scholarly journals Independence of a Marine Unicellular Diazotroph to the Presence of NO3−

2021 ◽  
Vol 9 (10) ◽  
pp. 2073
Author(s):  
Sophie Rabouille ◽  
Benjamin Randall ◽  
Amélie Talec ◽  
Patrick Raimbault ◽  
Thierry Blasco ◽  
...  
Keyword(s):  
Growth Rate ◽  
N2 Fixation ◽  
Carbon Fixation ◽  
Nitrogenase Activity ◽  
Cellular Growth ◽  
Energetic Cost ◽  
Cell Physiology ◽  
Fixation Rate ◽  
Unicellular Cyanobacterium ◽  
General Validity

Marine nitrogen (N2) fixation was historically considered to be absent or reduced in nitrate (NO3−) rich environments. This is commonly attributed to the lower energetic cost of NO3− uptake compared to diazotrophy in oxic environments. This paradigm often contributes to making inferences about diazotroph distribution and activity in the ocean, and is also often used in biogeochemical ocean models. To assess the general validity of this paradigm beyond the traditionally used model organism Trichodesmium spp., we grew cultures of the unicellular cyanobacterium Crocosphaera watsonii WH8501 long term in medium containing replete concentrations of NO3−. NO3− uptake was measured in comparison to N2 fixation to assess the cultures’ nitrogen source preferences. We further measured culture growth rate, cell stoichiometry, and carbon fixation rate to determine if the presence of NO3− had any effect on cell metabolism. We found that uptake of NO3− by this strain of Crocosphaera was minimal in comparison to other N sources (~2–4% of total uptake). Furthermore, availability of NO3− did not statistically alter N2 fixation rate nor any aspect of cell physiology or metabolism measured (cellular growth rate, cell stoichiometry, cell size, nitrogen fixation rate, nitrogenase activity) in comparison to a NO3− free control culture. These results demonstrate the capability of a marine diazotroph to fix nitrogen and grow independently of NO3−. This lack of sensitivity of diazotrophy to NO3− suggests that assumptions often made about, and model formulations of, N2 fixation should be reconsidered.

Estimating Nitrogenase Activity of Faba Bean (Vicia faba) by Acetylene Reduction (Ar) Assay

1990 ◽  
Vol 17 (5) ◽  
pp. 489 ◽  
Author(s):  
Herdina ◽  
JH Silsbury
Keyword(s):  
Diurnal Variation ◽  
Vicia Faba ◽  
Faba Bean ◽  
Closed System ◽  
N2 Fixation ◽  
Acetylene Reduction ◽  
Nitrogenase Activity ◽  
Electron Flow ◽  
Specific Rate ◽  
Rooting Medium

Methods of conducting acetylene reduction (AR) assay were appraised for estimating the nitrogenase activity of nodules of faba bean (Vicia faba L.). Factors considered were: (i) disturbance of plants when removing the rooting medium; (ii) assay temperature; (iii) the use of whole plants rather than detached, nodulated roots; (iv) diurnal variation in nodule activity; and (v) a decline in C2H4 production after exposure to C2H2. Plants growing in jars of 'oil dry' (calcined clay) had the same AR activity when assayed in situ in a closed system as when assayed after removal of the rooting medium. Assay temperatures of 12.5, 17.5 and 22.5°C influenced the specific rate of AR with the optimum at 17.5°C. Removal of the shoot resulted in a rapid decrease in AR activity in both vegetative and reproductive plants but the effect was much larger in the latter. AR and respiration by nodulated roots were closely linked and both varied markedly over a diurnal 12 h/12 h cycle. Since no fluctuation was found after nodules were detached, diurnal variation in the respiration of nodulated roots is attributed to change in nodule activity. Half of the dark respiration of nodulated roots was associated with respiration of the nodules and thus largely with N2 fixation. Since the AR assay provides no information on how electron flow in vivo is partitioned between reduction of N2 and reduction of protons, diurnal variation in hydrogen evolution (HE) in air and Ar/O2 in an open system was used to estimate this partitioning. Diurnal variation in apparent N2 fixation estimated in this manner was examined at a 'low' PPFD (300 μmol m-2 s-1) and at 'high' (1300 μmol m-2 s-1) to explore whether variation could be attributed to change in carbohydrate supply. Although HE in air and in Ar/O2 were both closely linked with the respiration of the nodulated root, apparent N2 fixation showed only a slight diurnal variation at 'low' light and almost none at 'high'. Vegetative plants showed no C2H2-induced decline in activity with exposure to C2H2 but reproductive plants did. This difference appears to be an age effect rather than attributable to flowering per se, since a decline occurred even when plants were kept vegetative by disbudding. A closed system for AR assay appears satisfactory for vegetative faba bean but such an assay over a 40-min period during the reproductive stage would underestimate nitrogenase activity by about 20%.

scholarly journals Whole-Genome Transcriptional Profiling of Bradyrhizobium japonicum during Chemoautotrophic Growth

2008 ◽  
Vol 190 (20) ◽  
pp. 6697-6705 ◽  
Author(s):  
William L. Franck ◽  
Woo-Suk Chang ◽  
Jing Qiu ◽  
Masayuki Sugawara ◽  
Michael J. Sadowsky ◽  
...  
Keyword(s):  
Bradyrhizobium Japonicum ◽  
Carbon Fixation ◽  
Cultured Cells ◽  
Isocitrate Lyase ◽  
Nitrogenase Activity ◽  
Glyoxylate Cycle ◽  
Transcriptional Profiling ◽  
Pentose Phosphate ◽  
Hydrogen Gas ◽  
Essential Components

ABSTRACT Bradyrhizobium japonicum is a facultative chemoautotroph capable of utilizing hydrogen gas as an electron donor in a respiratory chain terminated by oxygen to provide energy for cellular processes and carbon dioxide assimilation via a reductive pentose phosphate pathway. A transcriptomic analysis of B. japonicum cultured chemoautotrophically identified 1,485 transcripts, representing 17.5% of the genome, as differentially expressed when compared to heterotrophic cultures. Genetic determinants required for hydrogen utilization and carbon fixation, including the uptake hydrogenase system and components of the Calvin-Benson-Bassham cycle, were strongly induced in chemoautotrophically cultured cells. A putative isocitrate lyase (aceA; blr2455) was among the most strongly upregulated genes, suggesting a role for the glyoxylate cycle during chemoautotrophic growth. Addition of arabinose to chemoautotrophic cultures of B. japonicum did not significantly alter transcript profiles. Furthermore, a subset of nitrogen fixation genes was moderately induced during chemoautotrophic growth. In order to specifically address the role of isocitrate lyase and nitrogenase in chemoautotrophic growth, we cultured aceA, nifD, and nifH mutants under chemoautotrophic conditions. Growth of each mutant was similar to that of the wild type, indicating that the glyoxylate bypass and nitrogenase activity are not essential components of chemoautotrophy in B. japonicum.

scholarly journals Design and in vitro realization of carbon-conserving photorespiration

2018 ◽  
Vol 115 (49) ◽  
pp. E11455-E11464 ◽  
Author(s):  
Devin L. Trudeau ◽  
Christian Edlich-Muth ◽  
Jan Zarzycki ◽  
Marieke Scheffen ◽  
Moshe Goldsmith ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Calvin Cycle ◽  
Computational Design ◽  
Carbon Loss ◽  
Fixation Rate ◽  
Bisphosphate Carboxylase ◽  
Stoichiometric Model ◽  
Synthetic Routes ◽  
Coa Reductase

Photorespiration recycles ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) oxygenation product, 2-phosphoglycolate, back into the Calvin Cycle. Natural photorespiration, however, limits agricultural productivity by dissipating energy and releasing CO2. Several photorespiration bypasses have been previously suggested but were limited to existing enzymes and pathways that release CO2. Here, we harness the power of enzyme and metabolic engineering to establish synthetic routes that bypass photorespiration without CO2 release. By defining specific reaction rules, we systematically identified promising routes that assimilate 2-phosphoglycolate into the Calvin Cycle without carbon loss. We further developed a kinetic–stoichiometric model that indicates that the identified synthetic shunts could potentially enhance carbon fixation rate across the physiological range of irradiation and CO2, even if most of their enzymes operate at a tenth of Rubisco’s maximal carboxylation activity. Glycolate reduction to glycolaldehyde is essential for several of the synthetic shunts but is not known to occur naturally. We, therefore, used computational design and directed evolution to establish this activity in two sequential reactions. An acetyl-CoA synthetase was engineered for higher stability and glycolyl-CoA synthesis. A propionyl-CoA reductase was engineered for higher selectivity for glycolyl-CoA and for use of NADPH over NAD+, thereby favoring reduction over oxidation. The engineered glycolate reduction module was then combined with downstream condensation and assimilation of glycolaldehyde to ribulose 1,5-bisphosphate, thus providing proof of principle for a carbon-conserving photorespiration pathway.

scholarly journals Massive Phenotypic Measurements Reveal Complex Physiological Consequences of Differential Translation Efficacies

2017 ◽  
Author(s):  
Adam Paul Arkin ◽  
Guillaume Cambray
Keyword(s):  
Growth Rate ◽  
Translation Initiation ◽  
Protein Production ◽  
Protein Biosynthesis ◽  
Cellular Growth ◽  
Sequence Variants ◽  
Release Rates ◽  
Trade Offs ◽  
Fluctuating Environments ◽  
Protein Overproduction

ABSTRACTControl of protein biosynthesis is at the heart of resource allocation and cell adaptation to fluctuating environments. One gene’s translation often occurs at the expense of another’s, resulting in global energetic and fitness trade-offs during differential expression of various functions. Patterns of ribosome utilization—as controlled by initiation, elongation and release rates—are central to this balance. To disentangle their respective determinants and physiological impacts, we complemented measurements of protein production with highly parallelized quantifications of transcripts’ abundance and decay, ribosome loading and cellular growth rate for 244,000 precisely designed sequence variants of an otherwise standard reporter. We find highly constrained, non-monotonic relationships between measured phenotypes. We show that fitness defects derive either from protein overproduction, with efficient translation initiation and heavy ribosome flows; or from unproductive ribosome sequestration by highly structured, slowly initiated and overly stabilized transcripts. These observations demonstrate physiological impacts of key sequence features in natural and designed transcripts.

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