The Experts below are selected from a list of 186 Experts worldwide ranked by ideXlab platform
Luis M. Rubio - One of the best experts on this subject based on the ideXlab platform.
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Molybdenum trafficking for Nitrogen Fixation
Biochemistry, 2009Co-Authors: José A. Hernández, Simon J George, Luis M. RubioAbstract:The molybdenum Nitrogenase is responsible for most biological Nitrogen Fixation, a prokaryotic metabolic process that determines the global biogeochemical cycles of Nitrogen and carbon. Here we describe the trafficking of molybdenum for Nitrogen Fixation in the model diazotrophic bacterium Azotobacter vinelandii. The genes and proteins involved in molybdenum uptake, homeostasis, storage, regulation, and Nitrogenase cofactor biosynthesis are reviewed. Molybdenum biochemistry in A. vinelandii reveals unexpected mechanisms and a new role for iron-sulfur clusters in the sequestration and delivery of molybdenum.
José A. Hernández - One of the best experts on this subject based on the ideXlab platform.
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Molybdenum trafficking for Nitrogen Fixation
Biochemistry, 2009Co-Authors: José A. Hernández, Simon J George, Luis M. RubioAbstract:The molybdenum Nitrogenase is responsible for most biological Nitrogen Fixation, a prokaryotic metabolic process that determines the global biogeochemical cycles of Nitrogen and carbon. Here we describe the trafficking of molybdenum for Nitrogen Fixation in the model diazotrophic bacterium Azotobacter vinelandii. The genes and proteins involved in molybdenum uptake, homeostasis, storage, regulation, and Nitrogenase cofactor biosynthesis are reviewed. Molybdenum biochemistry in A. vinelandii reveals unexpected mechanisms and a new role for iron-sulfur clusters in the sequestration and delivery of molybdenum.
Ray Dixon - One of the best experts on this subject based on the ideXlab platform.
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Distribution of Nitrogen Fixation and Nitrogenase-like sequences amongst microbial genomes
BMC Genomics, 2012Co-Authors: Patricia C Dos Santos, Steven W Mason, João C Setubal, Zhong Yi-fang, Ray DixonAbstract:Background The metabolic capacity for Nitrogen Fixation is known to be present in several prokaryotic species scattered across taxonomic groups. Experimental detection of Nitrogen Fixation in microbes requires species-specific conditions, making it difficult to obtain a comprehensive census of this trait. The recent and rapid increase in the availability of microbial genome sequences affords novel opportunities to re-examine the occurrence and distribution of Nitrogen Fixation genes. The current practice for computational prediction of Nitrogen Fixation is to use the presence of the nifH and/or nifD genes. Results Based on a careful comparison of the repertoire of Nitrogen Fixation genes in known diazotroph species we propose a new criterion for computational prediction of Nitrogen Fixation: the presence of a minimum set of six genes coding for structural and biosynthetic components, namely NifHDK and NifENB. Using this criterion, we conducted a comprehensive search in fully sequenced genomes and identified 149 diazotrophic species, including 82 known diazotrophs and 67 species not known to fix Nitrogen. The taxonomic distribution of Nitrogen Fixation in Archaea was limited to the Euryarchaeota phylum; within the Bacteria domain we predict that Nitrogen Fixation occurs in 13 different phyla. Of these, seven phyla had not hitherto been known to contain species capable of Nitrogen Fixation. Our analyses also identified protein sequences that are similar to Nitrogenase in organisms that do not meet the minimum-gene-set criteria. The existence of Nitrogenase-like proteins lacking conserved co-factor ligands in both diazotrophs and non-diazotrophs suggests their potential for performing other, as yet unidentified, metabolic functions. Conclusions Our predictions expand the known phylogenetic diversity of Nitrogen Fixation, and suggest that this trait may be much more common in nature than it is currently thought. The diverse phylogenetic distribution of Nitrogenase-like proteins indicates potential new roles for anciently duplicated and divergent members of this group of enzymes.
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distribution of Nitrogen Fixation and Nitrogenase like sequences amongst microbial genomes
BMC Genomics, 2012Co-Authors: Patricia Dos C Santos, Steven W Mason, João C Setubal, Zhong Yi-fang, Ray DixonAbstract:The metabolic capacity for Nitrogen Fixation is known to be present in several prokaryotic species scattered across taxonomic groups. Experimental detection of Nitrogen Fixation in microbes requires species-specific conditions, making it difficult to obtain a comprehensive census of this trait. The recent and rapid increase in the availability of microbial genome sequences affords novel opportunities to re-examine the occurrence and distribution of Nitrogen Fixation genes. The current practice for computational prediction of Nitrogen Fixation is to use the presence of the nifH and/or nifD genes. Based on a careful comparison of the repertoire of Nitrogen Fixation genes in known diazotroph species we propose a new criterion for computational prediction of Nitrogen Fixation: the presence of a minimum set of six genes coding for structural and biosynthetic components, namely NifHDK and NifENB. Using this criterion, we conducted a comprehensive search in fully sequenced genomes and identified 149 diazotrophic species, including 82 known diazotrophs and 67 species not known to fix Nitrogen. The taxonomic distribution of Nitrogen Fixation in Archaea was limited to the Euryarchaeota phylum; within the Bacteria domain we predict that Nitrogen Fixation occurs in 13 different phyla. Of these, seven phyla had not hitherto been known to contain species capable of Nitrogen Fixation. Our analyses also identified protein sequences that are similar to Nitrogenase in organisms that do not meet the minimum-gene-set criteria. The existence of Nitrogenase-like proteins lacking conserved co-factor ligands in both diazotrophs and non-diazotrophs suggests their potential for performing other, as yet unidentified, metabolic functions. Our predictions expand the known phylogenetic diversity of Nitrogen Fixation, and suggest that this trait may be much more common in nature than it is currently thought. The diverse phylogenetic distribution of Nitrogenase-like proteins indicates potential new roles for anciently duplicated and divergent members of this group of enzymes.
Douglas G. Capone - One of the best experts on this subject based on the ideXlab platform.
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Emerging patterns of marine Nitrogen Fixation
Nature reviews. Microbiology, 2011Co-Authors: Jill A. Sohm, Eric A. Webb, Douglas G. CaponeAbstract:Biological Nitrogen Fixation is an important part of the marine Nitrogen cycle, supporting carbon export and sequestration. In this Review, Sohm, Webb and Capone describe the nutrients that limit Nitrogen Fixation and the distribution of diazotrophic species in the world's oceans.
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Nitrogen Fixation and denitrification
Methods in Microbiology, 2004Co-Authors: Douglas G. Capone, Joseph P. MontoyaAbstract:Publisher Summary The chapter discusses Nitrogen Fixation, denitrification, and their applications. It discusses the most widely used enzyme-based and direct tracer procedures in the N cycle- N 2 Fixation and denitrification. Biological Nitrogen Fixation is the enzymological capacity of certain bacteria and Archaea to convert gaseous diNitrogen to ammonium on a pathway to amino acid synthesis. In marine systems, the attention is focused on diazotrophic cyanobacteria, because of their quantitative importance in supplying new N to the upper ocean. Nitrogenase activity is routinely determined in many laboratories using the C 2 H 2 reduction procedure. Denitrification is measured conveniently in many microbial systems by addition of C 2 H 2 , which inhibits N 2 O reductase, the last step of the denitrification pathway. The presence of C 2 H 2 results in the accumulation of N 2 O, which is detected selectively and sensitively by electron capture gas chromatography. Many of the procedures and conceptual design of denitrification experiments parallel those of the C 2 H 2 reduction procedure. As for Nitrogen Fixation, denitrification can also be measured directly by the introduction of enriched 15-N nitrate (or nitrite) into a system, with the determination of progressive enrichment of 15N in the N 2 pool.
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Marine Nitrogen Fixation: what's the fuss?
Current opinion in microbiology, 2001Co-Authors: Douglas G. CaponeAbstract:Biological Nitrogen Fixation is a much more important process in the Nitrogen cycle of the oceans than previously thought. Further, Nitrogen Fixation may have an influence on the capacity of the oceans to sequester carbon. A greater diversity of marine Nitrogen fixers has also been uncovered but their quantitative significance remains to be determined.
Mark C Moore - One of the best experts on this subject based on the ideXlab platform.
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large scale distribution of atlantic Nitrogen Fixation controlled by iron availability
Nature Geoscience, 2009Co-Authors: Julie Laroche, Mark C Moore, Matthew M Mills, Eric P Achterberg, Richard J Geider, Mike Lucas, Elaine L Mcdonagh, Xi Pan, Alex J PoultonAbstract:Oceanic fixed-Nitrogen concentrations are controlled by the balance between Nitrogen Fixation and denitrification1, 2, 3, 4. A number of factors, including iron limitation5, 6, 7, can restrict Nitrogen Fixation, introducing the potential for decoupling of Nitrogen inputs and losses2, 5, 8. Such decoupling could significantly affect the oceanic fixed-Nitrogen inventory and consequently the biological component of ocean carbon storage and hence air–sea partitioning of carbon dioxide2, 5, 8, 9. However, the extent to which nutrients limit Nitrogen Fixation in the global ocean is uncertain. Here, we examined rates of Nitrogen Fixation and nutrient concentrations in the surface waters of the Atlantic Ocean along a north–south 10,000 km transect during October and November 2005. We show that rates of Nitrogen Fixation were markedly higher in the North Atlantic compared with the South Atlantic Ocean. Across the two basins, Nitrogen Fixation was positively correlated with dissolved iron and negatively correlated with dissolved phosphorus concentrations. We conclude that inter-basin differences in Nitrogen Fixation are controlled by iron supply rather than phosphorus availability. Analysis of the nutrient content of deep waters suggests that the fixed Nitrogen enters North Atlantic Deep Water. Our study thus supports the suggestion that iron significantly influences Nitrogen Fixation5, and that subsequent interactions with ocean circulation patterns contribute to the decoupling of Nitrogen Fixation and loss2, 4, 8.