitatively assessed through a new, fast, semi-automated, and taxonfree morphometric analysis of benthic foraminiferal tests, developed and calibrated using Eastern North Pacific (ENP) and the Eastern South Pacific (ESP) OMZs samples. This new approach is based on an average size and circularity index for each sample. This method, as well as two already published micropalaeontological approaches based on benthic foraminiferal assemblages variability and porosity investigation of a single species, were here calibrated based on availability of new data from 23 core tops recovered along an oxygen gradient (from 0.03 to 1.79 mL.L−1) from the ENP, ESP, AS (Arabian Sea) and WNP (Western North Pacific, including its marginal seas) OMZs. Global calibrated transfer functions are thus herein proposed for each of these methods. These micropalaeontological reconstruction approaches were then applied on a paleorecord from the ENP OMZ to examine the consistency and limits of these methods, as well as the relative influence of bottom and pore waters on these micropalaeontological tools. Both the assemblages and morphometric approaches (that is also ultimately based on the ecological response of the complete assemblage and faunal succession according to BWO) gave similar and consistent past BWO reconstructions, while the porosity approach (based on a single species and its unique response to a mixed signal of bottom and pore waters) shown ambiguous estimations.

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