Rhodopseudomonas palustris shapes bacterial community, reduces Cd bioavailability in Cd contaminated flooding paddy soil, and improves rice performance

Photosynthetic bacteria (PSB) are suitable to live and remediate cadmium (Cd) in the slightly oxygenated or anaerobic flooding paddy field. However, there is currently limited study on the inhibition of Cd accumulation in rice by PSB, and the relevant mechanisms has yet to be elucidated. In the current study, we firstly used Rhodopseudomonas palustris SC06 (a typical PSB) as research target and combined physiology, biochemistry, microbiome and metabolome to evaluate the mechanisms of remeding Cd pollution in paddy field and inhibiting Cd accumulation in rice. Microbiome analysis results revealed that intensive inoculation with R. palustris SC06 successfully survived and multiplied in flooding paddy soil, and significantly increased the relatively abundance of anaerobic bacteria including Desulfobacterota, Anaerolineaceae, Geobacteraceae, and Gemmatimonadaceae by 46.40 %, 45.00 %, 50.12 %, and 21.30 %, respectively. Simultaneously, the structure of microbial community was regulated to maintain relative stability in the rhizosphere soil of rice under Cd stress. In turn, these bacteria communities reduced bioavailable Cd and enhanced residual Cd in soil, and induced the upregulation of sugar and organic acids in the rice roots, which further inhibited Cd uptake in rice seedlings, and dramatically improved the photosynthetic efficiency in the leaves and the activities of antioxidative enzymes in the roots. Finally, Cd content of the roots, stems, leaves, and grains significantly decreased by 38.14 %, 69.10 %, 83.40 %, and 37.24 % comparing with the control, respectively. This study provides a new strategy for the remediation of Cd-contaminated flooding paddy fields and the safe production of rice.

Evolution of Rhodopseudomonas palustris to degrade halogenated aromatic compounds involves changes in pathway regulation and enzyme specificity

Halogenated aromatic compounds are used in a variety of industrial applications but can be harmful to humans and animals when released into the environment. Microorganisms that degrade halogenated aromatic compounds anaerobically have been isolated but the evolutionary path that they may have taken to acquire this ability is not well understood. A strain of the purple nonsulfur bacterium, Rhodopseudomonas palustris, RCB100, can use 3-chlorobenzoate (3-CBA) as a carbon source whereas a closely related strain, CGA009, cannot. To reconstruct the evolutionary events that enabled RCB100 to degrade 3-CBA, we isolated an evolved strain derived from CGA009 capable of growing on 3-CBA. Comparative whole-genome sequencing of the evolved strain and RCB100 revealed both strains contained large deletions encompassing badM, a transcriptional repressor of genes for anaerobic benzoate degradation. It was previously shown that in strain RCB100, a single nucleotide change in an alicyclic acid coenzyme A ligase gene, named aliA, gives rise to a variant AliA enzyme that has high activity with 3-CBA. When the RCB100 aliA allele and a deletion in badM were introduced into R. palustris CGA009, the resulting strain grew on 3-CBA at a similar rate as RCB100. This work provides an example of pathway evolution in which regulatory constraints were overcome to enable the selection of a variant of a promiscuous enzyme with enhanced substrate specificity.IMPORTANCEBiodegradation of man-made compounds often involves the activity of promiscuous enzymes whose native substrate is structurally similar to the man-made compound. Based on the enzymes involved, it is possible to predict what microorganisms are likely involved in biodegradation of anthropogenic compounds. However, there are examples of organisms that contain the required enzyme(s) and yet cannot metabolize these compounds. We found that even when the purple nonsulfur bacterium, Rhodopseudomonas palustris, encodes all the enzymes required for degradation of a halogenated aromatic compound, it is unable to metabolize that compound. Using adaptive evolution, we found that a regulatory mutation and a variant of promiscuous enzyme with increased substrate specificity were required. This work provides insight into how an environmental isolate evolved to use a halogenated aromatic compound.

Full quantitative resource utilization of raw mustard waste through integrating a comprehensive approach for producing hydrogen and soil amendments

BACKGROUND

Pickled mustard, the largest cultivated vegetable in China, generates substantial waste annually, leading to significant environmental pollution due to challenges in timely disposal, leading to decomposition and sewage issues. Consequently, the imperative to address this concern centers on the reduction and comprehensive resource utilization of raw mustard waste (RMW). To achieve complete and quantitative resource utilization of RMW, this study employs novel technology integration for optimizing its higher-value applications.

RESULTS

Initially, subcritical hydrothermal technology was applied for rapid decomposition, with subsequent ammonia nitrogen removal via zeolite. Thereafter, photosynthetic bacteria, Rhodopseudomonas palustris, were employed to maximize hydrogen and methane gas production using various fermentation enhancement agents. Subsequent solid-liquid separation yielded liquid fertilizer from the fermented liquid and soil amendment from solid fermentation remnants. Results indicate that the highest glucose yield (29.6 ± 0.14) was achieved at 165-173℃, with a total sugar content of 50.2 g/L and 64% glucose proportion. Optimal ammonia nitrogen removal occurred with 8 g/L zeolite and strain stable growth at 32℃, with the highest OD600 reaching 2.7. Several fermentation promoters, including FeSO4, Neutral red, Na2S, flavin mononucleotide, Nickel titanate, Nickel oxide, and Mixture C, were evaluated for hydrogen production. Notably, Mixture C resulted in the maximum hydrogen production (756 mL), a production rate of 14 mL/h, and a 5-day stable hydrogen production period. Composting experiments enhanced humic acid content and organic matter (OM) by 17% and 15%, respectively.

CONCLUSIONS

This innovative technology not only expedites RMW treatment and hydrogen yield but also substantially enriches soil fertility. Consequently, it offers a novel approach for low-carbon, zero-pollution RMW management. The study's double outcomes extend to large-scale RMW treatment based on the aim of full quantitative resource utilization of RMW. Our method provides a valuable reference for waste management in similar perishable vegetable plantations.

Multidimensional optimization for accelerating light-powered biocatalysis in Rhodopseudomonas palustris

BACKGROUND

Whole-cell biocatalysis has been exploited to convert a variety of substrates into high-value bulk or chiral fine chemicals. However, the traditional whole-cell biocatalysis typically utilizes the heterotrophic microbes as the biocatalyst, which requires carbohydrates to power the cofactor (ATP, NAD (P)H) regeneration.

RESULTS

In this study, we sought to harness purple non-sulfur photosynthetic bacterium (PNSB) as the biocatalyst to achieve light-driven cofactor regeneration for cascade biocatalysis. We substantially improved the performance of Rhodopseudomonas palustris-based biocatalysis using a highly active and conditional expression system, blocking the side-reactions, controlling the feeding strategy, and attenuating the light shading effect. Under light-anaerobic conditions, we found that 50 mM ferulic acid could be completely converted to vanillyl alcohol using the recombinant strain with 100% efficiency, and > 99.9% conversion of 50 mM p-coumaric acid to p-hydroxybenzyl alcohol was similarly achieved. Moreover, we examined the isoprenol utilization pathway for pinene synthesis and 92% conversion of 30 mM isoprenol to pinene was obtained.

CONCLUSIONS

Taken together, these results suggested that R. palustris could be a promising host for light-powered biotransformation, which offers an efficient approach for synthesizing value-added chemicals in a green and sustainable manner.

Characterization of the Pyrroloquinoline Quinone Producing Rhodopseudomonas palustris as a Plant Growth-Promoting Bacterium under Photoautotrophic and Photoheterotrophic Culture Conditions

Rhodopseudomonas palustris is a purple non-sulfide bacterium (PNSB), and some strains have been proven to promote plant growth. However, the mechanism underlying the effect of these PNSBs remains limited. Based on genetic information, R. palustris possesses the ability to produce pyrroloquinoline quinone (PQQ). PQQ is known to play a crucial role in stimulating plant growth, facilitating phosphorous solubilization, and acting as a reactive oxygen species scavenger. However, it is still uncertain whether growth conditions influence R. palustris's production of PQQ and other characteristics. In the present study, it was found that R. palustris exhibited a higher expression of genes related to PQQ synthesis under autotrophic culture conditions as compared to acetate culture conditions. Moreover, similar patterns were observed for phosphorous solubilization and siderophore activity, both of which are recognized to contribute to plant-growth benefits. However, these PNSB culture conditions did not show differences in Arabidopsis growth experiments, indicating that there may be other factors influencing plant growth in addition to PQQ content. Furthermore, the endophytic bacterial strains isolated from Arabidopsis exhibited differences according to the PNSB culture conditions. These findings imply that, depending on the PNSB's growing conditions, it may interact with various soil bacteria and facilitate their infiltration into plants.

Performance of production of polyhydroxyalkanoates from food waste fermentation with Rhodopseudomonas palustris

The use of waste as a carbon source can significantly reduce the cost of production of Polyhydroxyalkanoates (PHAs). In this study, an acidified hydrolysate solution derived from food waste (FW) was used as a carbon source for the synthesis of PHAs by Rhodopseudomonas palustris (R. palustris) and optimized the process parameters. The results showed that the PHAs yield reached 48.62% under optimal conditions (an incubation time of 30 days, volatile fatty acids (VFAs) in substrate concentration of 2202.21 mg⋅L^-1, an initial pH of 8.0, and inoculum concentration of 15%). The fraction of VFAs affects the composition of PHAs, R. palustris first uses VFAs with an even number of carbons to synthesize poly(3-hydroxybutyrate)(3HB), and later uses VFAs with an odd number of carbons to synthesize poly-3-hydroxyvalerate (3HV). Pathways for the synthesis of PHAs by R. palustris were inferred. R. palustris is a strain with the potential to synthesize PHAs.

The effect of light emission spectrum on biohydrogen production by Rhodopseudomonas palustris

Photofermentative hydrogen production has gained increasing attention as a source of green energy. To make such photofermentation processes economically competitive, operating costs need to be reduced, possibly through outdoor operation. Because photofermentation processes are light dependent, the emission spectrum and intensity of light both have a significant influence on the hydrogen production and merit investigation. This study investigates the effect of light sources on the hydrogen production and growth of Rhodopseudomonas palustris, comparing the organism's productivity under longer-wavelength light and light mimicking sunlight. Hydrogen production is enhanced under longer-wavelength light, producing 26.8% (± 7.3%) more hydrogen as compared to under light mimicking that of sunlight; however, R. palustris is still able to produce a considerable volume of hydrogen under light with a spectrum mimicking that of sunlight, providing a promising avenue for future research.

The effect of diurnal light cycles on biohydrogen production in a thermosiphon photobioreactor

Hydrogen production via microbial photofermentation shows great promise as a method for sustainable hydrogen production; however, operating costs associated with photofermentative hydrogen production need to be reduced. Costs can be reduced using a passive circulation system like the thermosiphon photobioreactor, and by operating it under natural sunlight. In this study, an automated system was implemented to investigate the effect of diurnal light cycles on the hydrogen productivity and growth of Rhodopseudomonas palustris and on the operation of a thermosiphon photobioreactor, under controlled conditions. Diurnal light cycles, simulating daylight times, were found to reduce hydrogen production in the thermosiphon photobioreactor demonstrating a low maximum production rate of 0.015 mol m^-3 h^-1 (± 0.002 mol m^-3 h^-1) as compared to 0.180 mol m^-3 h^-1 (± 0.0003 mol m^-3 h^-1) under continuous illumination. Glycerol consumption as well as hydrogen yield also decreased under diurnal light cycles. Nonetheless, hydrogen production in a thermosiphon photobioreactor under outdoor conditions was demonstrated as possible avenue for further investigation.

Evolving a New Electron Transfer Pathway for Nitrogen Fixation Uncovers an Electron Bifurcating-Like Enzyme Involved in Anaerobic Aromatic Compound Degradation

Nitrogenase is the key enzyme involved in nitrogen fixation and uses low potential electrons delivered by ferredoxin (Fd) or flavodoxin (Fld) to reduce dinitrogen gas (N₂) to produce ammonia, generating hydrogen gas (H₂) as an obligate product of this activity. Although the phototrophic alphaproteobacterium Rhodopseudomonas palustris encodes multiple proteins that can reduce Fd, the FixABCX complex is the only one shown to support nitrogen fixation, and R. palustris Fix^- mutants grow poorly under nitrogen-fixing conditions. To investigate how native electron transfer chains (ETCs) can be redirected toward nitrogen fixation, we leveraged the strong selective pressure of nitrogen limitation to isolate a suppressor of an R. palustris ΔfixC strain that grows under nitrogen-fixing conditions. We found two mutations were required to restore growth under nitrogen-fixing conditions in the absence of functional FixABCX. One mutation was in the gene encoding the primary Fd involved in nitrogen fixation, fer1, and the other mutation was in aadN, which encodes a homolog of NAD⁺-dependent Fd:NADPH oxidoreductase (Nfn). We present evidence that AadN plays a role in electron transfer to benzoyl coenzyme A reductase, the key enzyme involved in anaerobic aromatic compound degradation. Our data support a model where the ETC for anaerobic aromatic compound degradation was repurposed to support nitrogen fixation in the ΔfixC suppressor strain. IMPORTANCE There is increasing evidence that protein electron carriers like Fd evolved to form specific partnerships with select electron donors and acceptors to keep native electron transfer pathways insulated from one another. This makes it challenging to integrate a Fd-dependent pathway such as biological nitrogen fixation into non-nitrogen-fixing organisms and provide the high-energy reducing power needed to fix nitrogen. Here, we show that amino acid substitutions in an electron donor for anaerobic aromatic compound degradation and an Fd involved in nitrogen fixation enabled electron transfer to nitrogenase. This study provides a model system to understand electron transfer chain specificity and how new electron transfer pathways can be evolved for biotechnologically valuable pathways like nitrogen fixation.

Simultaneous functioning of different light-harvesting complexes-a strategy of adaptation of purple bacterium Rhodopseudomonas palustris to low illumination conditions

Novel peripheral light-harvesting (LH) complex designated as LL LH2 was isolated along with LH4 complex from Rhodopseudomonas palustris cells grown under low light intensity (LL). FPLC-MS/MS allowed to reveal PucABd and PucBabc apoproteins in LL LH2 complex, which is different from previously described LH4 complex containing PucABd, PucABa and PucBb. The main carotenoids in LL LH2 complex were rhodopin and 3,4-didehydrorhodopin. Three-dimensional modeling demonstrated which amino acid residues of all the β-subunits could interact with carotenoids (Car) and bacteriochlorophyll a (BChl a). Analysis of amino acid sequences of α-subunits of both LL complexes showed presence of different C-terminal motifs, IESSVNVG in αa subunit and IESSIKAV in αd subunit, in the same positions of C-termini, which could reflect different retention force of LL LH2 and LH4 on hydroxyl apatite, facilitating successful isolation of these complexes. Differences of these LL complexes in protein and carotenoid composition, in efficiency of energy transfer from Car to BChl a, which is two times lower in LL LH2 than in LH4, allow to assign it to a novel type of light-harvesting complex in Rhodopseudomonas palustris.

Modelling and testing of a light reflector system for the enhancement of biohydrogen production in a thermosiphon photobioreactor

One of the main factors affecting hydrogen production and growth of photofermentative microorganisms is light; low light penetration and utilization are significant bottlenecks in photofermentative hydrogen production systems. In this study, light distribution in a thermosiphon photobioreactor operated with Rhodopseudomonas palustris was investigated. Radiation fields were modelled and simulated using computational fluid dynamics (ANSYS® Fluent, 2019 R2) and a reflector system was evaluated for the enhancement of light distribution in a thermosiphon photobioreactor. The effect of the reflector system was investigated experimentally in terms of hydrogen production, carbon substrate consumption and biomass circulation in the reactor. With the addition of the reflector system, hydrogen production was increased by 48% while glycerol consumption was increased from approximately 24% to 32%. After 336 h, the concentration of R. palustris cells still in suspension ranged from 0.13 to 0.18 g∙L^-1, with no discernible difference in concentration between the systems with and without reflectors. Collectively, the reflector system was shown to be a viable option in enhancing light distribution in photobioreactors, with an associated increase in both hydrogen production as well as glycerol consumption.

Culture optimization to enhance carotenoid production of a selected purple nonsulfur bacterium and its activity against acute hepatopancreatic necrosis disease-causing Vibrio parahaemolyticus

Purple nonsulfur bacteria (PNSB) were investigated for their carotenoid production and anti-vibrio activity against acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio parahaemolyticus. To test carotenoid production, selected strains were cultivated in basic isolation medium (BIM), glutamate acetate medium, G5 medium and artificial acetic acid wastewater (AAW) medium. From 144 PNSB, Rhodopseudomonas palustris KTSSG46 was selected to produce carotenoids under microaerobic light conditions in BIM. When the culture medium was optimized, strain KTSSG46 grown in BIM modified with l-glutamate at 1 g/L more effectively inhibited AHPND-causing V. parahaemolyticus strains than standard BIM with 1 g/L (NH₄ )₂ SO₄ . BIM was further modified with 1.23 g/L MgSO₄ ·7H₂ O and carotenoid production increased 40.22%. Carotenoid production at day 2 by strain KTSSG46 grown in BIM modified with l-glutamate at 1 and 1.23 g/L MgSO₄ ·7H₂ O was the same as production in BIM modified with monosodium glutamate (MSG). Culture supernatants from all BIM formulations showed similar activity against the resistant AHPND strain SR2. Based on high-performance liquid chromatography, carotenoids of strain KTSSG46 might be canthaxanthin. Grown in BIM modified with MSG, strain KTSSG46 could produce inexpensive carotenoids and release anti-vibrio compounds that, applied as shrimp feed additive, would prevent AHPND strains.

Cryo-EM structures of light-harvesting 2 complexes from Rhodopseudomonas palustris reveal the molecular origin of absorption tuning

The light-harvesting (LH) complexes of phototrophic bacteria absorb solar energy for photosynthesis, and it is important to understand how the protein components influence the way bound pigments absorb light. We studied the LH2 complexes of Rhodopseudomonas palustris, which are encoded by a multigene family. Various combinations of LH2 genes were deleted, yielding strains that assemble only one of the four types of LH2. Following purification, the structures of four LH2 complexes were determined by cryogenic electron microscopy, revealing a basic nonameric ring structure comprising nine αβ-polypeptide pairs. An additional hitherto unknown polypeptide, γ, was found in each structure that binds six further bacteriochlorophylls. Comparison of these different structures shows how nature tunes their ability to absorb different wavelengths of light.

The genomes of some purple photosynthetic bacteria contain a multigene puc family encoding a series of α- and β-polypeptides that together form a heterogeneous antenna of light-harvesting 2 (LH2) complexes. To unravel this complexity, we generated four sets of puc deletion mutants in Rhodopseudomonas palustris, each encoding a single type of pucBA gene pair and enabling the purification of complexes designated as PucA-LH2, PucB-LH2, PucD-LH2, and PucE-LH2. The structures of all four purified LH2 complexes were determined by cryogenic electron microscopy (cryo-EM) at resolutions ranging from 2.7 to 3.6 Å. Uniquely, each of these complexes contains a hitherto unknown polypeptide, γ, that forms an extended undulating ribbon that lies in the plane of the membrane and that encloses six of the nine LH2 αβ-subunits. The γ-subunit, which is located near to the cytoplasmic side of the complex, breaks the C9 symmetry of the LH2 complex and binds six extra bacteriochlorophylls (BChls) that enhance the 800-nm absorption of each complex. The structures show that all four complexes have two complete rings of BChls, conferring absorption bands centered at 800 and 850 nm on the PucA-LH2, PucB-LH2, and PucE-LH2 complexes, but, unusually, the PucD-LH2 antenna has only a single strong near-infared (NIR) absorption peak at 803 nm. Comparison of the cryo-EM structures of these LH2 complexes reveals altered patterns of hydrogen bonds between LH2 αβ-side chains and the bacteriochlorin rings, further emphasizing the major role that H bonds play in spectral tuning of bacterial antenna complexes.

Construction of 5-aminolevulinic acid synthase variants by cysteine-targeted mutation to release heme inhibition

5-Aminolevulinic acid (5-ALA), a vital precursor for the biosynthesis of tetrapyrrole compounds, has been widely applied in agriculture and medicine, while extremely potential for the treatment of cancers, corona virus disease 2019 (COVID-19) and metabolic diseases in recent years. With the development of metabolic engineering and synthetic biology, the biosynthesis of 5-ALA has attracted increasing attention. 5-Aminolevulinic acid synthase (ALAS), the key enzyme for 5-ALA synthesis in the C4 pathway, is subject to stringent feedback inhibition by heme. In this work, cysteine-targeted mutation of ALAS was proposed to overcome this drawback. ALAS from Rhodopseudomonas palustris (RP-ALAS) and Rhodobacter capsulatus (RC-ALAS) were selected for mutation and eight variants were generated. Variants RP-C132A and RC-C201A increased enzyme activities and released hemin inhibition, respectively, maintaining 82.5% and 81.9% residual activities in the presence of 15 μM hemin. Moreover, the two variants exhibited higher stability than that of their corresponding wild-type enzymes. Corynebacterium glutamicum overexpressing RP-C132A and RC-C201A produced 14.0% and 21.6% higher titers of 5-ALA than the control, respectively. These results strongly suggested that variants RP-C132A and RC-C201A obtained by utilizing cysteine-targeted mutation strategy released hemin inhibition, broadening their applications in 5-ALA biosynthesis.

Framework to improve biohydrogen generation with estrogen co-metabolism under complete suppression of nitrogen source

The current work provides insights for improving the hydrogen output while degrading emerging contaminants using Rhodopseudomonas palustris. The changes in the growth rate of a microorganism due to different substrate inputs affects the hydrogen production due to metabolic route changes. The different ratios of glutamate and glycerol as nitrogen and carbon sources along with the presence of ethinylestradiol (EE2) in the photofermenter affected the flux of electrons being directed towards biosynthesis and biohydrogen generation. The combination of glutamate and glycerol in different ratios (Glu:Gly; 0, 0.20 and 0.54) along with estrogen showed no significant difference in the bacteriochlorophyll concentrations. The highest biomass concentration (0.013 h^-1) was in ratio of 0.54 while maximum specific hydrogen production (1.9 ± 0.05 ml g^-1 biomass h^-1) was observed under complete suppression of nitrogen (0; without Glu; non-growing condition) with resultant improved estrogen degradation of about 78% in 168 h by R. palustris strain MDOC01.

PioABC-Dependent Fe(II) Oxidation during Photoheterotrophic Growth on an Oxidized Carbon Substrate Increases Growth Yield

Microorganisms that carry out Fe(II) oxidation play a major role in biogeochemical cycling of iron in environments with low oxygen. Fe(II) oxidation has been largely studied in the context of autotrophy. Here, we show that the anoxygenic phototroph, Rhodopseudomonas palustris CGA010, carries out Fe(II) oxidation during photoheterotrophic growth with an oxidized carbon source, malate, leading to an increase in cell yield and allowing more carbon to be directed to cell biomass. We probed the regulatory basis for this by transcriptome sequencing (RNA-seq) and found that the expression levels of the known pioABC Fe(II) oxidation genes in R. palustris depended on the redox-sensing two-component system, RegSR, and the oxidation state of the carbon source provided to cells. This provides the first mechanistic demonstration of mixotrophic growth involving reducing power generated from both Fe(II) oxidation and carbon assimilation. IMPORTANCE The simultaneous use of carbon and reduced metals such as Fe(II) by bacteria is thought to be widespread in aquatic environments, and a mechanistic description of this process could improve our understanding of biogeochemical cycles. Anoxygenic phototrophic bacteria like Rhodopseudomonas palustris typically use light for energy and organic compounds as both a carbon and an electron source. They can also use CO₂ for carbon by carbon dioxide fixation when electron-rich compounds like H₂, thiosulfate, and Fe(II) are provided as electron donors. Here, we show that Fe(II) oxidation can be used in another context to promote higher growth yields of R. palustris when the oxidized carbon compound malate is provided. We further established the regulatory mechanism underpinning this observation.

A Thermosiphon Photobioreactor for Photofermentative Hydrogen Production by Rhodopseudomonas palustris

A thermosiphon photobioreactor (TPBR) can potentially be used for biohydrogen production, circumventing the requirement for external mixing energy inputs. In this study, a TPBR is evaluated for photofermentative hydrogen production by Rhodopseudomonas palustris (R. palustris). Experiments were conducted in a TPBR, and response surface methodology (RSM), varying biomass concentration, and light intensity and temperature were employed to determine the operating conditions for the enhancement of both hydrogen production as well as biomass suspension. Biomass concentration was found to have had the most pronounced effect on both hydrogen production as well as biomass suspension. RSM models predicted maximum specific hydrogen production rates of 0.17 mol m⁻³h⁻¹ and 0.21 mmol g_CDW⁻¹h⁻¹ at R. palustris concentrations of 1.21 and 0.4 g L⁻¹, respectively. The experimentally measured hydrogen yield was in the range of 45 to 77% (±3.8%), and the glycerol consumption was 8 to 19% (±0.48). At a biomass concentration of 0.40 g L⁻¹, the highest percentage of biomass (72.3%), was predicted to remain in suspension in the TPBR. Collectively, the proposed novel photobioreactor was shown to produce hydrogen as well as passively circulate biomass.

Rhodopseudomonas palustris: A biotechnology chassis

Rhodopseudomonas palustris is an attractive option for biotechnical applications and industrial engineering due to its metabolic versatility and its ability to catabolize a wide variety of feedstocks and convert them to several high-value products. Given its adaptable metabolism, R. palustris has been studied and applied in an extensive variety of applications such as examining metabolic tradeoffs for environmental perturbations, biodegradation of aromatic compounds, environmental remediation, biofuel production, agricultural biostimulation, and bioelectricity production. This review provides a holistic summary of the commercial applications for R. palustris as a biotechnology chassis and suggests future perspectives for research and engineering.

Biodegradation of synthetic estrogen using bioelectrochemical system and degradation pathway analysis through Quadrupole-time-of-flight-mass spectrometry

Synthetic estrogenic compounds such as 17α-ethinylestradiol (EE2) are significant environmental contaminants. This research studied the biodegradation of EE2 utilizing the EE2 adapted cells isolated from a dairy farm waste site in suspension flask vis-a-vis Bioelectrochemical System (BES) and compared the power output in the BES with and without EE2 as a co-substrate. 78% removal of EE2 was observed in the BES as against 60% removal in suspension flasks. The maximum power density in the BES increased about 53% when EE2 is used as a co-substrate. The EE2 biodegradation studied using HPLC and Q-TOF methods, also proposes a hypothetical pathway for EE2 degradation by the newly isolated strain Rhodopseudomonas palustris MDOC01 and reports the significant metabolites like nicotinic acid and oxoproline being detected during bioelectrochemical treatment process of EE2. Study also suggests that Plasma peroxide treatment of anode material enhanced the overall performance in terms of biodegradation efficiency and power output.

Heterologous phasin expression in Rhodopseudomonas palustris CGA009 for bioplastic production from lignocellulosic biomass

Rhodopseudomonas palustris CGA009 is a metabolically robust microbe that can utilize lignin breakdown products to produce polyhydroxyalkanoates (PHAs), biopolymers with the potential to replace conventional plastics. Our recent efforts suggest PHA granule formation is a limiting factor for maximum production of the bioplastic poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) by R. palustris. The Phap1 phasin (phaP1) from the PHB-producing model bacterium Cupriavidus necator H16 was expressed in R. palustris with the aim of overproducing PHBV from the lignin breakdown product p-coumarate by fostering smaller and more abundant granules. Expression of phaP1 yielded PHBV production from R. palustris aerobically (0.7 g/L), which does not occur in the wild-type strain, and led to a significantly higher PHBV titer than wild-type anaerobic production (0.41 g/L). The 3HV fractions were also significantly increased under both anaerobic and aerobic conditions, which boosts thermomechanical properties and potential for application. Thus, heterologous phasin expression in R. palustris provides flexibility for industrial processing and could foster compositional changes in copolymers with better thermomechanical properties compared to PHB alone.

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Heterologous phasin expression in R. palustris fostered aerobic bioplastic production.

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Offers flexibility for industrial processing of high-value products from lignocellosic biomass.

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Composition increases in desirable monomer fractions occurred due to phasin expression.

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Further develops the metabolically robust R. palustris as a biotechnology chassis.

Investigating and modelling the effect of light intensity on Rhodopseudomonas palustris growth

Photosynthetic bacteria can be useful biotechnological tools - they produce a variety of valuable products, including high purity hydrogen, and can simultaneously treat recalcitrant wastewaters. However, while photobioreactors have been designed and modelled for photosynthetic algae and cyanobacteria, there has been less work on understanding the effect of light in photosynthetic bacterial fermentations. In order to design photobioreactors, and processes using these organisms, robust models of light penetration, utilisation and conversion are needed. This article uses experimental data from a tubular photobioreactor designed to focus in on light intensity effects, to model the effect of light intensity on the growth of Rhodopseudomonas palustris, a model photosynthetic bacterium. The work demonstrates that growth is controlled by light intensity, and that this organism does experience photolimitation below 200 W/m2 and photoinhibition above 600 W/m2. This has implications for outdoor applications, as there will be low growth during the periods of limited light, and growth may be inhibited during the light intensive hours of mid-day. Further, the work presents a model for light penetration in cylindrical photobioreactors, which tends to be the most common geometry. The model developed showed good fit to the experimental data for each light intensity investigated, with high R2 values and NRMSE values all below 20%. The work extends the modelling tools for these organisms, and will allow for better photobioreactor design, and the integration of modelling tools in designing processes which use photosynthetic bacteria. This article is protected by copyright. All rights reserved.

GroEL protein from the potential biocontrol agent Rhodopseudomonas palustris enhances resistance to rice blast disease

BACKGROUND

GroEL, which is a chaperone, plays a key role in maintaining protein homeostasis and, among other functions, serves to prevent protein misfolding and aggregation. In addition, the GroEL protein also has a significant effect on enhancing plant resistance and inhibiting plant diseases. However, the function of the GroEL protein in the inhibition of rice blast remains unknown.

RESULTS

Field experiment results show that photosynthetic bacteria PSB-06 have a good control effect on Magnaporthe oryzae. PSB-06 also can promote rice growth and enhance stress resistance. A GroEL protein which was separated and purified from photosynthetic bacteria had a significant antagonistic effect on appressorial formation and pathogenicity of Magnaporthe oryzae, meanwhile transcriptional analysis demonstrated that the GroEL protein could improve the expression of defense gene of rice.

CONCLUSION

Our results show that the photosynthetic bacteria Rhodopseudomonas palustris significantly controls rice blast disease. Its action involves an extracellular GroEL protein, which inhibits appressoria formation, antagonizes the pathogenicity of Magnaporthe oryzae and promotes a host defense response. The research results provide evidence of the potential of this photosynthetic bacterium as a biocontrol agent at least for rice blast control. © 2021 Society of Chemical Industry.

Expression of Alternative Nitrogenases in Rhodopseudomonas palustris Is Enhanced Using an Optimized Genetic Toolset for Rapid, Markerless Modifications

The phototrophic bacterium Rhodopseudomonas palustris is emerging as a promising biotechnological chassis organism, due to its resilience to a range of harsh conditions, a wide metabolic repertoire, and the ability to quickly regenerate ATP using light. However, realization of this promise is impeded by a lack of efficient, rapid methods for genetic modification. Here, we present optimized tools for generating chromosomal insertions and deletions employing electroporation as a means of transformation. Generation of markerless strains can be completed in 12 days, approximately half the time for previous conjugation-based methods. This system was used for overexpression of alternative nitrogenase isozymes with the aim of improving biohydrogen productivity. Insertion of the pucBa promoter upstream of vnf and anf nitrogenase operons drove robust overexpression up to 4000-fold higher than wild-type. Transcript quantification was facilitated by an optimized high-quality RNA extraction protocol employing lysis using detergent and heat. Overexpression resulted in increased nitrogenase protein levels, extending to superior hydrogen productivity in bioreactor studies under nongrowing conditions, where promoter-modified strains better utilized the favorable energy state created by reduced competition from cell division. Robust heterologous expression driven by the pucBa promoter is thus attractive for energy-intensive biosyntheses suited to the capabilities of R. palustris. Development of this genetic modification toolset will accelerate the advancement of R. palustris as a biotechnological chassis organism, and insights into the effects of nitrogenase overexpression will guide future efforts in engineering strains for improved hydrogen production.

The structural basis for high-affinity uptake of lignin-derived aromatic compounds by proteobacterial TRAP transporters

The organic polymer lignin is a component of plant cell walls, which like (hemi)-cellulose is highly abundant in nature and relatively resistant to degradation. However, extracellular enzymes released by natural microbial consortia can cleave the β-aryl ether linkages in lignin, releasing monoaromatic phenylpropanoids that can be further catabolised by diverse species of bacteria. Biodegradation of lignin is therefore important in global carbon cycling, and its natural abundance also makes it an attractive biotechnological feedstock for the industrial production of commodity chemicals. Whilst the pathways for degradation of lignin-derived aromatics have been extensively characterised, much less is understood about how they are recognised and taken up from the environment. The purple phototrophic bacterium Rhodopseudomonas palustris can grow on a range of phenylpropanoid monomers and is a model organism for studying their uptake and breakdown. R. palustris encodes a tripartite ATP-independent periplasmic (TRAP) transporter (TarPQM) linked to genes encoding phenylpropanoid-degrading enzymes. The periplasmic solute-binding protein component of this transporter, TarP, has previously been shown to bind aromatic substrates. Here, we determine the high-resolution crystal structure of TarP from R. palustris as well as the structures of homologous proteins from the salt marsh bacterium Sagittula stellata and the halophile Chromohalobacter salexigens, which also grow on lignin-derived aromatics. In combination with tryptophan fluorescence ligand-binding assays, our ligand-bound co-crystal structures reveal the molecular basis for high-affinity recognition of phenylpropanoids by these TRAP transporters, which have potential for improving uptake of these compounds for biotechnological transformations of lignin.

Kinetic modeling of anaerobic degradation of plant-derived aromatic mixtures by Rhodopseudomonas palustris

Rhodopseudomonas palustris is a model microorganism for studying the anaerobic metabolism of aromatic compounds. While it is well documented which aromatics can serve as sole organic carbon sources, co-metabolism of other aromatics is poorly understood. This study used kinetic modeling to analyze the simultaneous degradation of aromatic compounds present in corn stover hydrolysates and model the co-metabolism of aromatics not known to support growth of R. palustris as sole organic substrates. The simulation predicted that p-coumaroyl amide and feruloyl amide were hydrolyzed to p-coumaric acid and ferulic acid, respectively, and further transformed via p-coumaroyl-CoA and feruloyl-CoA. The modeling also suggested that metabolism of p-hydroxyphenyl aromatics was slowed by substrate inhibition, whereas the transformation of guaiacyl aromatics was inhibited by their p-hydroxyphenyl counterparts. It also predicted that substrate channeling may occur during degradation of p-coumaroyl-CoA and feruloyl-CoA, resulting in no detectable accumulation of p-hydroxybenzaldehyde and vanillin, during the transformation of these CoA ligated compounds to p-hydroxybenzoic acid and vanillic acid, respectively. While the simulation correctly represented the known transformation of p-hydroxybenzoic acid via the benzoyl-CoA pathway, it also suggested co-metabolism of vanillic acid and syringic acid, which are known not to serve as photoheterotrophic growth substrate for R. palustris.

Rhodopseudomonas palustris Quorum Sensing Molecule pC-HSL Induces Systemic Resistance to TMV Infection via Upregulation of NbSIPK/NbWIPK Expressions in Nicotiana benthamiana

G-negative bacteria produce myriad N-acyl-homoserine lactones (AHLs) that can function as quorum sensing (QS) signaling molecules. AHLs are also known to regulate various plant biological activities. p-Coumaroyl-homoserine lactone (pC-HSL) is the only QS molecule produced by a photosynthetic bacterium, Rhodopseudomonas palustris. The role of pC-HSL in the interaction between R. palustris and plant has not been investigated. In this study, we investigated the effect of pC-HSL on plant immunity and found that this QS molecule can induce a systemic resistance to Tobacco mosaic virus (TMV) infection in Nicotiana benthamiana. The results show that pC-HSL treatment can prolong the activation of two mitogen-associated protein kinase genes (i.e., NbSIPK and NbWIPK) and increase the expression of transcription factor WRKY8 as well as immune response marker genes NbPR1 and NbPR10, leading to an increased accumulation of reactive oxygen species (ROS) in the TMV-infected plants. Our results also show that pC-HSL treatment can increase activities of two ROS-scavenging enzymes, peroxidase and superoxide dismutase. Knockdown of NbSIPK or NbWIPK expression in N. benthamiana plants through virus-induced gene silencing nullified or attenuated pC-HSL-induced systemic resistance, indicating that the functioning of pC-HSL relies on the activity of those two kinases. Meanwhile, pC-HSL-pretreated plants also showed a strong induction of kinase activities of NbSIPK and NbWIPK after TMV inoculation. Taken together, our results demonstrate that pC-HSL treatment increases plant resistance to TMV infection, which is helpful to uncover the outcome of interaction between R. palustris and its host plants.

Reductive tricarboxylic acid cycle enzymes and reductive amino acid synthesis pathways contribute to electron balance in a Rhodospirillum rubrum Calvin-cycle mutant

Purple non-sulfur bacteria (PNSB) use light for energy and organic substrates for carbon and electrons when growing photoheterotrophically. This lifestyle generates more reduced electron carriers than are required for biosynthesis, even during consumption of some of the most oxidized organic substrates like malate and fumarate. Reduced electron carriers not used in biosynthesis must still be oxidized for photoheterotrophic growth to occur. Diverse PNSB commonly rely on the CO₂-fixing Calvin cycle to oxidize reduced electron carriers. Some PNSB also produce H₂ or reduce terminal electron acceptors as alternatives to the Calvin cycle. Rhodospirillum rubrum Calvin-cycle mutants defy this trend by growing phototrophically on malate or fumarate without H₂ production or access to terminal electron acceptors. We used ¹³C-tracer experiments to examine how a Rs. rubrum Calvin-cycle mutant maintains electron balance under such conditions. We detected the reversal of some tricarboxylic acid cycle enzymes, carrying reductive flux from malate or fumarate to αKG. This pathway and the reductive synthesis of αKG-derived amino acids are likely important for electron balance, as supplementing the growth medium with αKG-derived amino acids prevented Rs. rubrum Calvin-cycle-mutant growth unless a terminal electron acceptor was provided. Flux estimates also suggested that the Calvin-cycle mutant preferentially synthesized isoleucine using the reductive threonine-dependent pathway instead of the less-reductive citramalate-dependent pathway. Collectively, our results suggest that alternative biosynthetic pathways can contribute to electron balance within the constraints of a relatively constant biomass composition.

Ribosome Purification from an α-proteobacterium and rRNA Analysis by Northern Blot

Ribosomes are an integral part of cellular life. They are complex molecular machines consisting of multiple ribosomal proteins and RNAs. To study different aspects of ribosome composition, many methods have been developed over the decades. Here, we describe how to purify ribosomes from the α-proteobacterium Rhodopseudomonas palustris. Following this protocol, RNA can be extracted from either purified ribosomes or directly from cell cultures, and ribosomal RNAs quantified using Northern blot. This protocol gives an example of studying ribosomes in a bacterium other than the commonly used E. coli. The challenge of performing Northern blots with rRNA is also addressed in detail.

Structural characterization and functional activity of an exopolysaccharide secreted by Rhodopseudomonas palustris GJ-22

One water exopolysaccharide, designated G-EPS, was secreted by Rhodopseudomonas palustris GJ-22 culture media. The structure of G-EPS was characterized with HPGPC, GC-MS, methylation, 1D and 2D NMR, along with UV and FT-IR spectrum. The G-EPS molecular weight was 10.026 kilodalton, and is composed of D-mannose (92.8%) and d-glucose (7.2%). The purified G-EPS promoted plant growth and induced systemic resistance against TMV in Nicotiana benthamiana. These results suggested that G-EPS is an important active component of the bio-control capacity of GJ-22.

A New Type of Light-Harvesting Complex Detected when Growing Rhodopseudomonas palustris under Low Light Intensity Conditions

The predominance of the maximum at 800 nm for the light-harvesting complex LH4 (B800) and at 850 nm for LH2 (B800-850) from Rps. palustris is determined by the composition of αβ-polypeptides and pigments. In low light (LL) for Rps. palustris, strain KM 286 (1e5), along with LH4, the LL LH2 complex was synthesized with the same absorption at 800 and 850 nm. It differed from the LH4 and LH2 complex, which is synthesized under high illumination, in the composition and content of carotenoids (Car) and bacteriochlorophyll a (BChl a). LH4 differed from LL LH2 and LH2 by an additional emission maximum at 766 nm in the BChl a fluorescence spectra. All three complexes had approximately the same level (about 45%) of the energy transfer efficiency from Car to BChl a. Isolation of LL LH2 complex from Rps. palustris confirms the hypothesis of the synthesis in these bacteria under low light conditions of other types of complexes, except LH4, which is due to the multiple biosynthesis genes of αβ-polypeptides and the possibility of their various combinations.

Genomic and genetic sequence information of strains assigned to the genus Rhodopseudomonas reveal the great heterogeneity of the group and identify strain Rhodopseudomonas palustris DSM 123T as the authentic type strain of this species

The genus Rhodopseudomonas, containing purple nonsulfur photosynthetic Proteobacteria, has a number of strains that belong to different species, although many of them are collectively called Rhodopseudomonas palustris. The type species R. palustris and closely related species are the focus of this paper. The comparison of available genome sequences indicate that the following Rhodopseudomonas species are well recognized: R. palustris (strains ATH 2.1.6^T=DSM 123^T=NBRC 100419^T and BisB5), Rhodopseudomonas rutila (strains R1^T, DSM 126, CGA009, ATH 2.1.37, Eli 1980, ATCC 17001 and TIE1), Rhodopseudomonas pentothenatexigens JA575^T and Rhodopseudomonas faecalis JCM 11668^T. Other strains for which genome sequences are available are distinct from these four species. Evidence is presented that R. palustris strain ATH 2.1.6^T-KCM as obtained directly from the van Niel collection by one of us (T.E.M.) is identical to the DSMZ deposit DSM 123^T of ATH 2.1.6^T, but not to the deposit at ATCC 17001. The amino acid sequences of the cytochromes C2 and C556 from R. palustris strain ATH 2.1.6^T-KCM are in complete agreement with the translated genome sequences of R. palustris DSM 123^T. In addition, the 16S rRNA gene sequence of R. palustris NBRC 100419^T completely matches that of strain DSM 123^T. In conclusion, the type strain of R. palustris ATH 2.1.6^T is correctly represented by DSM 123^T and NBRC 100419^T. However, the deposit at ATCC 17001 has properties that do not conform with properties of authentic R. palustris, but rather indicate that this is a strain of R. rutila. The previously suggested assignment of the type strain of R. palustris DSM 123^T to the new species R. pseudopalustris was incorrect because strain DSM 123^T is the authentic type strain of R. palustris.

A Disjointed Pathway for Malonate Degradation by Rhodopseudomonas palustris

The purple nonsulfur phototrophic bacterium Rhodopseudomonas palustris strain CGA009 uses the three-carbon dicarboxylic acid malonate as the sole carbon source under phototrophic conditions. However, this bacterium grows extremely slowly on this compound and does not have operons for the two pathways for malonate degradation that have been detected in other bacteria. Many bacteria grow on a spectrum of carbon sources, some of which are classified as poor growth substrates because they support low growth rates. This trait is rarely addressed in the literature, but slow growth is potentially useful in biotechnological applications where it is imperative for bacteria to divert cellular resources to value-added products rather than to growth. This prompted us to explore the genetic and physiological basis for the slow growth of R. palustris with malonate as a carbon source. There are two unlinked genes annotated as encoding a malonyl coenzyme A (malonyl-CoA) synthetase (MatB) and a malonyl-CoA decarboxylase (MatA) in the genome of R. palustris, which we verified as having the predicted functions. Additionally, two tripartite ATP-independent periplasmic transporters (TRAP systems) encoded by rpa2047 to rpa2049 and rpa2541 to rpa2543 were needed for optimal growth on malonate. Most of these genes were expressed constitutively during growth on several carbon sources, including malonate. Our data indicate that R. palustris uses a piecemeal approach to growing on malonate. The data also raise the possibility that this bacterium will evolve to use malonate efficiently if confronted with an appropriate selection pressure.IMPORTANCE There is interest in understanding how bacteria metabolize malonate because this three-carbon dicarboxylic acid can serve as a building block in bioengineering applications to generate useful compounds that have an odd number of carbons. We found that the phototrophic bacterium Rhodopseudomonas palustris grows extremely slowly on malonate. We identified two enzymes and two TRAP transporters involved in the uptake and metabolism of malonate, but some of these elements are apparently not very efficient. R. palustris cells growing with malonate have the potential to be excellent biocatalysts, because cells would be able to divert cellular resources to the production of value-added compounds instead of using them to support rapid growth. In addition, our results suggest that R. palustris is a candidate for directed evolution studies to improve growth on malonate and to observe the kinds of genetic adaptations that occur to make a metabolic pathway operate more efficiently.

Alleviation of tetrabromobisphenol A toxicity in soybean seedlings by Rhodopseudomonas palustris RP1n1

This study investigated the regulatory role of Rhodopseudomonas palustris RP11 in alleviating TBBPA-induced harmful effects in soybean seedlings. In this study, the characteristics of growth promotion by strain RP11 were studied by analysing 5-aminolevulinic acid (ALA) and indole-3-acetic acid (IAA) production, as well as phosphorus-solubilizing and potassium-solubilizing ability. In the pot culture conditions, we tested whether strain RP11 improved soybean seedlings tolerance against TBBPA by measuring the root length and physiological parameters of the seedlings treated with strain RP11 and different concentration of TBBPA (0, 5, 50, 100, and 1000 mg/kg) together. The results showed that strain RP11 secreted IAA and ALA, and solubilized phosphate and potassium. In pot trials, strain RP11 increased the root length, chlorophyll content, carotenoid content, soluble sugar and protein content of soybean seedlings treated with TBBPA, in comparison with the seedlings treated only with TBBPA. Furthermore, strain RP11 induced the activities of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD), decreased the malondialdehyde (MDA) content in soybean seedlings under TBBPA stress. It was concluded that strain RP11 alleviated TBBPA-induced harmful effects in soybean seedlings by the secretion of IAA and ALA, the accumulation of carotenoid, soluble sugar and soluble protein, and the induction of SOD, CAT and POD as well as nutrient adjustment of phosphorus and potassium levels.

Mechanistic evaluation of the exoelectrogenic activity of Rhodopseudomonas palustris under different nitrogen regimes

The operation of bioelectrochemical systems (BESs) relies on the ability of microbes to export electrons outside of their cells. However, microorganisms are not evolutionary conceived to power BESs as most of the redox processes occur within. In this study, a low cost strategy equivalent to the one used to improve hydrogen production is employed to divert electrons from the metabolism to an electrode. Varying the ratio of nitrogen to carbon concentration (0, 0.20 and 0.54) determines what fraction of the electron flux is directed towards biosynthesis, biohydrogen generation and extracellular electron transfer. The ratio of 0.54 produced a higher specific growth rate while the ratio of 0.20 resulted in combined higher maximum specific hydrogen production and exoelectrogenic activity, translating into a maximum power density of 2.39 ± 0.13 mW m^-2 in a novel hybrid hydrogen-photosynthetic microbial fuel cell. The current work sets a framework for the optimisation of R. palustris for bioenergy recovery.

ArsM-mediated arsenite volatilization is limited by efflux catalyzed by As efflux transporters

Arsenic (As) methylation is regarded as an efficient strategy for As contamination remediation by As volatilization. However, most microorganisms display low As volatilization efficiency, which is possibly linked to As efflux transporters competing for cytoplasmic As(III) as a substrate. Here, we developed two types of As biosensors in Escherichia coli to compare the As efflux rate of three efflux transporters and to further investigate the correlation between As efflux rates and As volatilization. The engineered As-sensitive E. coli AW3110 expressing arsB_RP, acr3_RP or arsB_EC displayed a higher As resistance compared to the control. The fluorescence intensity was in a linear correlation in the range of 0-2.0 μmol/L of As(III). The intracellular As(III) concentration was negatively related to As efflux activity of As efflux transporter, which was consistent with the As resistance assays. Moreover, arsM derived from R. palustris CGA009 was subsequently introduced to construct an E. coli AW3110 co-expressing arsB/acr3 and arsM, which exhibited higher As(III) resistance, lower fluorescence intensity and intracellular As concentration compared to the engineered E. coli AW3110 expressing only arsB/acr3. The As volatilization efficiency was negatively related to As efflux activity of efflux transporters, the recombinants without arsB/acr3 displayed the highest rate of As volatilization. This study provided new insights into parameters affecting As volatilization with As efflux being the main limiting factor for As methylation and subsequent volatilization in many microorganisms.

Transparent polyvinyl-alcohol cryogel as immobilisation matrix for continuous biohydrogen production by phototrophic bacteria

BACKGROUND

Phototrophic purple non-sulfur bacteria (PNSB) have gained attention for their ability to produce a valuable clean energy source in the form biohydrogen via photofermentation of a wide variety of organic wastes. For maturation of these phototrophic bioprocesses towards commercial feasibility, development of suitable immobilisation materials is required to allow continuous production from a stable pool of catalytic biomass in which energy is not diverted towards biomass accumulation, and optimal hydrogen production rates are realised. Here, the application of transparent polyvinyl-alcohol (PVA) cryogel beads to immobilisation of Rhodopseudomonas palustris for long-term hydrogen production is described. PVA cryogel properties are characterised and demonstrated to be well suited to the purpose of continuous photofermentation. Finally, analysis of the long-term biocompatibility of the material is illustrated.

RESULTS

The addition of glycerol co-solvent induces favourable light transmission properties in normally opaque PVA cryogels, especially well-suited to the near-infrared light requirements of PNSB. Material characterisation showed high mechanical resilience, low resistance to diffusion of substrates and high biocompatibility of the material and immobilisation process. The glycerol co-solvent in transparent cryogels offered additional benefit by reinforcing physical interactions to the extent that only a single freeze-thaw cycle was required to form durable cryogels, extending utility beyond only phototrophic bioprocesses. In contrast, conventional PVA cryogels require multiple cycles which compromise viability of entrapped organisms. Hydrogen production studies of immobilised Rhodopseudomonas palustris in batch photobioreactors showed higher specific hydrogen production rates which continued longer than planktonic cultures. Continuous cultivation yielded hydrogen production for at least 67 days from immobilised bacteria, demonstrating the suitability of PVA cryogel immobilisation for long-term phototrophic bioprocesses. Imaged organisms immobilised in cryogels showed a monolithic structure to PVA cryogels, and demonstrated a living, stable, photofermentative population after long-term immobilisation.

CONCLUSION

Transparent PVA cryogels offer ideal properties as an immobilisation matrix for phototrophic bacteria and present a low-cost photobioreactor technology for the further advancement of biohydrogen from waste as a sustainable energy source, as well as development of alternative photo-bioprocesses exploiting the unique capabilities of purple non-sulfur bacteria.

Beneficial effect of Rhodopseudomonas palustris on in vitro rumen digestion and fermentation

As a member of photosynthetic bacteria, Rhodopseudomonas palustris, which has extraordinary metabolic versatility, has been applied as one of potential probiotics in feed industry. To explore whether R. palustris can increase rumen microbial viability and thus improve microbial fermentation, a 2×5 factorial experiment was conducted to evaluate the effect of R. palustris at dose rates of 0, 1.3, 2.6, 3.9, 5.2×10⁶ cfu/ml on ruminal fermentation of two representative total mixed rations (HY, a ration for high-yield (>32 kg/d) lactating cows; LY, a ration for low-yield (<25 kg/d) lactating cows). After a 48 h in vitro rumen incubation, both rations resulted in different fermentation characteristics. The HY in comparison with LY group presented greater in vitro dry matter disappearance (IVDMD), cumulative gas production (GP₄₈) and total volatile fatty acids (VFA, P<0.01). Increasing R. palustris addition linearly increased IVDMD (P<0.01) and GP₄₈ (P<0.05), and the IVDMD increment in response to R. palustris addition was greater in LY than HY group (6.4% vs 1.4%). Meanwhile, increasing R. palustris addition also linearly enhanced microbial protein synthesis and increased total VFA production (P<0.01), especially in LY group (up to 21.5% and 24.5% respectively). Unchanged acetate and declined propionate in molar percentage were observed in response to the R. palustris addition. Furthermore, increasing R. palustris addition altered fermentation gas composition in which molar O₂ proportion in headspace of fermentation system was linearly reduced by 46.1% in LY and 32.9% in HY group, respectively (P<0.01), and methane production in both ration groups was enhanced by 1.9-4.1% (P=0.02). In summary, the R. palustris addition exhibited high potential for promoting the growth of rumen microorganism and enhancing microbial fermentation towards non-glucogenic energy supply by maintaining an anaerobic environment to microbe equilibrium.

Redox Regulation of a Light-Harvesting Antenna Complex in an Anoxygenic Phototroph

The purple nonsulfur bacterium Rhodopseudomonas palustris is a model for understanding how a phototrophic organism adapts to changes in light intensity because it produces different light-harvesting (LH) complexes under high light (LH2) and low light intensities (LH3 and LH4). Outside of this change in the composition of the photosystem, little is understood about how R. palustris senses and responds to low light intensity. On the basis of the results of transcription analysis of 17 R. palustris strains grown in low light, we found that R. palustris strains downregulate many genes involved in iron transport and homeostasis. The only operon upregulated in the majority of R. palustris exposed to low light intensity was pucBAd, which encodes LH4. In previous work, pucBAd expression was shown to be modulated in response to light quality by bacteriophytochromes that are part of a low-light signal transduction system. Here we found that this signal transduction system also includes a redox-sensitive protein, LhfE, and that its redox sensitivity is required for LH4 synthesis in response to low light. Our results suggest that R. palustris upregulates its LH4 system when the cellular redox state is relatively oxidized. Consistent with this, we found that LH4 synthesis was upregulated under high light intensity when R. palustris was grown semiaerobically or under nitrogen-fixing conditions. Thus, changes in the LH4 system in R. palustris are not dependent on light intensity per se but rather on cellular redox changes that occur as a consequence of changes in light intensity.IMPORTANCE An essential aspect of the physiology of phototrophic bacteria is their ability to adjust the amount and composition of their light-harvesting apparatus in response to changing environmental conditions. The phototrophic purple bacterium R. palustris adapts its photosystem to a range of light intensities by altering the amount and composition of its peripheral LH complexes. Here we found that R. palustris regulates its LH4 complex in response to the cellular redox state rather than in response to light intensity per se Relatively oxidizing conditions, including low light, semiaerobic growth, and growth under nitrogen-fixing conditions, all stimulated a signal transduction system to activate LH4 expression. By understanding how LH composition is regulated in R. palustris, we will gain insight into how and why a photosynthetic organism senses and adapts its photosystem to multiple environmental cues.

Immobilization of Rhodopseudomonas palustris P1 on glass pumice to improve the removal of NH4 + -N and NO2 - -N from aquaculture pond water

We conducted this research in order to investigate the potential of a new material called glass pumice for use as a microorganism immobilization carrier to improve aquaculture pond water quality. The pH adjustment capacity and the Rhodopseudomonas palustris P1 cell adsorption capacity of glass pumice were measured. The immobilized Rps. palustris P1 and the free sample were compared to determine which had an enhanced NH₄ ⁺ -N and NO₂ ^- -N removal efficiency. The results showed that glass pumice significantly affected the pH of the acid solution (P < 0.05); the pH increased from 3.0 ± 0.08 to 7.21 ± 0.13 in 12 H. Rps. palustris P1 adsorption to glass pumice was rapid and reached equilibrium within 60 Min. The Langmuir adsorption parameter data showed that glass pumice had a higher affinity for Rps. palustris P1 than SiO₂ powder, with an adsorption capacity of 4.02 × 10⁸  cells g^-1 . The maximum NH₄ ⁺ -N and NO₂ ^- -N removal rates by immobilized Rps. palustris P1 were 134.82 ± 0.67% and 93.68 ± 0.14% higher than those of nonimmobilized P1, respectively. Based on the above results, we propose that glass pumice is potential as a microorganism carrier material in aquaculture water treatment.

Anoxic growth optimization for metal respiration and photobiological hydrogen production by arsenic-resistant Rhodopseudomonas and Rhodobacter species

The current research focuses on anaerobic respiration of arsenic and other toxic metals by purple nonsulfur bacteria (PNSB). Among the optimization assays performed were carbon utilization, cross metal resistance, and metal respiration, along with a comparison of each assay in photoheterotrophic and chemoheterotrophic growth. The bacteria were identified by the classification of 16S ribosomal RNA gene sequences. Rhodobacter sp. PI3 proved to be more versatile in carbon source utilization (acetate, lactate, citrate, and oxalate), whereas Rhodopseudomonas palustris PI5 proved to be more versatile in metal resistance (arsenate, arsenite, cobalt, lead, selenium, and nickel). Both the strains were found to be positive for photofermentative hydrogen production along with arsenic respiration. This study reveals that anaerobic conditions are more appropriate for better efficiency of PNSB. Our study demonstrates that R. palustris PI5 and Rhodobacter sp. PI3 can be promising candidates for the biohydrogen production along with metal detoxification using heavy metal-polluted effluents as a substrate.

Bacterial Longevity Requires Protein Synthesis and a Stringent Response

Gram-negative bacteria in infections, biofilms, and industrial settings often stop growing due to nutrient depletion, immune responses, or environmental stresses. Bacteria in this state tend to be tolerant to antibiotics and are often referred to as dormant. Rhodopseudomonas palustris, a phototrophic alphaproteobacterium, can remain fully viable for more than 4 months when its growth is arrested. Here, we show that protein synthesis, specific proteins involved in translation, and a stringent response are required for this remarkable longevity. Because it can generate ATP from light during growth arrest, R. palustris is an extreme example of a bacterial species that will stay alive for long periods of time as a relatively homogeneous population of cells and it is thus an excellent model organism for studies of bacterial longevity. There is evidence that other Gram-negative species also continue to synthesize proteins during growth arrest and that a stringent response is required for their longevity as well. Our observations challenge the notion that growth-arrested cells are necessarily dormant and metabolically inactive and suggest that such bacteria may have a level of metabolic activity that is higher than many would have assumed. Our results also expand our mechanistic understanding of a crucial but understudied phase of the bacterial life cycle.IMPORTANCE We are surrounded by bacteria, but they do not completely dominate our planet despite the ability of many to grow extremely rapidly in the laboratory. This has been interpreted to mean that bacteria in nature are often in a dormant state. We investigated life in growth arrest of Rhodopseudomonas palustris, a proteobacterium that stays alive for months when it is not growing. We found that cells were metabolically active, and they continued to synthesize proteins and mounted a stringent response, both of which were required for their longevity. Our results suggest that long-lived bacteria are not necessarily inactive but have an active metabolism that is well adjusted to life without growth.

A genetic tool for production of GFP-expressing Rhodopseudomonas palustris for visualization of bacterial colonization

Development of a genetic tool for visualization of photosynthetic bacteria (PSB) is essential for understanding microbial function during their interaction with plant and microflora. In this study, Rhodopseudomonas palustris GJ-22-gfp harboring the vector pBBR1-pckA_PT-gfp was constructed using an electroporation transformation method and was used for dynamic tracing of bacteria in plants. The results showed that strain GJ-22-gfp was stable and did not affect the biocontrol function, and the Confocal Laser Scanning Microscopy (CLSM) results indicated it could successfully colonised on the surface of leaf and root of tobacco and rice. In tobacco leaves, cells formed aggregates on the mesophyll epidermal cells. While in rice, no aggregate was found. Instead, the fluorescent cells colonise the longitudinal intercellular spaces between epidermal cells. In addition, the results of strain GJ-22 on the growth promotion and disease resistance of tobacco and rice indicated that the different colonization patterns might be related to the bacteria could induce systemic resistance in tobacco.

Fermentative Escherichia coli makes a substantial contribution to H2 production in coculture with phototrophic Rhodopseudomonas palustris

Individual species within microbial communities can combine their attributes to produce services that benefit society, such as the transformation of renewable resources into valuable chemicals. Under defined genetic and environmental conditions, fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris exchange essential carbon and nitrogen, respectively, to establish a mutualistic relationship. In this relationship, each species produces H2 biofuel as a byproduct of its metabolism. However, the extent to which each species contributes to H2 production and the factors that influence their relative contributions were previously unknown. By comparing H2 yields in cocultures pairing R. palustris with either wild-type E. coli or a formate hydrogenlyase mutant that is incapable of H2 production, we determined the relative contribution of each species to total H2 production. Our results indicate that E. coli contributes between 32 and 86% of the H2 produced in coculture depending on the level of ammonium excreted by the R. palustris partner. The level of ammonium excretion influenced the time over which E. coliwas exposed to formate, the types of E. colifermentation products available to R. palustris, and the pH of the medium, all of which affected the contribution of each species to H2 production.

Phototrophic Lactate Utilization by Rhodopseudomonas palustris Is Stimulated by Coutilization with Additional Substrates

The phototrophic purple nonsulfur bacterium Rhodopseudomonas palustris is known for its metabolic versatility and is of interest for various industrial and environmental applications. Despite decades of research on R. palustris growth under diverse conditions, patterns of R. palustris growth and carbon utilization with mixtures of carbon substrates remain largely unknown. R. palustris readily utilizes most short-chain organic acids but cannot readily use lactate as a sole carbon source. Here we investigated the influence of mixed-substrate utilization on phototrophic lactate consumption by R. palustris We found that lactate was simultaneously utilized with a variety of other organic acids and glycerol in time frames that were insufficient for R. palustris growth on lactate alone. Thus, lactate utilization by R. palustris was expedited by its coutilization with additional substrates. Separately, experiments using carbon pairs that did not contain lactate revealed acetate-mediated inhibition of glycerol utilization in R. palustris This inhibition was specific to the acetate-glycerol pair, as R. palustris simultaneously utilized acetate or glycerol when either was paired with succinate or lactate. Overall, our results demonstrate that (i) R. palustris commonly employs simultaneous mixed-substrate utilization, (ii) mixed-substrate utilization expands the spectrum of readily utilized organic acids in this species, and (iii) R. palustris has the capacity to exert carbon catabolite control in a substrate-specific manner.IMPORTANCE Bacterial carbon source utilization is frequently assessed using cultures provided single carbon sources. However, the utilization of carbon mixtures by bacteria (i.e., mixed-substrate utilization) is of both fundamental and practical importance; it is central to bacterial physiology and ecology, and it influences the utility of bacteria as biotechnology. Here we investigated mixed-substrate utilization by the model organism Rhodopseudomonas palustris Using mixtures of organic acids and glycerol, we show that R. palustris exhibits an expanded range of usable carbon substrates when provided substrates in mixtures. Specifically, coutilization enabled the prompt consumption of lactate, a substrate that is otherwise not readily used by R. palustris Additionally, we found that R. palustris utilizes acetate and glycerol sequentially, revealing that this species has the capacity to use some substrates in a preferential order. These results provide insights into R. palustris physiology that will aid the use of R. palustris for industrial and commercial applications.

System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

Background

Living organisms need to allocate their limited resources in a manner that optimizes their overall fitness by simultaneously achieving several different biological objectives. Examination of these biological trade-offs can provide invaluable information regarding the biophysical and biochemical bases behind observed cellular phenotypes. A quantitative knowledge of a cell system’s critical objectives is also needed for engineering of cellular metabolism, where there is interest in mitigating the fitness costs that may result from human manipulation.

Results

To study metabolism in photoheterotrophs, we developed and validated a genome-scale model of metabolism in Rhodopseudomonas palustris, a metabolically versatile gram-negative purple non-sulfur bacterium capable of growing phototrophically on various carbon sources, including inorganic carbon and aromatic compounds. To quantitatively assess trade-offs among a set of important biological objectives during different metabolic growth modes, we used our new model to conduct an 8-dimensional multi-objective flux analysis of metabolism in R. palustris. Our results revealed that phototrophic metabolism in R. palustris is light-limited under anaerobic conditions, regardless of the available carbon source. Under photoheterotrophic conditions, R. palustris prioritizes the optimization of carbon efficiency, followed by ATP production and biomass production rate, in a Pareto-optimal manner. To achieve maximum carbon fixation, cells appear to divert limited energy resources away from growth and toward CO₂ fixation, even in the presence of excess reduced carbon. We also found that to achieve the theoretical maximum rate of biomass production, anaerobic metabolism requires import of additional compounds (such as protons) to serve as electron acceptors. Finally, we found that production of hydrogen gas, of potential interest as a candidate biofuel, lowers the cellular growth rates under all circumstances.

Conclusions

Photoheterotrophic metabolism of R. palustris is primarily regulated by the amount of light it can absorb and not the availability of carbon. However, despite carbon’s secondary role as a regulating factor, R. palustris’ metabolism strives for maximum carbon efficiency, even when this increased efficiency leads to slightly lower growth rates.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2844-z) contains supplementary material, which is available to authorized users.

Differences in possible TCA cycle replenishing pathways in purple non-sulfur bacteria possessing glyoxylate pathway

Pathways replenishing tricarboxylic acid cycle were divided into four major groups based on metabolite serving as source for oxaloacetic acid or other tricarboxylic acid cycle component synthesis. Using this metabolic map, the analysis of genetic potential for functioning of tricarboxylic acid cycle replenishment pathways was carried out for seven strains of purple non-sulfur bacterium Rhodopseudomonas palustris. The results varied from strain to strain. Published microarray data for phototrophic acetate cultures of Rps. palustris CGA009 were analyzed to validate activity of the putative pathways. All the results were compared with the results for another purple non-sulfur bacterium, Rhodobacter capsulatus SB1003 and species-specific differences were clarified.

Functional divergence of annotated l-isoaspartate O-methyltransferases in an α-proteobacterium

Spontaneous formation of isoaspartates (isoDs) often causes protein damage. l-Isoaspartate O-methyltransferase (PIMT) repairs isoD residues by catalyzing the formation of an unstable l-isoaspartyl methyl ester that spontaneously converts to an l-aspartyl residue. PIMTs are widely distributed in all three domains of life and have been studied most intensively in connection with their role in protein repair and aging in plants and animals. Studies of bacterial PIMTs have been limited to Escherichia coli, which has one PIMT. The α-proteobacterium Rhodopseudomonas palustris has three annotated PIMT genes, one of which (rpa2580) has been found to be important for cellular longevity in a growth-arrested state. However, the biochemical activities of these three R. palustris PIMTs are unknown. Here, we expressed and characterized all three annotated PIMT proteins, finding that two of them, RPA0376 and RPA2838, had PIMT activity, whereas RPA2580 did not. RPA0376 and RPA2838 single- and double-deletion mutants did not differ in longevity from WT R. palustris and did not exhibit elevated levels of isoD residues in aged cells. Comparative sequence analyses revealed that RPA2580 belongs to a separate phylogenetic group of annotated PIMT proteins present in the α-proteobacteria. Our results suggest that this group of proteins is not involved in repair of protein isoD residues. In addition, the bona fide bacterial PIMT enzymes may play a different or subtler role in bacterial physiology than previously suggested.

Enhancing thermostability and removing hemin inhibition of Rhodopseudomonas palustris 5-aminolevulinic acid synthase by computer-aided rational design

OBJECTIVE

To enhance the thermostability and deregulate the hemin inhibition of 5-aminolevulinic acid (ALA) synthase from Rhodopseudomonas palustris (RP-ALAS) by a computer-aided rational design strategy.

RESULTS

Eighteen RP-ALAS single variants were rationally designed and screened by measuring their residual activities upon heating. Among them, H29R and H15K exhibited a 2.3 °C and 6.0 °C higher melting temperature than wild-type, respectively. A 6.7-fold and 10.3-fold increase in specific activity after 1 h incubation at 37 °C was obtained for H29R (2.0 U/mg) and H15K (3.1 U/mg) compared to wild-type (0.3 U/mg). Additionally, higher residual activities in the presence of hemin were obtained for H29R and H15K (e.g., 64% and 76% at 10 μM hemin vs. 27% for wild-type). The ALA titer was increased by 6% and 22% in fermentation using Corynebacterium glutamicum ATCC 13032 expressing H29R and H15K, respectively.

CONCLUSION

H29R and H15K showed high thermostability, reduced hemin inhibition and slightly high activity, indicating that these two variants are good candidates for bioproduction of ALA.

Nitrogen fixation in Rhodopseudomonas palustris co-cultured with Bacillus subtilis in the presence of air

Nitrogen fixation in purple non-sulfur bacteria (PNSB) does not take place even in N-free medium when they are cultured under aerobic conditions. It is assumed that PNSB might possess inadequate capability to protect their cellular components from exposure to air (20.95 vol.% oxygen). In this study, therefore, Bacillus subtilis was inoculated together with a purple non-sulfur bacterium Rhodopseudomonas palustris in N-free medium in order to examine whether nitrogen fixation in Rps. palustris takes place when the co-culture is exposed to 20.95 vol.% oxygen. Rps. palustris grew and formed biofilm only when it was inoculated together with B. subtilis. When the biofilm formed in the co-culture was inoculated in N-free medium, diazotrophic growth was observed in the sequential subcultures. Expression of nifH gene, derepression of nitrogenase activity, an increase of total nitrogen, and a decrease of C/N in the co-culture of Rps. palustris and B. subtilis demonstrated the occurrence of nitrogen fixation under aerobic conditions. The diazotrophic growth was suppressed at a lower medium-to-air ratio in a sealed culture vessel, and growth of B. subtilis preceded growth of Rps. palustris in the co-culture. These results suggest that growth of B. subtilis, which is usually accompanied with oxygen consumption, might cause a decrease of dissolve oxygen concentration in medium and contribute to the occurrence of nitrogenase activity in Rps. palustris.

Two Distinct Aerobic Methionine Salvage Pathways Generate Volatile Methanethiol in Rhodopseudomonas palustris

5'-Methyl-thioadenosine (MTA) is a dead-end, sulfur-containing metabolite and cellular inhibitor that arises from S-adenosyl-l-methionine-dependent reactions. Recent studies have indicated that there are diverse bacterial methionine salvage pathways (MSPs) for MTA detoxification and sulfur salvage. Here, via a combination of gene deletions and directed metabolite detection studies, we report that under aerobic conditions the facultatively anaerobic bacterium Rhodopseudomonas palustris employs both an MTA-isoprenoid shunt identical to that previously described in Rhodospirillum rubrum and a second novel MSP, both of which generate a methanethiol intermediate. The additional R. palustris aerobic MSP, a dihydroxyacetone phosphate (DHAP)-methanethiol shunt, initially converts MTA to 2-(methylthio)ethanol and DHAP. This is identical to the initial steps of the recently reported anaerobic ethylene-forming MSP, the DHAP-ethylene shunt. The aerobic DHAP-methanethiol shunt then further metabolizes 2-(methylthio)ethanol to methanethiol, which can be directly utilized by O-acetyl-l-homoserine sulfhydrylase to regenerate methionine. This is in contrast to the anaerobic DHAP-ethylene shunt, which metabolizes 2-(methylthio)ethanol to ethylene and an unknown organo-sulfur intermediate, revealing functional diversity in MSPs utilizing a 2-(methylthio)ethanol intermediate. When MTA was fed to aerobically growing cells, the rate of volatile methanethiol release was constant irrespective of the presence of sulfate, suggesting a general housekeeping function for these MSPs up through the methanethiol production step. Methanethiol and dimethyl sulfide (DMS), two of the most important compounds of the global sulfur cycle, appear to arise not only from marine ecosystems but from terrestrial ones as well. These results reveal a possible route by which methanethiol might be biologically produced in soil and freshwater environments.IMPORTANCE Biologically available sulfur is often limiting in the environment. Therefore, many organisms have developed methionine salvage pathways (MSPs) to recycle sulfur-containing by-products back into the amino acid methionine. The metabolically versatile bacterium Rhodopseudomonas palustris is unusual in that it possesses two RuBisCOs and two RuBisCO-like proteins. While RuBisCO primarily serves as the carbon fixation enzyme of the Calvin cycle, RuBisCOs and certain RuBisCO-like proteins have also been shown to function in methionine salvage. This work establishes that only one of the R. palustris RuBisCO-like proteins functions as part of an MSP. Moreover, in the presence of oxygen, to salvage sulfur, R. palustris employs two pathways, both of which result in production of volatile methanethiol, a key compound of the global sulfur cycle. When total available sulfur was plentiful, methanethiol was readily released into the environment. However, when sulfur became limiting, methanethiol release decreased, presumably due to methanethiol utilization to regenerate needed methionine.