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.

Development of an electrochemical separation-Rhodopseudomonas palustris electrolysis cell-coupled system for resourceful treatment of mature leachate landfill

Electrochemical technology is a promising technique for separating ammonia from mature landfill leachate. However, the accompanying migration and transformation of coexisting pollutants and strategies for further high-value resourceful utilization of ammonia have rarely received attention. In this study, an electrochemical separation-Rhodopseudomonas palustris electrolysis cell coupled system was initially constructed for efficient separation and conversion of nitrogen in mature landfill leachate to microbial protein with synchronously tracking the transport and conversion of coexisting heavy metals accompanying the process. The results revealed that ammonia concentration in the cathode increased from 40.3 to 49.8% with increasing the current density from 20 to 40 mA/cm2, with less than 3% of ammonia transformation to NO2--N and NO3--N. During ammonia separation, approximately 95% of HM-DOMs (Cr, Cu, Ni, Pb, and Zn) were released into the anolyte due to humus degradation and further diffused to the cathode. A significant correlation was observed between the releases of HM-DOMs. Cu-DOMs accounted for 70.2% of the total Cu content, which was the highest proportion among the heavy metals (HMs). Among the HMs in anolyte, 57.4% of Pb, 52.5% of Ni, and 50.6% of Zn diffused to the cathode, and most of the HMs were removed in the form of hydroxide precipitations due to heavy alkaline catholyte. Compared with the open-circuit condition, the utilization efficiency of NH4+-N in the R. palustris electrolysis cell increased by 445.1% with 47% and 50% increases in final NH4+-N conversion rate and R. palustris biomass, respectively, due to bio-electrochemical enhanced phototrophic metabolism and acid generation for buffering the strong alkalinity of the electrolyte to maintain suitable growth conditions for R. palustris.

Outdoor biohydrogen production by thermotolerant Rhodopseudomonas pentothenatexigens KKU-SN1/1 in a cluster of ten bioreactors system

In tropical regions, the viability of outdoor photo-fermentative biohydrogen production faces challenges arising from elevated temperatures and varying light intensity. This research aimed to explore how high temperatures and outdoor environments impact both biohydrogen production and the growth of purple non-sulfur bacteria. Our findings revealed the potential of Rhodopseudomonas spp. as a robust outdoor hydrogen-producing bacteria, demonstrating its capacity to thrive and generate biohydrogen even at 40 °C and under fluctuating outdoor conditions. Rhodopseudomonas harwoodiae NM3/1-2 produced the highest cumulative biohydrogen of 223 mL/L under anaerobic light conditions at 40 °C, while Rhodopseudomonas harwoodiae 2M had the highest dry cell weight of 2.93 g/L. However, R. harwoodiae NM3/1-2 demonstrated the highest dry cell weight of 3.99 g/L and Rhodopseudomonas pentothenatexigens KKU-SN1/1 exhibited the highest cumulative biohydrogen production of 400 mL/L when grown outdoors. In addition, the outdoor enhancement of biohydrogen production was achieved through the utilization of a cluster of ten bioreactors system. The outcomes demonstrated a notable improvement in biohydrogen production efficiency, marked by the highest daily biohydrogen production of 493 mL/L d by R. pentothenatexigens KKU-SN1/1. Significantly, the highest biohydrogen production rate was noted to be 17 times greater than that observed in conventional batch production methods. This study is the first to utilize R. pentothenatexigens and R. harwoodiae for sustained biohydrogen production at high temperatures and in outdoor conditions over an extended operational period. The successful utilization of a clustered system of ten bioreactors demonstrates potential to scale-up for industrial biohydrogen production.

Effect of the addition of an inorganic carbon source on the degradation of sotol vinasse by Rhodopseudomonastelluris

The difficulty of the microbial conversion process for the degradation of sotol vinasse due to its high acidity and organic load makes it an effluent with high potential for environmental contamination, therefore its treatment is of special interest. Calcium carbonate is found in great abundance and has the ability to act as a neutralizing agent, maintaining the alkalinity of the fermentation medium as well as, through its dissociation, releasing CO2 molecules that can be used by phototrophic CO2-fixing bacteria. This study evaluated the use of Rhodopseudomonas telluris (OR069658) for the degradation of vinasse in different concentrations of calcium carbonate (0, 2, 4, 6, 8 and 10% m/v). The results showed that calcium carbonate concentration influenced volatile fatty acids (VFA), alkalinity and pH, which in turn influenced changes in the degradation of chemical oxygen demand (COD), phenol and sulfate. Maximum COD and phenol degradation values of 83.16 ± 0.15% and 90.16 ± 0.30%, respectively, were obtained at a calcium carbonate concentration of 4%. At the same time, the lowest COD and phenol degradation values of 52.01 ± 0.38% and 68.21 ± 0.81%, respectively, were obtained at a calcium carbonate concentration of 0%. The data obtained also revealed to us that at high calcium carbonate concentrations of 6-10%, sotol vinasse can be biosynthesized by Rhodopseudomonas telluris (OR069658) to VFA, facilitating the degradation of sulfates. The findings of this study confirmed the potential for using Rhodopseudomonas telluris (OR069658) at a calcium carbonate concentration of 4% as an appropriate alternative treatment for sotol vinasse degradation.

Phototrophic Fe(II) oxidation by Rhodopseudomonas palustris TIE-1 in organic and Fe(II)-rich conditions

Rhodopseudomonas palustris TIE-1 grows photoautotrophically with Fe(II) as an electron donor and photoheterotrophically with a variety of organic substrates. However, it is unclear whether R. palustris TIE-1 conducts Fe(II) oxidation in conditions where organic substrates and Fe(II) are available simultaneously. In addition, the effect of organic co-substrates on Fe(II) oxidation rates or the identity of Fe(III) minerals formed is unknown. We incubated R. palustris TIE-1 with 2 mM Fe(II), amended with 0.6 mM organic co-substrate, and in the presence/absence of CO2 . We found that in the absence of CO2 , only the organic co-substrates acetate, lactate and pyruvate, but not Fe(II), were consumed. When CO2 was present, Fe(II) and all organic substrates were consumed. Acetate, butyrate and pyruvate were consumed before Fe(II) oxidation commenced, whereas lactate and glucose were consumed at the same time as Fe(II) oxidation proceeded. Lactate, pyruvate and glucose increased the Fe(II) oxidation rate significantly (by up to threefold in the case of lactate). 57 Fe Mössbauer spectroscopy revealed that short-range ordered Fe(III) oxyhydroxides were formed under all conditions. This study demonstrates phototrophic Fe(II) oxidation proceeds even in the presence of organic compounds, and that the simultaneous oxidation of organic substrates can stimulate Fe(II) oxidation.

Synergistic molecular mechanism of degradation in dye wastewater by Rhodopseudomonas palustris intimately coupled carbon nanotube - Silver modified titanium dioxide photocatalytic composite with sodium alginate

The intimately coupled photocatalysis and biodegradation (ICPB), which combined the advantages of high oxidation capacity of photocatalysis and high mineralization rate of biodegradation, has demonstrated excellent removal performance in the degradation of azo dyes with highly toxic, refractory, mutagenic and carcinogenic. In order to explore the metagenomics mechanism of the ICPB system, a novel ICPB was prepared by coupling Rhodopseudomonas palustris (R. Palustris), carbon nanotube - silver modified titanium dioxide photocatalytic composite (CNT-Ag -TiO2, CAT) and sodium alginate (SA) (R. palustris/CAT@SA, R-CAT). Metagenomics sequencing was used to investigate the molecular mechanism of adaptation and degradation of dyes by photosynthetic microorganisms and the adaptive and synergistic interaction between photosynthetic microorganisms and photocatalyst. Experiments on the adaptability and degradability of photosynthetic microorganisms have proved that low concentration azo dyes could be utilized as carbon sources for growth of photosynthetic microorganisms. Metagenomics sequencing revealed that R. palustris was the main degrading bacterium in photosynthetic microorganisms and the functional genes related to carbohydrate metabolism, biological regulation and catalytic activity were abundant. It was found that the addition of photocatalyst significantly up-regulated the functional genes related to the catabolic process, electron transport, oxidoreductase activity and superoxide metabolism of organic matter in the photosynthetic microorganisms. Moreover, many key gene such as alpha-amylase, 1-acyl-sn-glycerol-3-phosphate acyltransferase, aldehyde dehydrogenase enrichment in microbial basal metabolism, such as enoyl-CoA hydratase, malate dehydrogenase, glutathione S-transferase enrichment in degrading azo dyes and electron transport, and many key gene such as undecaprenyl-diphosphatase, carbon storage regulator, DNA ligase enrichment in response to dyes and photocatalysts were discovered. These findings would contribute to a comprehensive understanding of the mechanism of degradation of dye wastewater by ICPB system, a series of genes was produced to adapt to environmental changes, and played synergistic role in terms of intermediate product degradation and electron transfer for degrading azo dyes. The photosynthetic microorganisms might be a promising microorganism for constructing ICPB system.

Removal of pollutants and accumulation of high-value cell inclusions in a batch reactor containing Rhodopseudomonas for treating real heavy oil refinery wastewater

Treating wastewater using purple non-sulfur bacteria (PNSB) is an environmentally friendly technique that can simultaneously remove pollutants and lead to the accumulation of high-value cell inclusions. However, no PNSB system for treating heavy oil refinery wastewater (HORW) and recovering high-value cell inclusions has yet been developed. In this study, five batch PNSB systems dominated by Rhodopseudomonas were used to treat real HORW for 186 d. The effects of using different hydraulic retention times (HRT), sludge retention times (SRT), trace element solutions, phosphate loads, and influent loads were investigated, and the bacteriochlorophyll, carotenoid, and coenzyme Q10 concentrations were determined. The community structure and quantity of Rhodopseudomonas in the systems were determined using a high-sequencing technique and quantitative polymerase chain reaction technique. The long-term results indicated that phosphate was the limiting factor for treating HORW in the PNSB reactor. The soluble chemical oxygen demand (SCOD) removal rates were 67.03% and 85.26% without and with phosphate added, respectively, and the NH4+-N removal rates were 32.18% and 89.22%, respectively. The NO3--N concentration in the effluent was stable at 0-3 mg/L with or without phosphate added. Adding phosphate increased the Rhodopseudomonas relative abundance and number by 13.21% and 41.61%, respectively, to 57.35% and 8.52 × 106 gene copies/μL, respectively. The SRT was the limiting factor for SCOD removal, and the bacteria concentration was the limiting factor for nitrogen removal. Once the inflow load had been increased, the total nitrogen (TN) removal rate increased as the HRT increased. Maximum TN removal rates of 64.46%, 68.06%, 73.89%, 82.15%, and 89.73% were found at HRT of 7, 10, 13, 16, and 19 d, respectively. The highest bacteriochlorophyll, carotenoid, and coenzyme Q10 concentrations were 2.92, 4.99, and 4.53 mg/L, respectively. This study provided a simple and efficient method for treating HORW and reutilizing resources, providing theoretical support and parameter guidance for the application of Rhodopseudomonas in treating HORW.

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.

on recovery of soil properties damaged by Al3+ and Fe2+ toxins and enhancement of rice yield in acid sulfate soil

In the Mekong Delta Vietnam, rice is heavily affected by Al3+ and Fe2+ ions appearing in local acid sulfate soils (AAS). Therefore, the current study was carried out to assess the efficacy of a liquid biofertilizer (LB) containing nitrogen-fixing and phosphorus-solubilizing bacterial strains of Rhodopseudomonas spp. on remediation of soil characteristics and improvements of rice uptakes, growth, and yield. The experiment was designed in a randomized block design with nine treatments and four replications in an ASS. The results have shown that the LB application could contribute to the remediation of soil properties, including an increase in concentrations of NH4+ by 12.9%-19.4%, soluble P by 25.7%-42.6%, total N uptake by 40.7-64.0 kg ha-1 and total P uptake by 5.60-12.6 kg ha-1, and a decrease in concentrations of toxins, such as Al3+ by 12.1%-19.7% and Fe2+ by 16.6%-19.0%, compared to the treatment with the farmer-based fertilization. Thereby, grain yield was improved by 31.9%-32.2% with the LB versus the treatments without the bacteria and by 9.5%-11.1% compared to the commercial biofertilizer treatments. The application of LB reduced 25% N and 50% P of the recommendation versus the farmers' fertilization and improved performance of rice growth and yield cultivated on ASS which suffered from Al3+ and Fe2+ ions.

Intensification of Hydrogen Production by a Co-culture of Syntrophomonas wolfei and Rhodopseudomonas palustris Employing High Concentrations of Butyrate as a Substrate

The purpose of this study is to present an effective form of developing a sequential dark (DF) and photo (PF) fermentation using volatile fatty acids (VFAs) and nitrogen compounds as bonding components between both metabolic networks of microbial growing in each fermentation. A simultaneous (co-)culture of Syntrophomonas wolfei (with its ability to consume butyrate and produce acetate) and Rhodopseudomonas palustris (that can use the produced acetate as a carbon source) performed a syntrophic metabolism. The former bacteria consumed the acetate/butyrate mixture reducing the butyrate concentration below 2.0 g/L, permitting Rhodopseudomonas palustris to produce hydrogen. Considering that the inoculum composition (Syntrophomonas wolfei/Rhodopseudomonas palustris) and the nitrogen source (yeast extract) define the microbial biomass specific productivity and the butyrate consumption, a response surface methodology defined the best inoculum design and yeast extract (YE) yielding to the highest biomass concentration of 1.1 g/L after 380.00 h. A second culture process (without a nitrogen source) showed the biomass produced in the previous culture process yields to produce a total cumulated hydrogen concentration of 3.4 mmol. This value was not obtained previously with the pure strain Rhodopseudomonas palustris if the culture medium contained butyrate concentration above 2.0 g/L, representing a contribution to the sequential fermentation scheme based on DF and PF.

A broad specificity β-propeller enzyme from Rhodopseudomonas palustris that hydrolyzes many lactones including γ-valerolactone

Lactones are prevalent in biological and industrial settings, yet there is a lack of information regarding enzymes used to metabolize these compounds. One compound, γ-valerolactone (GVL), is used as a solvent to dissolve plant cell walls into sugars and aromatic molecules for subsequent microbial conversion to fuels and chemicals. Despite the promise of GVL as a renewable solvent for biomass deconstruction, residual GVL can be toxic to microbial fermentation. Here, we identified a Ca2+-dependent enzyme from Rhodopseudomonas palustris (Rpa3624) and showed that it can hydrolyze aliphatic and aromatic lactones and esters, including GVL. Maximum-likelihood phylogenetic analysis of other related lactonases with experimentally determined substrate preferences shows that Rpa3624 separates by sequence motifs into a subclade with preference for hydrophobic substrates. Additionally, we solved crystal structures of this β-propeller enzyme separately with either phosphate, an inhibitor, or a mixture of GVL and products to define an active site where calcium-bound water and calcium-bound aspartic and glutamic acid residues make close contact with substrate and product. Our kinetic characterization of WT and mutant enzymes combined with structural insights inform a reaction mechanism that centers around activation of a calcium-bound water molecule promoted by general base catalysis and close contacts with substrate and a potential intermediate. Similarity of Rpa3624 with other β-propeller lactonases suggests this mechanism may be relevant for other members of this emerging class of versatile catalysts.

Extracellular electron uptake for CO2 fixation by Rhodopseudomonas palustris during electro-cultivation in darkness

As a vital part of the global carbon cycle, photosynthesis helps in fixing CO₂ to produce diverse biomass. However, over-reliance on optical density results in inadequate photosynthesis under limited light sources. The coupling of extracellular respiration and photosynthetic chain via the quinone pool provides a possibility for electrically driven photosynthesis in darkness, which is not well understood. In this study, CO₂ fixation of photosynthetic bacteria Rhodopseudomonas palustris was enhanced in the dark via extracellular electron uptake from the electrode at -0.4 V. The copy number of R. palustris increased by 35 folds during 28 days of operation, accompanied by the increase of ATP content, NADH/NAD⁺, and NADPH/NADP⁺ of cells. Especially, the activity of Rubisco, the key enzyme of the Calvin cycle, increased by 28 % during electro-cultivation. Accordingly, the electrochemical activity of R. palustris was found to increase, which might be attributed to the structural modification of protein-like substances due to the enhanced proton-coupled electron transfer (PCET) process in electro-cultivation, which was further confirmed by in situ Fourier transform infrared spectroscopy and kinetic isotope effect tests. This study indicated that extracellular respiration could be electrostimulated via PCET to maintain photosynthesis in R. palustris in the dark.

Isolation, Molecular Identification and Amino Acid Profiling of Single-Cell-Protein-Producing Phototrophic Bacteria Isolated from Oil-Contaminated Soil Samples

In the current study, soil samples were gathered from different places where petrol and diesel filling stations were located for isolation of photosynthetic bacteria under anaerobic conditions using the paraffin wax-overlay pour plate method with Biebl and Pfennig’s medium. The three isolated strains were named Rhodopseudomonas palustris SMR 001 (Mallapur), Rhodopseudomonas palustris NR MPPR (Nacahram) and Rhodopseudomonas faecalis N Raju MPPR (Karolbagh). The morphologies of the bacteria were examined with a scanning electron microscope (SEM). The phylogenetic relationship between R. palustris strains was examined by means of 16S rRNA gene sequence analysis using NCBI-BLAST search and a phylogenetic tree. The sequenced data for R. palustris were deposited with the National Centre for Biotechnology Research (NCBI). The total amino acids produced by the isolated bacteria were determined by HPLC. A total of 14 amino acids and their derivatives were produced by the R. palustris SMR 001 strain. Among these, carnosine was found in the highest concentration (8553.2 ng/mL), followed by isoleucine (1818.044 ng/mL) and anserine (109.5 ng/mL), while R. palustris NR MPPR was found to produce 12 amino acids. Thirteen amino acids and their derivatives were found to be produced from R. faecalis N Raju MPPR, for which the concentration of carnosine (21601.056 ng/mL) was found to be the highest, followed by isoleucine (2032.6 ng/mL) and anserine (227.4 ng/mL). These microbes can be explored for the scaling up of the process, along with biohydrogen and single cell protein production.

Characterizing the Interplay of Rubisco and Nitrogenase Enzymes in Anaerobic-Photoheterotrophically Grown Rhodopseudomonas palustris CGA009 through a Genome-Scale Metabolic and Expression Model

Rhodopseudomonas palustris CGA009 is a Gram-negative purple nonsulfur bacterium that grows phototrophically by fixing carbon dioxide and nitrogen or chemotrophically by fixing or catabolizing a wide array of substrates, including lignin breakdown products for its carbon and fixing nitrogen for its nitrogen requirements. It can grow aerobically or anaerobically and can use light, inorganic, and organic compounds for energy production. Due to its ability to convert different carbon sources into useful products during anaerobic growth, this study reconstructed a metabolic and expression (ME) model of R. palustris to investigate its anaerobic-photoheterotrophic growth. Unlike metabolic (M) models, ME models include transcription and translation reactions along with macromolecules synthesis and couple these reactions with growth rate. This unique feature of the ME model led to nonlinear growth curve predictions, which matched closely with experimental growth rate data. At the theoretical maximum growth rate, the ME model suggested a diminishing rate of carbon fixation and predicted malate dehydrogenase and glycerol-3 phosphate dehydrogenase as alternate electron sinks. Moreover, the ME model also identified ferredoxin as a key regulator in distributing electrons between major redox balancing pathways. Because ME models include the turnover rate for each metabolic reaction, it was used to successfully capture experimentally observed temperature regulation of different nitrogenases. Overall, these unique features of the ME model demonstrated the influence of nitrogenases and rubiscos on R. palustris growth and predicted a key regulator in distributing electrons between major redox balancing pathways, thus establishing a platform for in silico investigation of R. palustris metabolism from a multiomics perspective. IMPORTANCE In this work, we reconstructed the first ME model for a purple nonsulfur bacterium (PNSB). Using the ME model, different aspects of R. palustris metabolism were examined. First, the ME model was used to analyze how reducing power entering the R. palustris cell through organic carbon sources gets partitioned into biomass, carbon dioxide fixation, and nitrogen fixation. Furthermore, the ME model predicted electron flux through ferredoxin as a major bottleneck in distributing electrons to nitrogenase enzymes. Next, the ME model characterized different nitrogenase enzymes and successfully recapitulated experimentally observed temperature regulations of those enzymes. Identifying the bottleneck responsible for transferring an electron to nitrogenase enzymes and recapitulating the temperature regulation of different nitrogenase enzymes can have profound implications in metabolic engineering, such as hydrogen production from R. palustris. Another interesting application of this ME model can be to take advantage of its redox balancing strategy to gain an understanding of the regulatory mechanism of biodegradable plastic production precursors, such as polyhydroxybutyrate (PHB).

Rapid degradation of Congo red wastewater by Rhodopseudomonas palustris intimately coupled carbon nanotube - Silver modified titanium dioxide photocatalytic composite with sodium alginate

With a large number of Congo red used in textiles, Congo red wastewater was not easily degraded, resulting in environmental and health-related problems. In order to improve the degradation efficiency of Congo red wastewater, A novel intimately coupled photocatalysis and biodegradation (ICPB) system was prepared by coupling Rhodopseudomonas palustris (R. Palustris), carbon nanotube - silver modified titanium dioxide photocatalytic composite (CNT-Ag -TiO₂, CAT) and sodium alginate (SA) (R. palustris/CAT@SA). Compared with immobilized CAT and R. palustris, the R. palustris/CAT@SA improved the degradation and removal rates of Congo red by 14.3% and 42.1%, and the COD removal rates by 76% and 44.6%, respectively. The mechanism of the degradation of Congo red by the new ICPB was that the Congo red on the surface of the support was degraded into long-chain alkanes by the superoxide and hydroxyl radicals of CAT product, and then the long-chain alkanes were completely mineralization by R. Palustris, which reduced the accumulation of intermediates in the photocatalysis. Most of the Congo red was adsorbed to the interior of the carrier was degraded into aromatic hydrocarbons by R. Palustris, and then oxidized and degraded by CAT, and a small part of the Congo red would be directly mineralized by R. Palustris. A novel technical solution of R. palustris/CAT@SA provided a potential application to the degradation of dye wastewater.

Distinct gene clusters drive formation of ferrosome organelles in bacteria

Cellular iron homeostasis is vital and maintained through tight regulation of iron import, efflux, storage and detoxification1-3. The most common modes of iron storage use proteinaceous compartments, such as ferritins and related proteins4,5. Although lipid-bounded iron compartments have also been described, the basis for their formation and function remains unknown6,7. Here we focus on one such compartment, herein named the 'ferrosome', that was previously observed in the anaerobic bacterium Desulfovibrio magneticus6. Using a proteomic approach, we identify three ferrosome-associated (Fez) proteins that are responsible for forming ferrosomes in D. magneticus. Fez proteins are encoded in a putative operon and include FezB, a P1B-6-ATPase found in phylogenetically and metabolically diverse species of bacteria and archaea. We show that two other bacterial species, Rhodopseudomonas palustris and Shewanella putrefaciens, make ferrosomes through the action of their six-gene fez operon. Additionally, we find that fez operons are sufficient for ferrosome formation in foreign hosts. Using S. putrefaciens as a model, we show that ferrosomes probably have a role in the anaerobic adaptation to iron starvation. Overall, this work establishes ferrosomes as a new class of iron storage organelles and sets the stage for studying their formation and structure in diverse microorganisms.

Enhanced pollutants removal and high-value cell inclusions accumulation with Fe2+ in heavy oil refinery treatment system using Rhodopseudomonas and Pseudomonas

Metal ions has been widely used as a method of improving pollutant removal efficiency in wastewater biological treatment system. In order to enhance pollutants removal and high-value cell inclusions accumulation in heavy oil refinery wastewater treatment systems using PSB, different reactors were built feeding with different Fe²⁺ concentrations respectively, and run with enriching Rhodopseudomonas and Pseudomonas in the reactors. Solute chemical oxygen demand (SCOD), ammonia (NH₄⁺-N), nitrate nitrogen (NO₃^--N), nitrous nitrogen (NO₂^--N), Fe²⁺, and related cell inclusions were all detected, moreover, microbial community structure and the quantity of Rhodopseudomonas and Pseudomonas were also detected. The results showed that at the optimal dosage of Fe²⁺ with 20 mg/L, the corresponding removal ratios of solute chemical oxygen demand and ammonia were 73.51% and 92.26%, respectively. The yields of carotenoid, bacteriochlorophyll, and coenzyme Q₁₀ were 11.18, 6.75, and 9.84 mg/g-DCW respectively. Furthermore, with 20 mg/L Fe²⁺ dosage, the relative abundance and gene number of Rhodopseudomonas were the highest in the system, which were 91.57% and 1.843 × 10⁶ gene copies/μL, while Fe²⁺ had no obvious effect on the growth of Pseudomonas. The results showed that adding Fe²⁺ has improved the removal of pollutants and accumulation of high-value cells inclusions, also provided theoretical guidance for the treatment of heavy oil refinery wastewater using PSB.

Lactic acid wastewater treatment by photosynthetic bacteria and simultaneous production of protein and pigments

Photosynthetic bacteria (PSB) can be used in wastewater treatment to simultaneously remove pollutants and produce valuable biomass. In this study, PSB were used to treat lactic acid wastewater and produce high-value substances (protein, carotenoid and bacteriochlorophyll). The results showed that the PSB biomass increase, COD and NH4+-N removal reached 55%, 89% and 94% in 5 days, respectively. The protein content, carotenoid and bacteriochlorophyll concentrations reached 69.1%, 2.3 and 0.8 mg/L, respectively. Furthermore, kinetic analysis showed that both NH4+-N removal and protein content fitted the Boltzmann equation, and the NH4+-N removal was positively related with the content of protein and concentration of pigments. This novel wastewater treatment method can adapt to the changes of light-oxygen condition, F/M and pH conditions.Highlights(1) PSB effectively treated real lactic acid wastewater with zero excess sludge.(2) 69% of protein and 2.3 mg/L of carotenoid were produced in the process.(3) NH4+-N removal was positively related with the content of protein and pigments.

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.

Metagenomic insights into the "window" effect of static magnetic field on nitrous oxide emission from biological nitrogen removal process at low temperature

This study aimed to explore whether the "window" effect of static magnetic field (SMF) on nitrous oxide (N₂O) emission from the biological nitrogen removal process at low temperature existed and reveal its biological mechanism at the gene level. Four sequencing batch reactors (SBRs) with SMFs of 0, 10, 45, and 75 mT were operated continuously for 110 days at 10 °C and the lowest N₂O-Gas cumulative emission (5.50 mg N/day) and N₂O conversion rate (4.28 %) in 45 mT SMF-SBR verified the existence of the "window" effect. In 45 mT SMF-SBR, nearly all enzymatic activities related to N₂O reduction and corresponding functional gene abundances improved significantly. Metagenomic high-throughput sequencing analysis revealed that Alicycliphilus denitricans, Paracoccus denitrificans, Rhodopseudomonas palustris, Pseudomonas stutzeri, and Dechloromonas aromatica, as species related to N₂O reduction, could be separately enriched by applying suitable SMF intensity. Gene functions annotation based on KEGG and CAZy databases indicated that SMF not only accelerated the rate of free ammonia into ammonia-oxidizing bacteria and electrons delivered to the corresponding denitrification reductases, but also enhanced the degradation of complex organic matter into smaller molecules, and thus reducing the production of N₂O via nitrifier denitrification and incomplete denitrification pathways at 10 °C. These findings provided a guideline and presented a blueprint of ecophysiology for the future application of magnetic field to the reduction of N₂O emission in wastewater treatment plants in the cold region.

Microbial food from light, carbon dioxide and hydrogen gas: Kinetic, stoichiometric and nutritional potential of three purple bacteria

The urgency for a protein transition towards more sustainable solutions is one of the major societal challenges. Microbial protein is one of the alternative routes, in which land- and fossil-free production should be targeted. The photohydrogenotrophic growth of purple bacteria, which builds on the H₂- and CO₂-economy, is unexplored for its microbial protein potential. The three tested species (Rhodobacter capsulatus, Rhodobacter sphaeroides and Rhodopseudomonas palustris) obtained promising growth rates (2.3-2.7 d^-1 at 28°C) and protein productivities (0.09-0.12 g protein L^-1 d^-1), rendering them likely faster and more productive than microalgae. The achieved protein yields (2.6-2.9 g protein g^-1 H₂) transcended the ones of aerobic hydrogen oxidizing bacteria. Furthermore, all species provided full dietary protein matches for humans and their fatty acid content was dominated by vaccenic acid (82-86%). Given its kinetic and nutritional performance we recommend to consider Rhodobacter capsulatus as a high-potential sustainable source of microbial food.

Influence of supplemented nutrients in tequila vinasses for hydrogen and polyhydroxybutyrate production by photofermentation with Rhodopseudomonas pseudopalustris

There is a great interest for replacing petroleum-derived chemical processes with biological processes to obtain fuels and plastics from industrial waste. Accordingly, Rhodopseudomonas species are capable of producing hydrogen and polyhydroxybutyrate. Culture conditions for production of both hydrogen and polyhydroxybutyrate with Rhodopseudomonas pseudopalustris (DSM 123) from tequila vinasses were analyzed. The production of hydrogen using tequila vinasses was higher with respect to two synthetic media. Replacing the headspace with N₂ increased the production of hydrogen with respect to Argon, while a higher concentration of polyhydroxybutyrate was achieved using Argon as compared to N₂. A higher concentration of phosphates increased the production of hydrogen (250 mL), while the highest concentration of polyhydroxybutyrate (305 mg/L) was accomplished when the bacteria were cultivated only with phosphates contained in tequila vinasses. This study revealed that the culture conditions for Rhodopseudomonas pseudopalustris (DSM 123) for production of hydrogen are the opposite of those for production of polyhydroxybutyrate.

Single-phase and two-phase cultivations using different light regimes to improve production of valuable substances in the anoxygenic photosynthetic bacterium Rhodopseudomonas faecalis PA2

This study aimed to improve biomass, carotenoid, bacteriochlorophyll, protein, lipid, and carbohydrate contents of Rhodopseudomonas faecalis PA2 using different light regimes. Light intensity (4000, 6000, 8000, and 10,000 lx), together with photoperiod (24:0, 16:8, 12:12, and 8:16 h light/dark), was assigned as single-phase (SP) cultivation while two-phase (TP) cultivation used two light intensities (using 4000 lx as the first phase), together with the control of phase shift (3, 6, and 9 days) and photoperiod. Biomass, carotenoid, and bacteriochlorophyll contents were maximized by SP cultivation; light at 8000 lx with light-dark cycle of 24:0 was optimal for pigments synthesis. In contrast, TP was useful to enhance storage compounds; protein, lipid, and carbohydrate productivities were significantly increased by 121.69%, 101.69%, and 92.44%, respectively, in TP when compared with SP. This indicates that the novel light strategy proposed in this study was able to manipulate the production of valuable substances in this strain.

Augmenting the biodegradation of recalcitrant ethinylestradiol using Rhodopseudomonas palustris in a hybrid photo-assisted microbial fuel cell with enhanced bio-hydrogen production

This study presents the biodegradation potential of ethinylestradiol (EE2) in anaerobic environments using exoelectrogenic activity of Rhodopseudomonas palustris. EE2, a basic ingredient in oral contraceptives, is a significant estrogenic micropollutant in various wastewaters and is considered highly recalcitrant. This recalcitrance of EE2 has caused anoxic areas to become repositories for these pollutants. Thus, it is essential to find the microorganisms and suitable methods to degrade this compound. An initial EE2 concentration of 1 mg/L, used in an anaerobic photobioreactor, resulted in 70% EE2 degradation over a period of 16 days with an increase of 63% in hydrogen production when EE2 was used with glycerol as the main carbon source in the culture medium. Furthermore, in the novel setup of hybrid photo-assisted microbial fuel cell (h-PMFC) employed here, EE2 degradation enhanced to 89.82% with a maximum power density of 0.633 ± 0.04 mW/m². The hybrid MFC employed here could metabolize EE2 and sustained the bio-hydrogen production for 14 days to run the hydrogen fuel cell which otherwise could not be sustained with glycerol only and thus increased the overall power output. The current work highlights the use of R. palustris and the significance of co-metabolism in bioremediation of pollutants and bioenergy generation.

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.

Cocultivating aerobic heterotrophs and purple bacteria for microbial protein in sequential photo- and chemotrophic reactors

Aerobic heterotrophic bacteria (AHB) and purple non-sulfur bacteria (PNSB) are typically explored as two separate types of microbial protein, yet their properties as respectively a bulk and added-value feed ingredient make them appealing for combined use. The feasibility of cocultivation in a sequential photo- and chemotrophic approach was investigated. First, mapping the chemotrophic growth kinetics for four Rhodobacter, Rhodopseudomonas and Rhodospirillum species on different carbon sources showed a preference for fructose (µ_max 2.4-3.9 d^-1 28 °C; protein 36-59%_DW). Secondly, a continuous photobioreactor inoculated with Rhodobacter capsulatus (VFA as C-source) delivered the starter culture for an aerobic batch reactor (fructose as C-source). This two-stage system showed an improved nutritional quality compared to AHB production: higher protein content (45-71%_DW), more attractive amino/fatty acid profile and contained up to 10% PNSB. The findings strengthen protein production with cocultures and might enable the implementation of the technology for resource recovery on streams such as wastewater.

Upgrading industrial effluent for agricultural reuse: effects of digestate concentration and wood vinegar dosage on biosynthesis of plant growth promotor

Emphasis on water reuse in agricultural sector receives a renewed interest to close the loop in circular economy, especially in dry and water-stressed regions. In this work, wastewater from cooperative smoked sheet rubber factory and the effluent (digestate) from its treatment system (anaerobic digester) were used as medium to grow purple non-sulfur bacteria (PNSB), Rhodopseudomonas palustris strain PP803, with wood vinegar supplement at mid-log growth phase to stimulate the release of 5-aminolevulinic acid (ALA), a plant growth promotor. Wastewater-to-digestate ratios (D:W) represented by soluble chemical oxygen demand (SCOD) were found to influence both the growth of R. palustris and synthesis of ALA. The highest ALA release of 16.02 ± 0.75 μM and the biomass accumulation of 1302 ± 78 mg/L were obtained from the medium SCOD of 4953 mg/L. Although retarding biomass accumulation by 28-36%, wood vinegar (WV) addition was proven to improve ALA release by 40%. Result suggested that SCOD of 3438 mg/L (75:25 D:W) contained sufficient carbon source for PNSB growth and was chosen to subsequently run the photo-bioreactor (PBR) to sustain R. palustris PP803 cells production. In continuous PBR operation, PNSB proliferation suffered from the low organic concentration in PBR at low organic loading. An organic loading increase to 1.21 g COD/L day was found to attain highest biomass concentration and longest PNSB dominant period over microalgea. In this study, a real-time monitoring protocol of PNSB and microalgae was specifically developed based on image color analysis at acceptable accuracy (R² = 0.94). In the final assay, verification of the PBR-grown inoculant was conducted and ALA release efficiency was discussed under various wood vinegar dosages and dosing frequencies. This work has advanced our understandings closer to practical field application.

Enhanced removal of veterinary antibiotic from wastewater by photoelectroactive biofilm of purple anoxygenic phototroph through photosynthetic electron uptake

Purple anoxygenic phototrophs have been recently attracted substantial attention for their growing potential in wastewater treatment and their diverse metabolic patterns can be regulated for process control and optimization. In this study, the photoheterotrophic metabolism of Rhodopseudomonas palustris (R. palustris) was modified by photosynthetic electron uptake using a poised electrode which was explored to enhance removal of veterinary antibiotic from aqueous medium. The results showed that R. palustris grown as biofilm on electrode surface had excellent photoelectroactive activity and the photosynthetic electron uptake from the photoelectroactive biofilm significantly enhanced antibiotic florfenicol (FLO) degradation. The specific degradation rate of FLO at the set electrode potential of 0 V was 2.59-fold higher than that without applied potential. Enhanced co-metabolic reductive dehalogenation by use of the photosynthetic electrons extracted from co-substrate was mainly responsible for FLO degradation which eliminated the antibacterial activity of FLO. The electrode potential controlled the processes of photosynthetic electron uptake and its resultant FLO degradation. The fastest degradation of FLO was achieved at 0 V because the electrode poised at this potential stroke a proper balance between the enhancing photosynthetic electron uptake by serving as electron acceptor and minimizing competition with FLO for the photosynthetic electron from co-substrate. The activity of photoelectroactive biofilm was not negatively affected by FLO at environmental relevant concentration, suggesting its great potential for removal of antibiotic contaminants in wastewater. R. palustris could serve as a reservoir for floR resistance gene but its abundance can be diminished by choosing appropriate electrode potential.

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.

Effects of light intensity and photoperiod on pigments production and corresponding key gene expression of Rhodopseudomonas palustris in a photobioreactor system

Light intensity and photoperiod significantly affect Rhodopseudomonas palustris growth and pigments production and their optimization is necessary for pigment biosynthesis. In this study, the impacts of different light intensity and light/dark cycles were investigated on biomass, carotenoids, bacteriochlorophyll production, together with pollutant removal, in a photobioreactor system. Results showed that R. palustris had the highest carotenoids and bacteriochlorophyll productions with light intensity of 150 μmol-photons/m²/s and light/dark cycle of 4/2 (16 h/8h). The corresponding values were 1.94 mg/g-biomass and 1.17 mg/g-biomass, respectively. The effects of light/dark cycle on crtA and bchE gene expression in pigments biosynthesis were also studied. Mechanism analysis revealed that carotenoids and bacteriochlorophyll yields represented good synergistic effect, which was consistent with the up-regulation of crtA and bchE gene expressions under optimal light/dark cycle of 4/2.

RETRACTED: Clothianidin wastewater treatment and the accumulation of high-value biochemical by Rhodopseudomonas spheroides

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the Authors and the Editor-in-Chief. The paper is retracted because of a high level of duplication of "Rhodopseudomonas palustris wastewater treatment: cyhalofop-butyl removal, biochemicals production and mathematical model establishment. Bioresource. Tech. 2019, 282: 390-397 As such this article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process. The first author, Pan Wu, takes full responsibility for these actions, a stance supported by Dalian Minzu University and Northeast Agricultural University, Harbin, where the research took place.

Grid columnar flat panel photobioreactor with immobilized photosynthetic bacteria for continuous photofermentative hydrogen production

A biophotoreactor with a transparent glass flat panel with polymethyl methacrylate (PMMA) grid columnar for enhanced biofilm growth with Rhodopseudomonas palustris GCA009 was developed and tested at 590 nm incident light. Continuous photofermentative hydrogen production from glucose was tested using this novel reactor. At light intensity of 210 W/m², feed substrate concentration of 56.0 mmol/L, and crossflow velocity of 1.68 × 10^-6 m/s, a maximum hydrogen production rate of 32.6 mmol/L-d (3.56 mmol/m²-h), hydrogen yield of 1.15 mol H₂/mol glucose and light conversion efficiency of 5.34% can be achieved. Since the revised grid columnar effectively enlarged the surface area of reactor and enhanced cell attachment, the present reactor design led to higher hydrogen production rates than literature works.

One-step treatment and resource recovery of high-concentration non-toxic organic wastewater by photosynthetic bacteria

In order to achieve simple pollutant removal and simultaneous resource recovery in high-COD-non-toxic wastewater treatment, a one-step photosynthetic bacteria (PSB) method was established using batch study experiment. The effluent COD met the national discharge standard, and biomass with rich protein and high-value substances was efficiently produced. It eliminated the demand of post-treatment for conventional PSB treatment. Results showed that Rhodopseudomonas effectively treated brewery wastewater and achieved biomass proliferation. Yeast extract was the best additive for PSB growth and the effluent COD was below 80 mg/L with 400 mg/L yeast extract, meeting the national discharge standard. In addition, the PSB biomass increased by 2.6 times, and the cells were rich in protein, polysaccharide, carotenoids, bacteriochlorophyll and coenzyme Q10, reaching 420.9, 177.6, 2.53, 10.75 and 38.6 mg/g respectively. This work demonstrated the great potential of PSB for high-COD non-toxic wastewater treatment in one-step process.

Optimization of the yield of dark microaerobic production of hydrogen from lactate by Rhodopseudomonas palustris

Hydrogen yields of dark fermentation are limited due to the need to also produce reduced side products, and photofermentation, an alternative, is limited by the need for light. A relatively new strategy, dark microaerobic fermentation, could potentially overcome both these constraints. Here, application of this strategy demonstrated for the first time significant hydrogen production from lactate by a single organism in the dark. Response surface methodology (RSM) was used to optimize substrate and oxygen concentration as well as inoculum using both (1) regular batch and (2) O₂ fed batch cultures. The highest hydrogen yield (HY) was observed under regular batch (1.4±0.1molH₂/mollactate) and the highest hydrogen production (HP) (173.5µmolH₂) was achieved using O₂ fed batch. This study has provided proof of principal for the ability of microaerobic fermentation to drive thermodynamically difficult reactions, such as the conversion of lactate to hydrogen.

for wastewater treatment

The future wastewater treatment requires high-efficiency and energy-saving technology. Anoxygenic photosynthetic bacteria (APB) is deemed as an eco-friendly microorganism, which could be employed in wastewater treatment. Here, monochromatic near-infrared (MNIR) light emitting diode (LED) was used, and three key factors (light quality, light intensity and photoperiod) of it were analyzed by a response surface methodology (RSM) in APB wastewater treatment. The results showed that light quality was the biggest impact factor in APB wastewater treatment, and nearly 58.07% of NH₄⁺-N and 70.62% of chemical oxygen demand (COD) could be removed based on 46.4% of that theoretically possible. The light quality's study revealed that APB had the highest NH₄⁺-N and COD removal, biomass production, and bacteriochlorophyll a production with 850nm IR LED. Moreover, the application of optimal MNIR LED could not only save energy, but also avoid algae bloom of photo-bioreactors (PBR).

[Microorganisms effect with probiotic potential in water quality and growth of the shrimp Litopenaeus vannamei (Decapoda: Penaeidae) in intensive culture]

The use of probiotics has gained acceptance in aquaculture, particularly in maintaining water quality and enhancing growth in organisms. This study analyzed the effect of the commercial (EM, Japan) natural product composed by (Rhodopseudomonas palustris, Lactobacillus plantarum, Lactobacillus casei and Saccharomyces cerevisiae) added to the water, in order to determine its effect in water quality, sediment and growth of L. vannamei under intensive culture. The evaluation included three treatments with a weekly addition of EM: i) tanks without probiotics (C), ii) tanks with a dose of 4 L/ha (EM1) and iii) tanks with a dose of 10 L/ha (EM2). The treatment C was carried out three times, while treatments EM1 and EM2 were carried out four times. A total of 4 350 shrimps were measured for total length and weight, to calculate total and porcentual weight gain, daily weight gain, specific growth rate (TCE), and food conversion factor (FCA); besides, the survival rate was estimated. The use of probiotics allowed a shorter harvest time in treatments EM1 (90 d) and EM2 (105 d) with relation to the treatment C (120d). Treatments EM1 and EM2 were within the recommended intervals for culture, with respect to treatment C. The use of probiotic bacteria significantly regulated pH (EM1, 8.03 +/- 0.33; EM2, 7.77 +/- 0.22; C, 9.08 +/- 0.35) and reduced nitrate concentration (EM1, 0.64 +/- 0.25 mg/L; EM2, 0.39 +/- 0.26 mg/L; C, 0.71 mg/L). Water pH mostly explained the variance with respect to the treatments. Treatment EM2 presented the greatest removal of organic matter (1.77 +/- 0.45%), whereas the contents of extractable phosphorus increased significantly in treatment EM1 with 21.6 +/- 7.99 mg/kg and in treatment EM2 with 21.6 +/- 8.45 mg/kg with control relation (14.3 +/- 5.47). The shrimp growth was influenced by dissolved oxygen, salinity and pH in the sediment, establishing that salinity was the most important variable in the weight with a negative association. Treatment EM1 recorded an improved TCE (2.69 +/- 0.35%/d) and FCA (1.46 +/- 0.20) with relation to the control treatment (TCE, 1.88 +/- 0.25%/d; FCA, 2.13 +/- 0.48). Survival was significantly greater in treatments containing probiotics with 61 +/- 8.76% and 60 +/- 10.5% for EM1 and EM2, respectively. This study indicated the positive effect obtained with the use of this commercial probiotic, to improve culture conditions and growth parameters in an intensive culture of L. vannamei.

Inelastic neutron scattering study of light-induced dynamics of a photosynthetic membrane system

Inelastic neutron scattering was employed to study photoeffects on the molecular dynamics of membranes of the photosynthetic bacterium Rhodopseudomonas viridis. The main photoactive parts of this biomolecular system are the chlorophyll molecules whose dynamics were found to be affected under illumination by visible light in a twofold manner. First, vibrational modes are excited at energies of 12(2) and 88(21) cm(-1). Second, a partial "freezing" of rotational modes is observed at energies of 1.2(3) and 2.9(5) cm(-1). These results are attributed to a possible coupling between molecular motions and particular mechanisms in the photosynthetic process.

Robust estimation of peptide abundance ratios and rigorous scoring of their variability and bias in quantitative shotgun proteomics

The abundance ratio between the light and heavy isotopologues of an isotopically labeled peptide can be estimated from their selected ion chromatograms. However, quantitative shotgun proteomics measurements yield selected ion chromatograms at highly variable signal-to-noise ratios for tens of thousands of peptides. This challenge calls for algorithms that not only robustly estimate the abundance ratios of different peptides but also rigorously score each abundance ratio for the expected estimation bias and variability. Scoring of the abundance ratios, much like scoring of sequence assignment for tandem mass spectra by peptide identification algorithms, enables filtering of unreliable peptide quantification and use of formal statistical inference in the subsequent protein abundance ratio estimation. In this study, a parallel paired covariance algorithm is used for robust peak detection in selected ion chromatograms. A peak profile is generated for each peptide, which is a scatterplot of ion intensities measured for the two isotopologues within their chromatographic peaks. Principal component analysis of the peak profile is proposed to estimate the peptide abundance ratio and to score the estimation with the signal-to-noise ratio of the peak profile (profile signal-to-noise ratio). We demonstrate that the profile signal-to-noise ratio is inversely correlated with the variability and bias of peptide abundance ratio estimation.

A comparison of stigmatellin conformations, free and bound to the photosynthetic reaction center and the cytochrome bc1 complex

We describe in detail the conformations of the inhibitor stigmatellin in its free form and bound to the ubiquinone-reducing (Q(B)) site of the reaction center and to the ubiquinol-oxidizing (Q(o)) site of the cytochrome bc(1) complex. We present here the first structures of a stereochemically correct stigmatellin in complexes with a bacterial reaction center and the yeast cytochrome bc1 complex. The conformations of the inhibitor bound to the two enzymes are not the same. We focus on the orientations of the stigmatellin side-chain relative to the chromone head group, and on the interaction of the stigmatellin side-chain with these membrane protein complexes. The different conformations of stigmatellin found illustrate the structural variability of the Q sites, which are affected by the same inhibitor. The free rotation about the chi1 dihedral angle is an essential factor for allowing stigmatellin to bind in both the reaction center and the cytochrome bc1 pocket.

ProRata: A Quantitative Proteomics Program for Accurate Protein Abundance Ratio Estimation with Confidence Interval Evaluation

A profile likelihood algorithm is proposed for quantitative shotgun proteomics to infer the abundance ratios of proteins from the abundance ratios of isotopically labeled peptides derived from proteolysis. Previously, we have shown that the estimation variability and bias of peptide abundance ratios can be predicted from their profile signal-to-noise ratios. Given multiple quantified peptides for a protein, the profile likelihood algorithm probabilistically weighs the peptide abundance ratios by their inferred estimation variability, accounts for their expected estimation bias, and suppresses contribution from outliers. This algorithm yields maximum likelihood point estimation and profile likelihood confidence interval estimation of protein abundance ratios. This point estimator is more accurate than an estimator based on the average of peptide abundance ratios. The confidence interval estimation provides an "error bar" for each protein abundance ratio that reflects its estimation precision and statistical uncertainty. The accuracy of the point estimation and the precision and confidence level of the interval estimation were benchmarked with standard mixtures of isotopically labeled proteomes. The profile likelihood algorithm was integrated into a quantitative proteomics program, called ProRata, freely available at www.MSProRata.org.

Hydrophobic pockets at the membrane interface: an original mechanism for membrane protein interactions

The effect of partial digestion by trypsin and GluC protease on the association of the membrane polypeptides of LH1 from Rhodospirillum (Rsp.) rubrum was studied. Trypsin and GluC protease treatments of LH1 result in the cleavage of the first three amino acids from the alpha polypeptide and of the first 18 amino acids from the beta polypeptide, respectively, without any noticeable reorganization of their secondary structure, as measured by attenuated total reflectance Fourier transform IR spectroscopy. However, the enthalpy variation accompanying dimer formation was dramatically reduced by the protease attacks by as much as 80%. Our results show that the alphabeta heterodimer is mainly stabilized by hydrophobic interactions which involve the amino-terminal extensions of the participating polypeptides. Using the close homology between the polypeptides of Rsp. rubrum LH1 and that of Rsp. molischianum LH2, whose structure is known, a structural model for these "hydrophobic pockets" lying close to the membrane interface is proposed.