The Experts below are selected from a list of 126 Experts worldwide ranked by ideXlab platform

Toshiaki Kudo - One of the best experts on this subject based on the ideXlab platform.

  • phylogenetic diversity of Nitrogen fixation genes in the symbiotic microbial community in the gut of diverse termites
    Applied and Environmental Microbiology, 1999
    Co-Authors: Moriya Ohkuma, Satoko Noda, Toshiaki Kudo
    Abstract:

    Nitrogen fixation by the microOrganisms in the gut of termites is one of the crucial aspects of symbiosis, since termites usually thrive on a Nitrogen-poor diet. The phylogenetic diversity of the Nitrogen-Fixing Organisms within the symbiotic community in the guts of various termite species was investigated without culturing the resident microOrganisms. A portion of the diNitrogenase reductase gene (nifH) was directly amplified from DNA extracted from the mixed population in the termite gut. Analysis of deduced amino acid sequences of the products of the clonally isolated nifH genes revealed the presence of diverse nifH sequences in most of the individual termite species, and their constituents were considerably different among termite species. A majority of the nifH sequences from six lower termites, which showed significant levels of Nitrogen fixation activity, could be assigned to either the anaerobic nif group (consisting of clostridia and sulfur reducers) or the alternative nif methanogen group among the nifH phylogenetic groups. In the case of three higher termites, which showed only low levels of Nitrogen fixation activity, a large number of the sequences were assigned to the most divergent nif group, probably functioning in some process other than Nitrogen fixation and being derived from methanogenic archaea. The nifH groups detected were similar within each termite family but different among the termite families, suggesting an evolutionary trend reflecting the diazotrophic habitats in the symbiotic community. Within these phylogenetic groups, the sequences from the termites formed lineages distinct from those previously recognized in studies using classical microbiological techniques, and several sequence clusters unique to termites were found. The results indicate the presence of diverse potentially Nitrogen-Fixing microbial assemblages in the guts of termites, and the majority of them are as yet uncharacterized.

  • diversity of Nitrogen fixation genes in the symbiotic intestinal microflora of the termite reticulitermes speratus
    Applied and Environmental Microbiology, 1996
    Co-Authors: Moriya Ohkuma, Satoko Noda, Koki Horikoshi, Ron Usami, Toshiaki Kudo
    Abstract:

    The diversity of Nitrogen-Fixing Organisms in the symbiotic intestinal microflora of a lower termite, Reticulitermes speratus, was investigated without culturing the resident microOrganisms. Fragments of the nifH gene, which encodes the diNitrogenase reductase, were directly amplified from the DNA of the mixed microbial population in the termite gut and were clonally isolated. The phylogenetic analysis of the nifH product amino acid sequences showed that there was a remarkable diversity of Nitrogenase genes in the termite gut. A large number of the termite nifH sequences were most closely related to those of a firmicute, Clostridium pasteurianum, with a few being most closely related to either the (gamma) subclass of the proteobacteria or a sequence of Desulfovibrio gigas. Some of the others were distantly related to those of the bacteria and were seemingly derived from the domain Archaea. The phylogenetic positions of these nifH sequences corresponded to those of genera found during a previous determination of rRNA-based phylogeny of the termite intestinal microbial community, of which a majority consisted of new, yet-uncultivated species. The results revealed that we have little knowledge of the Organisms responsible for Nitrogen fixation in termites.

Beat Christen - One of the best experts on this subject based on the ideXlab platform.

  • co catabolism of arginine and succinate drives symbiotic Nitrogen fixation
    Molecular Systems Biology, 2020
    Co-Authors: Carlos Eduardo Florestinoco, Flavia Tschan, Tobias Fuhrer, Celine Margot, Uwe Sauer, Matthias Christen, Beat Christen
    Abstract:

    Biological Nitrogen fixation emerging from the symbiosis between bacteria and crop plants holds promise to increase the sustainability of agriculture. One of the biggest hurdles for the engineering of Nitrogen-Fixing Organisms is an incomplete knowledge of metabolic interactions between microbe and plant. In contrast to the previously assumed supply of only succinate, we describe here the CATCH-N cycle as a novel metabolic pathway that co-catabolizes plant-provided arginine and succinate to drive the energy-demanding process of symbiotic Nitrogen fixation in endosymbiotic rhizobia. Using systems biology, isotope labeling studies and transposon sequencing in conjunction with biochemical characterization, we uncovered highly redundant network components of the CATCH-N cycle including transaminases that interlink the co-catabolism of arginine and succinate. The CATCH-N cycle uses N2 as an additional sink for reductant and therefore delivers up to 25% higher yields of Nitrogen than classical arginine catabolism-two alanines and three ammonium ions are secreted for each input of arginine and succinate. We argue that the CATCH-N cycle has evolved as part of a synergistic interaction to sustain bacterial metabolism in the microoxic and highly acid environment of symbiosomes. Thus, the CATCH-N cycle entangles the metabolism of both partners to promote symbiosis. Our results provide a theoretical framework and metabolic blueprint for the rational design of plants and plant-associated Organisms with new properties to improve Nitrogen fixation.

Moriya Ohkuma - One of the best experts on this subject based on the ideXlab platform.

  • phylogenetic diversity of Nitrogen fixation genes in the symbiotic microbial community in the gut of diverse termites
    Applied and Environmental Microbiology, 1999
    Co-Authors: Moriya Ohkuma, Satoko Noda, Toshiaki Kudo
    Abstract:

    Nitrogen fixation by the microOrganisms in the gut of termites is one of the crucial aspects of symbiosis, since termites usually thrive on a Nitrogen-poor diet. The phylogenetic diversity of the Nitrogen-Fixing Organisms within the symbiotic community in the guts of various termite species was investigated without culturing the resident microOrganisms. A portion of the diNitrogenase reductase gene (nifH) was directly amplified from DNA extracted from the mixed population in the termite gut. Analysis of deduced amino acid sequences of the products of the clonally isolated nifH genes revealed the presence of diverse nifH sequences in most of the individual termite species, and their constituents were considerably different among termite species. A majority of the nifH sequences from six lower termites, which showed significant levels of Nitrogen fixation activity, could be assigned to either the anaerobic nif group (consisting of clostridia and sulfur reducers) or the alternative nif methanogen group among the nifH phylogenetic groups. In the case of three higher termites, which showed only low levels of Nitrogen fixation activity, a large number of the sequences were assigned to the most divergent nif group, probably functioning in some process other than Nitrogen fixation and being derived from methanogenic archaea. The nifH groups detected were similar within each termite family but different among the termite families, suggesting an evolutionary trend reflecting the diazotrophic habitats in the symbiotic community. Within these phylogenetic groups, the sequences from the termites formed lineages distinct from those previously recognized in studies using classical microbiological techniques, and several sequence clusters unique to termites were found. The results indicate the presence of diverse potentially Nitrogen-Fixing microbial assemblages in the guts of termites, and the majority of them are as yet uncharacterized.

  • diversity of Nitrogen fixation genes in the symbiotic intestinal microflora of the termite reticulitermes speratus
    Applied and Environmental Microbiology, 1996
    Co-Authors: Moriya Ohkuma, Satoko Noda, Koki Horikoshi, Ron Usami, Toshiaki Kudo
    Abstract:

    The diversity of Nitrogen-Fixing Organisms in the symbiotic intestinal microflora of a lower termite, Reticulitermes speratus, was investigated without culturing the resident microOrganisms. Fragments of the nifH gene, which encodes the diNitrogenase reductase, were directly amplified from the DNA of the mixed microbial population in the termite gut and were clonally isolated. The phylogenetic analysis of the nifH product amino acid sequences showed that there was a remarkable diversity of Nitrogenase genes in the termite gut. A large number of the termite nifH sequences were most closely related to those of a firmicute, Clostridium pasteurianum, with a few being most closely related to either the (gamma) subclass of the proteobacteria or a sequence of Desulfovibrio gigas. Some of the others were distantly related to those of the bacteria and were seemingly derived from the domain Archaea. The phylogenetic positions of these nifH sequences corresponded to those of genera found during a previous determination of rRNA-based phylogeny of the termite intestinal microbial community, of which a majority consisted of new, yet-uncultivated species. The results revealed that we have little knowledge of the Organisms responsible for Nitrogen fixation in termites.

Carlos Eduardo Florestinoco - One of the best experts on this subject based on the ideXlab platform.

  • co catabolism of arginine and succinate drives symbiotic Nitrogen fixation
    Molecular Systems Biology, 2020
    Co-Authors: Carlos Eduardo Florestinoco, Flavia Tschan, Tobias Fuhrer, Celine Margot, Uwe Sauer, Matthias Christen, Beat Christen
    Abstract:

    Biological Nitrogen fixation emerging from the symbiosis between bacteria and crop plants holds promise to increase the sustainability of agriculture. One of the biggest hurdles for the engineering of Nitrogen-Fixing Organisms is an incomplete knowledge of metabolic interactions between microbe and plant. In contrast to the previously assumed supply of only succinate, we describe here the CATCH-N cycle as a novel metabolic pathway that co-catabolizes plant-provided arginine and succinate to drive the energy-demanding process of symbiotic Nitrogen fixation in endosymbiotic rhizobia. Using systems biology, isotope labeling studies and transposon sequencing in conjunction with biochemical characterization, we uncovered highly redundant network components of the CATCH-N cycle including transaminases that interlink the co-catabolism of arginine and succinate. The CATCH-N cycle uses N2 as an additional sink for reductant and therefore delivers up to 25% higher yields of Nitrogen than classical arginine catabolism-two alanines and three ammonium ions are secreted for each input of arginine and succinate. We argue that the CATCH-N cycle has evolved as part of a synergistic interaction to sustain bacterial metabolism in the microoxic and highly acid environment of symbiosomes. Thus, the CATCH-N cycle entangles the metabolism of both partners to promote symbiosis. Our results provide a theoretical framework and metabolic blueprint for the rational design of plants and plant-associated Organisms with new properties to improve Nitrogen fixation.

Anne M L Kraepiel - One of the best experts on this subject based on the ideXlab platform.

  • Molybdenum limitation of asymbiotic Nitrogen fixation in tropical forest soils
    Nature Geoscience, 2009
    Co-Authors: Alexander R. Barron, Anne M L Kraepiel, Nina Wurzburger, Jean Phillipe Bellenger, S. Joseph Wright, Lars O. Hedin
    Abstract:

    Biological Nitrogen fixation limits plant growth and carbon exchange at local to global scales. Long-term nutrient manipulation experiments in forests and short-term manipulation experiments in microcosms suggest that the micronutrient molybdenum, a component of the Nitrogen-Fixing enzyme Nitrogenase, limits Nitrogen fixation by asymbiotic bacteria in tropical soils in Panama. Nitrogen fixation, the biological conversion of di-Nitrogen to plant-available ammonium, is the primary natural input of Nitrogen to ecosystems^ 1 , and influences plant growth and carbon exchange at local to global scales^ 2 , 3 , 4 , 5 , 6 . The role of this process in tropical forests is of particular concern, as these ecosystems harbour abundant Nitrogen-Fixing Organisms^ 1 , 4 and represent one third of terrestrial primary production^ 4 , 7 , 8 . Here we show that the micronutrient molybdenum, a cofactor in the Nitrogen-Fixing enzyme Nitrogenase, limits Nitrogen fixation by free-living heterotrophic bacteria in soils of lowland Panamanian forests. We measured the fixation response to long-term nutrient manipulations in intact forests, and to short-term manipulations in soil microcosms. Nitrogen fixation increased sharply in treatments of molybdenum alone, in micronutrient treatments that included molybdenum by design and in treatments with commercial phosphorus fertilizer, in which molybdenum was a ‘hidden’ contaminant. Fixation did not respond to additions of phosphorus that were not contaminated by molybdenum. Our findings show that molybdenum alone can limit asymbiotic Nitrogen fixation in tropical forests and raise new questions about the role of molybdenum and phosphorus in the tropical Nitrogen cycle. We suggest that molybdenum limitation may be common in highly weathered acidic soils, and may constrain the ability of some forests to acquire new Nitrogen in response to CO_2 fertilization^ 9 .

  • uptake of molybdenum and vanadium by a Nitrogen Fixing soil bacterium using siderophores
    Nature Geoscience, 2008
    Co-Authors: Adam B Kustka, Jeanphilippe Bellenger, Thomas Wichard, Anne M L Kraepiel
    Abstract:

    Biological availability of molybdenum and vanadium is facilitated by siderophores that are produced by cultures of the bacterium Azotobacter vinelandii during the fixation of atmospheric Nitrogen. This suggests that the production of strong binding compounds may be a widespread strategy for metal acquisition by bacteria and implies that the availability of molybdenum and vanadium may be critical for the Nitrogen cycle of terrestrial ecosystems. Nitrogen fixation, the reaction that transforms atmospheric Nitrogen into bioavailable ammonia and is responsible for the supply of Nitrogen to Earth’s ecosystems, is mediated by the enzyme Nitrogenase. This reaction requires molybdenum (Mo) or vanadium (V) in addition to iron (Fe) (refs 1, 2). Therefore, the availability of these trace metals may control the Earth’s Nitrogen cycle3,4. Many bacteria release strong iron-binding compounds (siderophores) for iron acquisition5,6, but the effect of these compounds on Mo and V availability to Nitrogen-Fixing Organisms is not well understood. Here, we show that the siderophores produced in cultures of Azotobacter vinelandii while Fixing atmospheric Nitrogen under limitation by Mo or V form strong complexes with molybdate and vanadate, and that these complexes are available for uptake. We also show that addition of these siderophores rapidly reverses the effect of other natural binding compounds that make Mo and V unavailable for uptake. Our results resolve the long-standing debate regarding the existence of bacterial ‘molybdophores’7,8,9, as well as the corollary question regarding ‘vanadophores’. We conclude that the production of strong binding compounds may be a widespread strategy for metal acquisition by bacteria, implying that the availability of Mo and V may be critical for the Nitrogen cycle of terrestrial ecosystems.