Regulation of Nitrogen Fixation. In: Hunter CN, Daldal F, Thurnauer MC, Beatty JT, editors. The Purple Phototrophic Bacteria. Dordrecht: Springer Netherlands; 2009. pp. 759-75. [DOI: 10.1007/978-1-4020-8815-5_38]

Ammonia impact on the selection of a phototrophic - chemotrophic consortium for polyhydroxyalkanoates production under light-feast / dark-aerated-famine conditions

Phototrophic polyhydroxyalkanoate (PHA) production is an emerging technology for recovering carbon and nutrients from diverse wastewater streams. However, reliable selection methods for the enrichment of PHA accumulating purple phototrophic bacteria (PPB) in phototrophic mixed cultures (PMC) are needed. This research evaluates the impact of ammonia on the selection of a PHA accumulating phototrophic-chemotrophic consortium, towards the enrichment of PHA accumulating PPB. The culture was operated under light-feast/dark-aerated-famine and winter simulated-outdoor conditions (13.2 ± 0.9 °C, transient light, 143.5 W/m2), using real fermented domestic wastewater with molasses as feedstock. Three ammonia supply strategies were assessed: 1) ammonia available only in the light phase, 2) ammonia always present and 3) ammonia available only during the dark-aerated-famine phase. Results showed that the PMC selected under 1) ammonia only in the light and 3) dark-famine ammonia conditions, presented the lowest PHA accumulation capacity during the light period (11.1 % g PHA/g VSS and 10.4 % g PHA/g VSS, respectively). In case 1), the absence of ammonia during the dark-aerated-famine phase did not promote the selection of PHA storing PPB, whereas in case 3) the absence of ammonia during the light period favoured cyanobacteria growth as well as purple sulphur bacteria with increased non-PHA inclusions, resulting in an overall decrease of phototrophic PHA accumulation capacity. The best PHA accumulation performance was obtained with selection under permanent presence of ammonia (case 2), which attained a PHA content of 21.6 % g PHA/g VSS (10.2 Cmmol PHA/L), at a production rate of 0.57 g PHA/L·day, during the light period in the selection reactor. Results in case 2 also showed that feedstock composition impacts the PMC performance, with feedstocks richer in more reduced volatile fatty acids (butyric and valeric acids) decreasing phototrophic performance and leading to acids entering the dark-aerated phase. Nevertheless, the presence of organic carbon in the aerated phase was not detrimental to the system. In fact, it led to the establishment of a phototrophic-chemotrophic consortium that could photosynthetically accumulate a PHA content of 13.2 % g PHA/g VSS (6.7 Cmmol PHA/L) at a production rate of 0.20 g PHA/L·day in the light phase, and was able to further increase that storage up to 18.5 % g PHA/g VSS (11.0 Cmmol PHA/L) at a production rate of 1.35 g PHA/L·day in the dark-aerated period. Furthermore, the light-feast/dark-aerated-famine operation was able to maintain the performance of the selection reactor under winter conditions, unlike non-aerated PMC systems operated under summer conditions, suggesting that night-time aeration coupled with the constant presence of ammonia can contribute to overcoming the seasonal constraints of outdoor operation of PMCs for PHA production.

Structures of Rhodopseudomonas palustris RC-LH1 complexes with open or closed quinone channels

The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes from Rhodopseudomonas palustris A 2.65-Å resolution structure of the RC-LH1₁₄-W complex consists of an open 14-subunit LH1 ring surrounding the RC interrupted by protein-W, whereas the complex without protein-W at 2.80-Å resolution comprises an RC completely encircled by a closed, 16-subunit LH1 ring. Comparison of these structures provides insights into quinone dynamics within RC-LH1 complexes, including a previously unidentified conformational change upon quinone binding at the RC Q_B site, and the locations of accessory quinone binding sites that aid their delivery to the RC. The structurally unique protein-W prevents LH1 ring closure, creating a channel for accelerated quinone/quinol exchange.

Transcriptome analysis of Rhodobacter capsulatus grown on different nitrogen sources

This study investigated the effect of different nitrogen sources, namely, ammonium chloride and glutamate, on photoheterotrophic metabolism of Rhodobacter capsulatus grown on acetate as the carbon source. Genes that were significantly differentially expressed according to Affymetrix microarray data were categorized into Clusters of Orthologous Groups functional categories and those in acetate assimilation, hydrogen production, and photosynthetic electron transport pathways were analyzed in detail. Genes related to hydrogen production metabolism were significantly downregulated in cultures grown on ammonium chloride when compared to those grown on glutamate. In contrast, photosynthetic electron transport and acetate assimilation pathway genes were upregulated. In detail, aceA encoding isocitrate lyase, a unique enzyme of the glyoxylate cycle and ccrA encoding the rate limiting crotonyl-CoA carboxylase/reductase enzyme of ethylmalonyl-coA pathway were significantly upregulated. Our findings indicate for the first time that R. capsulatus can operate both glyoxylate and ethylmalonyl-coA cycles for acetate assimilation.

Pigment carbon and nitrogen isotopic signatures in euxinic basins

The carbon and nitrogen isotopic signatures of chloropigments and porphyrins from the sediments of redox-stratified lakes and marine basins reveal details of past biogeochemical nutrient cycling. Such interpretations are strengthened by modern calibration studies, and here, we report on the C and N isotopic composition of pigments and nutrients in the water column and surface sediment of redox-stratified Fayetteville Green Lake (FGL; New York). We also report δ¹³ C and δ¹⁵ N values for pyropheophytin a (Pphe a) and bacteriochlorophyll e (Bchl e) deposited in the Black Sea during its transition to a redox-stratified basin ca. 7.8 ka. We propose a model for evolving nutrient cycling in the Black Sea from 7.8 to 6.4 ka, informed by the new pigment data from FGL. The seasonal study of water column nutrients and pigments at FGL revealed population dynamics in surface and deep waters that were also captured in the sediments. Biomass was greatest near the chemocline, where cyanobacteria, purple sulfur bacteria (PSB), and green sulfur bacteria (GSB) had seasonally variable populations. Bulk organic matter in the surface sediment, however, was derived mainly from the oxygenated surface waters. Surface sediment pigment δ¹³ C and δ¹⁵ N values indicate intact chlorophyll a (Chl a) was derived from near the chemocline, but its degradation product pheophytin a (Phe a) was derived primarily from surface waters. Bacteriopheophytin a (Bphe a) and Bchl e in the sediments came from chemocline populations of PSB and GSB, respectively. The distinctive δ¹³ C and δ¹⁵ N values for Chl a, Phe a, and Bphe a in the surface sediment are inputs to an isotopic mixing model that shows their decomposition to a common porphyrin derivative can produce non-specific sedimentary isotope signatures. This model serves as a caveat for paleobiogeochemical interpretations in basins that had diverse populations near a shallow chemocline.

Phosphoribulokinase mediates nitrogenase-induced carbon dioxide fixation gene repression in Rhodobacter sphaeroides

In many organisms there is a balance between carbon and nitrogen metabolism. These observations extend to the nitrogen-fixing, nonsulfur purple bacteria, which have the classic family of P(II) regulators that coordinate signals of carbon and nitrogen status to regulate nitrogen metabolism. Curiously, these organisms also possess a reverse mechanism to regulate carbon metabolism based on cellular nitrogen status. In this work, studies in Rhodobacter sphaeroides firmly established that the activity of the enzyme that catalyses nitrogen fixation, nitrogenase, induces a signal that leads to repression of genes encoding enzymes of the Calvin–Benson–Bassham (CBB) CO₂ fixation pathway. Additionally, genetic and metabolomic experiments revealed that NADH-activated phosphoribulokinase is an intermediate in the signalling pathway. Thus, nitrogenase activity appears to be linked to cbb gene repression through phosphoribulokinase.

Pathways involved in reductant distribution during photobiological H(2) production by Rhodobacter sphaeroides

We used global transcript analyses and mutant studies to investigate the pathways that impact H(2) production in the photosynthetic bacterium Rhodobacter sphaeroides. We found that H(2) production capacity is related to the levels of expression of the nitrogenase and hydrogenase enzymes and the enzymes of the Calvin-Benson-Bassham pathway.

Relevance of individual Mo-box nucleotides to DNA binding by the related molybdenum-responsive regulators MopA and MopB in Rhodobacter capsulatus

Either of two related molybdenum-responsive regulators, MopA and MopB, of Rhodobacter capsulatus is sufficient to repress the nitrogen-fixation gene anfA. In contrast, MopA (but not MopB) activates mop, which codes for a molybdate (Mo)-binding molbindin. Both regulators bind to conserved cis-regulatory elements called Mo-boxes. Single-base substitution of two highly conserved nucleotides within the anfA-Mo-box (T21C and C24T) had little effect on regulator binding and anfA expression as shown by DNA mobility shift assays and reporter gene fusions, respectively. In contrast to C24T, mutation C24A strongly diminished binding and repression by MopA and MopB, showing that different nucleotide substitutions at the same position may have very different effects. A triple mutation destroying the left half-site of the mop-Mo-box completely abolished mop expression by MopA, demonstrating the importance of the mop-Mo-box for mop activation. Two point mutations (T23A and T24C) still allowed binding by MopA, but abolished mop activation, most likely because these nucleotides overlap with the RNA polymerase-binding site. A mutant mop promoter, in which the mop-Mo-box was exchanged against the anfA-Mo-box, allowed activation by MopA, showing that a former repressor-binding site may act as an activator-binding site depending on its location relative to the other promoter elements.