scholarly journals Mechanistic Model for the Coexistence of Nitrogen Fixation and Photosynthesis in Marine Trichodesmium

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Keisuke Inomura ◽  
Samuel T. Wilson ◽  
Curtis Deutsch
Keyword(s):  
Nitrogen Fixation ◽  
Mechanistic Model ◽  
Model Organism ◽  
Extracellular Polysaccharide ◽  
Physiological Model ◽  
Cellular Growth ◽  
Energetic Cost ◽  
Respiratory Protection ◽  
Nitrogen Fixing ◽  
Low Oxygen

ABSTRACT The cyanobacterium Trichodesmium is an important contributor of new nitrogen (N) to the surface ocean, but its strategies for protecting the nitrogenase enzyme from inhibition by oxygen (O2) remain poorly understood. We present a dynamic physiological model to evaluate hypothesized conditions that would allow Trichodesmium to carry out its two conflicting metabolic processes of N2 fixation and photosynthesis. First, the model indicates that managing cellular O2 to permit N2 fixation requires high rates of respiratory O2 consumption. The energetic cost amounts to ∼80% of daily C fixation, comparable to the observed diminution of the growth rate of Trichodesmium relative to other phytoplankton. Second, by forming a trichome of connected cells, Trichodesmium can segregate N2 fixation from photosynthesis. The transfer of stored C to N-fixing cells fuels the respiratory O2 consumption that protects nitrogenase, while the reciprocal transfer of newly fixed N to C-fixing cells supports cellular growth. Third, despite Trichodesmium lacking the structural barrier found in heterocystous species, the model predicts low diffusivity of cell membranes, a function that may be explained by the presence of Gram-negative membrane, production of extracellular polysaccharide substances (EPS), and “buffer cells” that intervene between N2-fixing and photosynthetic cells. Our results suggest that all three factors—respiratory protection, trichome formation, and diffusion barriers—represent essential strategies that, despite their energetic costs, facilitate the growth of Trichodesmium in the oligotrophic aerobic ocean and permit it to be a major source of new reactive nitrogen. IMPORTANCE Trichodesmium is a major nitrogen-fixing cyanobacterium and exerts a significant influence on the oceanic nitrogen cycle. It is also a widely used model organism in laboratory studies. Since the nitrogen-fixing enzyme nitrogenase is extremely sensitive to oxygen, how these surface-dwelling plankton manage the two conflicting processes of nitrogen fixation and photosynthesis has been a long-standing question. In this study, we developed a simple model of metabolic fluxes of Trichodesmium capturing observed daily cycles of photosynthesis, nitrogen fixation, and boundary layer oxygen concentrations. The model suggests that forming a chain of cells for spatially segregating nitrogen fixation and photosynthesis is essential but not sufficient. It also requires a barrier against oxygen diffusion and high rates of oxygen scavenging by respiration. Finally, the model indicates an extremely short life span of oxygen-enabling cells to instantly create a low-oxygen environment upon deactivation of photosynthesis.

scholarly journals Characterisation of a Novel Nitrogen-Fixing, Polyhydroxyalkanoate-Producing Bacterium, Novosphingobium Nitrogenifigens Y88T

2021 ◽  
Author(s):  
◽  
Anne-Marie Smit
Keyword(s):  
Nitrogen Fixation ◽  
Model Organism ◽  
Dry Weight ◽  
Growth Conditions ◽  
Biofuel Production ◽  
Nitrogen Fixing ◽  
Production Environment ◽  
Amino Terminal ◽  
Nitrogen Utilisation ◽  
Pha Production

<p>The novel sphingomonad Novosphingobium nitrogenifigens Y88T (Y88T) is an obligate aerobe able to grow in nutrient-imbalanced environments where nitrogen is naturally limiting, but carbon is found in abundance. Due to its ability to fix atmospheric nitrogen and produce the bioplastic polyhydroxyalkanoate (PHA), Y88T is well-suited for growth in a nitrogenlimited but carbon-enriched environment. Because of these metabolic abilities, Y88T is of interest as a model organism for PHA production unconstrained by nitrogen-limiting conditions. Growth profiles and PHA production profiles were determined for Y88T under conditions of carbon enrichment, nitrogen sufficiency and depletion to investigate carbon and nitrogen utilisation as well as PHA production in this organism. Also, since the nitrogenase enzyme required for nitrogen fixation is oxygen labile, the effect of DO concentration and the relationship between aerobic metabolism and the nitrogen-fixing and PHA-producing abilities of Y88T was investigated. This study demonstrated: that glucose is the preferred growth substrate for Y88T; that no direct relationship exists between nitrogen fixation and PHB accumulation in Y88T; that Y88T can reliably produce in excess of 80 % of its dry weight as polyhydroxybutyrate (PHB), a type of PHA, from glucose under nitrogenlimiting conditions. Proteomic signatures were determined for the various physiological responses of Y88T to growth, nitrogen utilisation, PHB production and exposure to different levels of DO. More than 250 unique proteins, including the core nitrogen-fixation, PHB-synthetic and glycolytic proteins were identified. Y88T apparently converts glucose to PHB via three interrelated glucose catabolic pathways and proteins likely involved in these pathways were identified. This study revealed that, regardless of growth conditions and despite decreased abundance of the Y88T nitrogenase enzyme, growth and PHB synthesis were not inhibited at DOhigh concentrations. Proteomic characterisation of the Y88T phasin, a PHA granule-associated protein, iii identified an amino-terminal, low complexity alanine and proline rich segment found only in other sphingomonads. The expression level of the Y88T phasin correlated well with PHB yields, suggesting the use of this protein as a biomarker to optimise PHB yield in a production environment. Y88T has the potential to be a useful production strain in pure culture, utilising its natural and robust propensity to metabolise glucose to preferentially produce PHB. Targets for biotechnological improvement and the potential for application of Y88T to biofuel production are discussed.</p>

scholarly journals Contrasted Reactivity to Oxygen Tensions inFrankiasp. Strain CcI3 throughout Nitrogen Fixation and Assimilation

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Faten Ghodhbane-Gtari ◽  
Karima Hezbri ◽  
Amir Ktari ◽  
Imed Sbissi ◽  
Nicholas Beauchemin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nitrogen Fixation ◽  
Mrna Level ◽  
Mrna Levels ◽  
Respiratory Protection ◽  
Oxygen Species ◽  
Nitrogen Fixing ◽  
Structural Genes ◽  
Oxygen Tensions ◽  
Strain Cci3

Reconciling the irreconcilable is a primary struggle in aerobic nitrogen-fixing bacteria. Although nitrogenase is oxygen and reactive oxygen species-labile, oxygen tension is required to sustain respiration. In the nitrogen-fixingFrankia, various strategies have been developed through evolution to control the respiration and nitrogen-fixation balance. Here, we assessed the effect of different oxygen tensions onFrankiasp. strain CcI3 growth, vesicle production, and gene expression under different oxygen tensions. Both biomass and vesicle production were correlated with elevated oxygen levels under both nitrogen-replete and nitrogen-deficient conditions. The mRNA levels for the nitrogenase structural genes (nifHDK) were high under hypoxic and hyperoxic conditions compared to oxic conditions. The mRNA level for the hopanoid biosynthesis genes (sqhC andhpnC) was also elevated under hyperoxic conditions suggesting an increase in the vesicle envelope. Under nitrogen-deficient conditions, thehup2 mRNA levels increased with hyperoxic environment, whilehup1 mRNA levels remained relatively constant. Taken together, these results indicate thatFrankiaprotects nitrogenase by the use of multiple mechanisms including the vesicle-hopanoid barrier and increased respiratory protection.

scholarly journals Metabolic model of nitrogen-fixing obligate aerobe Azotobacter vinelandii demonstrates adaptation to oxygen concentration and metal availability

2021 ◽  
Author(s):  
Alexander B Alleman ◽  
Florence Mus ◽  
John W Peters
Keyword(s):  
Nitrogen Fixation ◽  
Biological Nitrogen Fixation ◽  
Azotobacter Vinelandii ◽  
Metabolic Model ◽  
Metal Availability ◽  
Respiratory Protection ◽  
Nitrogen Fixing ◽  
A Genome ◽  
Biological Nitrogen ◽  
Genome Scale

There is considerable interest in promoting biological nitrogen fixation as a mechanism to reduce the inputs of nitrogenous fertilizers in agriculture, a problem of agronomic, economic, and environmental importance. For the potential impact of biological nitrogen fixation in agriculture to be realized, there are considerable fundamental knowledge gaps that need to be addressed. Biological nitrogen fixation or the reduction of N2 to NH3 is catalyzed by nitrogenase which requires a large amount of energy in the form of ATP and low potential electrons. Nitrogen-fixing organisms that respire aerobically have an advantage in meeting the energy demands of biological nitrogen fixation but face challenges of protecting nitrogenase from inactivation in the presence of oxygen. Here, we have constructed a genome-scale metabolic model of the aerobic metabolism of nitrogen-fixing bacteria Azotobacter vinelandii, which uses a complex electron transport system, termed respiratory protection, to consume oxygen at a high rate keeping intracellular conditions microaerobic. Our model accurately determines growth rate under high oxygen and high substrate concentration conditions, demonstrating the large flux of energy directed to respiratory protection. While respiratory protection mechanisms compensate the energy balance in high oxygen conditions, it does not account for all substrate intake, leading to increased maintenance rates. We have also shown how A. vinelandii can adapt under different oxygen concentrations and metal availability by rearranging flux through the electron transport system. Accurately determining the energy balance in a genome-scale metabolic model is required for future engineering approaches.

scholarly journals Active nitrogen fixation by Crocosphaera expands their niche despite the presence of ammonium – A case study

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Keisuke Inomura ◽  
Takako Masuda ◽  
Julia M. Gauglitz
Keyword(s):  
Nitrogen Fixation ◽  
Mechanistic Model ◽  
Energy Costs ◽  
High Electron ◽  
Nitrogen Fixing ◽  
Active Nitrogen ◽  
State Culture ◽  
Nitrogen Fixers ◽  
Efficient Alternative

Abstract Unicellular nitrogen fixer Crocosphaera contributes substantially to nitrogen fixation in oligotrophic subtropical gyres. They fix nitrogen even when significant amounts of ammonium are available. This has been puzzling since fixing nitrogen is energetically inefficient compared with using available ammonium. Here we show that by fixing nitrogen, Crocosphaera can increase their population and expand their niche despite the presence of ammonium. We have developed a simple but mechanistic model of Crocosphaera based on their growth in steady state culture. The model shows that the growth of Crocosphaera can become nitrogen limited despite their capability to fix nitrogen. When they fix nitrogen, the population increases by up to 78% relative to the case without nitrogen fixation. When we simulate a simple ecological situation where Crocosphaera exists with non-nitrogen-fixing phytoplankton, the relative abundance of Crocosphaera increases with nitrogen fixation, while the population of non-nitrogen-fixing phytoplankton decreases since a larger fraction of fixed nitrogen is consumed by Crocosphaera. Our study quantitatively supports the benefit of nitrogen fixation despite the high electron/energy costs, even when an energetically efficient alternative is available. It demonstrates a competitive aspect of Crocosphaera, permitting them to be regionally significant nitrogen fixers.

scholarly journals Characterisation of a Novel Nitrogen-Fixing, Polyhydroxyalkanoate-Producing Bacterium, Novosphingobium Nitrogenifigens Y88T

2021 ◽  
Author(s):  
◽  
Anne-Marie Smit
Keyword(s):  
Nitrogen Fixation ◽  
Model Organism ◽  
Dry Weight ◽  
Growth Conditions ◽  
Biofuel Production ◽  
Nitrogen Fixing ◽  
Production Environment ◽  
Amino Terminal ◽  
Nitrogen Utilisation ◽  
Pha Production

<p>The novel sphingomonad Novosphingobium nitrogenifigens Y88T (Y88T) is an obligate aerobe able to grow in nutrient-imbalanced environments where nitrogen is naturally limiting, but carbon is found in abundance. Due to its ability to fix atmospheric nitrogen and produce the bioplastic polyhydroxyalkanoate (PHA), Y88T is well-suited for growth in a nitrogenlimited but carbon-enriched environment. Because of these metabolic abilities, Y88T is of interest as a model organism for PHA production unconstrained by nitrogen-limiting conditions. Growth profiles and PHA production profiles were determined for Y88T under conditions of carbon enrichment, nitrogen sufficiency and depletion to investigate carbon and nitrogen utilisation as well as PHA production in this organism. Also, since the nitrogenase enzyme required for nitrogen fixation is oxygen labile, the effect of DO concentration and the relationship between aerobic metabolism and the nitrogen-fixing and PHA-producing abilities of Y88T was investigated. This study demonstrated: that glucose is the preferred growth substrate for Y88T; that no direct relationship exists between nitrogen fixation and PHB accumulation in Y88T; that Y88T can reliably produce in excess of 80 % of its dry weight as polyhydroxybutyrate (PHB), a type of PHA, from glucose under nitrogenlimiting conditions. Proteomic signatures were determined for the various physiological responses of Y88T to growth, nitrogen utilisation, PHB production and exposure to different levels of DO. More than 250 unique proteins, including the core nitrogen-fixation, PHB-synthetic and glycolytic proteins were identified. Y88T apparently converts glucose to PHB via three interrelated glucose catabolic pathways and proteins likely involved in these pathways were identified. This study revealed that, regardless of growth conditions and despite decreased abundance of the Y88T nitrogenase enzyme, growth and PHB synthesis were not inhibited at DOhigh concentrations. Proteomic characterisation of the Y88T phasin, a PHA granule-associated protein, iii identified an amino-terminal, low complexity alanine and proline rich segment found only in other sphingomonads. The expression level of the Y88T phasin correlated well with PHB yields, suggesting the use of this protein as a biomarker to optimise PHB yield in a production environment. Y88T has the potential to be a useful production strain in pure culture, utilising its natural and robust propensity to metabolise glucose to preferentially produce PHB. Targets for biotechnological improvement and the potential for application of Y88T to biofuel production are discussed.</p>

scholarly journals Pseudomonas azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from a compost pile

2005 ◽  
Vol 55 (4) ◽  
pp. 1539-1544 ◽  
Author(s):  
Kouta Hatayama ◽  
Satomi Kawai ◽  
Hirofumi Shoun ◽  
Yasuichi Ueda ◽  
Akira Nakamura
Keyword(s):  
Nitrogen Fixation ◽  
Nitrogenase Activity ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Pseudomonas Stutzeri ◽  
Sensu Stricto ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Low Oxygen ◽  
Close Relationship

A nitrogen-fixing bacterium, designated strain 6H33bT, was isolated from a compost pile in Japan. The nitrogenase activity of this strain was detected based on its acetylene-reducing activity under low oxygen concentrations (2–4 %). An analysis of the genes responsible for nitrogen fixation in this strain, nifH and nifD, indicated a close relationship to those of Pseudomonas stutzeri A15 (A1501). Sequence similarity searches based on the 16S rRNA gene sequences showed that strain 6H33bT belongs within the genus Pseudomonas sensu stricto; closest similarity was with Pseudomonas indica (97·3 %). A comparison of several taxonomic characteristics of 6H33bT with those of P. indica and some type strains of the genus Pseudomonas sensu stricto indicated that 6H33bT could be distinguished from P. indica based on the presence of nitrogen fixation ability, the absence of nitrate reduction and denitrification abilities and the utilization of some sugars and organic acids. Phylogenetic analyses and the results of DNA–DNA hybridization experiments also indicated that strain 6H33bT represents a species distinct from P. indica. From these results, it is proposed that strain 6H33bT (=ATCC BAA-1049T=JCM 12708T) is classified as the type strain of a novel species of the genus Pseudomonas sensu stricto under the name Pseudomonas azotifigens sp. nov.

scholarly journals Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae

2020 ◽  
Vol 12 (11) ◽  
pp. 2002-2014
Author(s):  
Ling-Ling Yang ◽  
Zhao Jiang ◽  
Yan Li ◽  
En-Tao Wang ◽  
Xiao-Yang Zhi
Keyword(s):  
Nitrogen Fixation ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Symbiotic Nitrogen Fixation ◽  
Gene Families ◽  
Time Span ◽  
Soil Conditions ◽  
Gene Gain ◽  
Nitrogen Fixing ◽  
Pan Genome

Abstract Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host’s physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.

scholarly journals Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Luz K. Medina-Cordoba ◽  
Aroon T. Chande ◽  
Lavanya Rishishwar ◽  
Leonard W. Mayer ◽  
Lina C. Valderrama-Aguirre ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Nitrogen Fixation ◽  
Plant Growth ◽  
Phosphate Solubilization ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Promising Tool ◽  
A Genome ◽  
Plant Growth Promoting ◽  
Growth Promoting

AbstractPrevious studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potential biofertilizers. A genome-enabled computational phenotyping approach was developed to prioritize sugarcane associated diazotrophs according to their potential as biofertilizers. This method selects isolates that have potential for nitrogen fixation and other plant growth promoting (PGP) phenotypes while showing low risk for virulence and antibiotic resistance. Intact nitrogenase (nif) genes and operons were found in 18 of the isolates. Isolates also encode phosphate solubilization and siderophore production operons, and other PGP genes. The majority of sugarcane isolates showed uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent and validated computational phenotype predictions. A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity. Our results indicate that computational phenotyping is a promising tool for the assessment of bacteria detected in agricultural ecosystems.

scholarly journals Use of design of experiments to optimize the production of microbial probiotic biofilms

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4826 ◽  
Author(s):  
Barbara Speranza ◽  
Arcangelo Liso ◽  
Maria Rosaria Corbo
Keyword(s):  
Design Of Experiments ◽  
Growth Phase ◽  
Lactobacillus Reuteri ◽  
Model Organism ◽  
Cellular Growth ◽  
Effects Of Ph ◽  
Probiotic Strains ◽  
Maximum Cell ◽  
Short Time ◽  
Control Samples

Here, we describe the production of a probiotic biofilm through three intermediate steps: (1) measurement of the adhesion capacity of 15 probiotic strains to evaluate their tendency to form biofilm on different surfaces (stainless steel, glass, and polycarbonate); (2) evaluation of the effects of pH, temperature, cellular growth phase, agitation, and presence of surfactants on probiotic biofilm formation (BF) through the Design of Experiments (DoE) approach; (3) study of the effects of pH, temperature and surfactants concentration on probiotic BF using the Central Composite Design. Finally, we show that biofilms pre-formed by selected probiotics can delay the growth of pathogens, such asListeria monocytogeneschosen as model organism. Among the tested strains,Bifidobacterium infantisDSM20088 andLactobacillus reuteriDSM20016 were found to be as the probiotics able to ensure the greatest adhesion (over 6 Log CFU cm2) to the surfaces tested in a very short time (<24 h). Cellular growth phase and agitation of the medium were factors not affecting BF, pH exerted a very bland effect and a greater tendency to adhesion was observed when the temperature was about 30 °C. The results obtained in the last experimental phase suggest that our probiotic biofilms can be used as an efficient mean to delay the growth ofL. monocytogenes: the λ phase length, in fact, was longer in samples containing probiotic biofilms (0.30–1.02 h) against 0.08 h observed in the control samples. A reduction of the maximum cell load was also observed (6.99–7.06 Log CFU mL−1against about 8 Log CFU mL−1observed in the control samples).

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