Bacterial adenine cross-feeding stems from a purine salvage bottleneck

Diverse ecosystems host microbial relationships that are stabilized by nutrient cross-feeding. Cross-feeding can involve metabolites that should hold value for the producer. Externalization of such communally valuable metabolites is often unexpected and difficult to predict. Previously, we discovered purine externalization by Rhodopseudomonas palustris by its ability to rescue an Escherichia coli purine auxotroph. Here we found that an E. coli purine auxotroph can stably coexist with R. palustris due to purine cross-feeding. We identified the cross-fed purine as adenine. Adenine was externalized by R. palustris under diverse growth conditions. Computational modeling suggested that adenine externalization occurs via diffusion across the cytoplasmic membrane. RNAseq analysis led us to hypothesize that adenine accumulation and externalization stems from a salvage pathway bottleneck at the enzyme encoded by apt. Ectopic expression of apt eliminated adenine externalization, supporting our hypothesis. A comparison of 49 R. palustris strains suggested that purine externalization is relatively common, with 16 strains exhibiting the trait. Purine externalization was correlated with the genomic orientation of apt, but apt orientation alone could not always explain purine externalization. Our results provide a mechanistic understanding of how a communally valuable metabolite can participate in cross-feeding. Our findings also highlight the challenge in identifying genetic signatures for metabolite externalization.

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.

Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired

Denitrification is a form of anaerobic respiration wherein nitrate (NO3-) is sequentially reduced via nitrite (NO2-), nitric oxide, and nitrous oxide (N2O) to dinitrogen gas (N2) by four reductase enzymes. Partial denitrifying bacteria possess only one or some of these four reductases and use them as independent respiratory modules. However, it is unclear if partial denitrifiers sense and respond to denitrification intermediates outside of their reductase repertoire. Here, we tested the denitrifying capabilities of two purple nonsulfur bacteria, Rhodopseudomonas palustris CGA0092 and Rhodobacter capsulatus SB1003. Each had denitrifying capabilities that matched their genome annotation; CGA0092 reduced NO2- to N2, and SB1003 reduced N2O to N2. For each bacterium, N2O reduction could be used both for electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in darkness. However, N2O reduction required supplementation with a denitrification intermediate, including those for which there was no associated denitrification enzyme. For CGA0092, NO3- served as a stable, non-catalyzable molecule that was sufficient to activate N2O reduction. Using a β-galactosidase reporter, we found that NO3- acted, at least in part, by stimulating N2O reductase gene expression. In SB1003, NO2- but not NO3- activated N2O reduction, but NO2- was slowly removed, likely by a promiscuous enzyme activity. Our findings reveal that partial denitrifiers can still be subject to regulation by denitrification intermediates that they cannot use.IMPORTANCEDenitrification is a form of microbial respiration wherein nitrate is converted via several nitrogen oxide intermediates into harmless dinitrogen gas. Partial denitrifying bacteria, which individually have some but not all denitrifying enzymes, can achieve complete denitrification as a community by cross-feeding nitrogen oxide intermediates. However, the last intermediate, nitrous oxide (N2O), is a potent greenhouse gas that often escapes, motivating efforts to understand and improve the efficiency of denitrification. Here, we found that at least some partial denitrifying N2O reducers can sense and respond to nitrogen oxide intermediates that they cannot otherwise use. The regulatory effects of nitrogen oxides on partial denitrifiers are thus an important consideration in understanding and applying denitrifying bacterial communities to combat greenhouse gas emissions.

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.

Protein Interactions in Rhodopseudomonas palustris TIE-1 Reveal the Molecular Basis for Resilient Photoferrotrophic Iron Oxidation

Rhodopseudomonas palustris is an alphaproteobacterium with impressive metabolic versatility, capable of oxidizing ferrous iron to fix carbon dioxide using light energy. Photoferrotrophic iron oxidation is one of the most ancient metabolisms, sustained by the pio operon coding for three proteins: PioB and PioA, which form an outer-membrane porin-cytochrome complex that oxidizes iron outside of the cell and transfers the electrons to the periplasmic high potential iron-sulfur protein (HIPIP) PioC, which delivers them to the light-harvesting reaction center (LH-RC). Previous studies have shown that PioA deletion is the most detrimental for iron oxidation, while, the deletion of PioC resulted in only a partial loss. The expression of another periplasmic HiPIP, designated Rpal_4085, is strongly upregulated in photoferrotrophic conditions, making it a strong candidate for a PioC substitute. However, it is unable to reduce the LH-RC. In this work we used NMR spectroscopy to map the interactions between PioC, PioA, and the LH-RC, identifying the key amino acid residues involved. We also observed that PioA directly reduces the LH-RC, and this is the most likely substitute upon PioC deletion. By contrast, Rpal_4085 demontrated significant electronic and structural differences from PioC. These differences likely explain its inability to reduce the LH-RC and highlight its distinct functional role. Overall, this work reveals the functional resilience of the pio operon pathway and further highlights the use of paramagnetic NMR for understanding key biological processes.

Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60

Mitochondrial cristae expand the surface area of respiratory membranes and ultimately allow for the evolutionary scaling of respiration with cell volume across eukaryotes. The discovery of Mic60 homologs among alphaproteobacteria, the closest extant relatives of mitochondria, suggested that cristae might have evolved from bacterial intracytoplasmic membranes (ICMs). Here, we investigated the predicted structure and function of alphaproteobacterial Mic60, and a protein encoded by an adjacent gene Orf52, in two distantly related purple alphaproteobacteria, Rhodobacter sphaeroides and Rhodopseudomonas palustris. In addition, we assessed the potential physical interactors of Mic60 and Orf52 in R. sphaeroides. We show that the three α helices of mitochondrial Mic60's mitofilin domain, as well as its adjacent membrane-binding amphipathic helix, are present in alphaproteobacterial Mic60. The disruption of Mic60 and Orf52 caused photoheterotrophic growth defects, which are most severe under low light conditions, and both their disruption and overexpression led to enlarged ICMs in both studied alphaproteobacteria. We also found that alphaproteobacterial Mic60 physically interacts with BamA, the homolog of Sam50, one of the main physical interactors of eukaryotic Mic60. This interaction, responsible for making contact sites at mitochondrial envelopes, has been conserved in modern alphaproteobacteria despite more than a billion years of evolutionary divergence. Our results suggest a role for Mic60 in photosynthetic ICM development and contact site formation at alphaproteobacterial envelopes. Overall, we provide support for the hypothesis that mitochondrial cristae evolved from alphaproteobacterial ICMs and have therefore improved our understanding of the nature of the mitochondrial ancestor.

strain AZUL predicts genome plasticity and adaptation to chemical homeostasis

The genus Rhodopseudomonas comprises purple non-sulfur bacteria with extremely versatile metabolisms. Characterization of several strains revealed that each is a distinct ecotype highly adapted to its specific micro-habitat. Here we present the sequencing, genomic comparison and functional annotation of AZUL, a Rhodopseudomonas strain isolated from a high altitude Andean lagoon dominated by extreme conditions and fluctuating levels of chemicals. Average nucleotide identity (ANI) analysis of 39 strains of this genus showed that the genome of AZUL is 96.2% identical to that of strain AAP120, which suggests that they belong to the same species. ANI values also show clear separation at the species level with the rest of the strains, being more closely related to R. palustris. Pangenomic analyses revealed that the genus Rhodopseudomonas has an open pangenome and that its core genome represents roughly 5 to 12% of the total gene repertoire of the genus. Functional annotation showed that AZUL has genes that participate in conferring genome plasticity and that, in addition to sharing the basal metabolic complexity of the genus, it is also specialized in metal and multidrug resistance and in responding to nutrient limitation. Our results also indicate that AZUL might have evolved to use some of the mechanisms involved in resistance as redox reactions for bioenergetic purposes. Most of those features are shared with strain AAP120, and mainly involve the presence of additional orthologs responsible for the mentioned processes. Altogether, our results suggest that AZUL, one of the few bacteria from its habitat with a sequenced genome, is highly adapted to the extreme and changing conditions that constitute its niche.

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.

Biotreatment and bacterial succession in an upflow immobilized cell bioreactor fed with fludioxonil wastewater

The large quantities and the persistent nature of fungicide wastewaters have increased the efforts towards a sustainable technological solution. In this context, fludioxonil-contaminated wastewater was treated in an upflow immobilized cell bioreactor, resulting in chemical oxygen demand (COD) removal efficiency even higher than 80%, whereas the electrical conductivity (EC) of the effluent was gradually increased. Organic-F was mineralized by 94.0 ± 5.2%, which was in accordance with the high fludioxonil removal efficiency (95.4 ± 4.0%). In addition, effluent total Kjeldahl nitrogen (TKN) concentration reduced significantly during bioprocessing. A strong relationship among COD removal, TKN/total nitrogen removal, and effluent EC increase (p < 0.01) was identified. Despite the adequate aeration provided, effluent nitrite and nitrate concentrations were negligible. Illumina sequencing revealed a reduction in the relative abundances of Betaproteobacteria, Chloroflexi, Planctomycetes, and Firmicutes and an increase in the proportion of Alphaproteobacteria and Actinobacteria. A shift in bacterial communities occurred during fludioxonil treatment, resulting in the significant increase of the relative abundances of Empedobacter, Sphingopyxis, and Rhodopseudomonas (from 0.67 ± 0.13% at the start-up to 34.34 ± 1.60% at the end of biotreatment). In conclusion, the immobilized cell bioreactor permitted the proliferation of specialized activated sludge microbiota with an active role in the depuration of postharvest fungicides.

Covert Cross-Feeding Revealed by Genome-Wide Analysis of Fitness Determinants in a Synthetic Bacterial Mutualism

Microbial interactions abound in natural ecosystems and shape community structure and function. Substantial attention has been given to cataloging mechanisms by which microbes interact, but there is a limited understanding of the genetic landscapes that promote or hinder microbial interactions. We previously developed a mutualistic coculture pairing Escherichia coli and Rhodopseudomonas palustris, wherein E. coli provides carbon to R. palustris in the form of glucose fermentation products and R. palustris fixes N₂ gas and provides nitrogen to E. coli in the form of NH₄ ⁺ The stable coexistence and reproducible trends exhibited by this coculture make it ideal for interrogating the genetic underpinnings of a cross-feeding mutualism. Here, we used random barcode transposon sequencing (RB-TnSeq) to conduct a genome-wide search for E. coli genes that influence fitness during cooperative growth with R. palustris RB-TnSeq revealed hundreds of genes that increased or decreased E. coli fitness in a mutualism-dependent manner. Some identified genes were involved in nitrogen sensing and assimilation, as expected given the coculture design. The other identified genes were involved in diverse cellular processes, including energy production and cell wall and membrane biogenesis. In addition, we discovered unexpected purine cross-feeding from R. palustris to E. coli, with coculture rescuing growth of an E. coli purine auxotroph. Our data provide insight into the genes and gene networks that can influence a cross-feeding mutualism and underscore that microbial interactions are not necessarily predictable a priori IMPORTANCE Microbial communities impact life on Earth in profound ways, including driving global nutrient cycles and influencing human health and disease. These community functions depend on the interactions that resident microbes have with the environment and each other. Thus, identifying genes that influence these interactions will aid the management of natural communities and the use of microbial consortia as biotechnology. Here, we identified genes that influenced Escherichia coli fitness during cooperative growth with a mutualistic partner, Rhodopseudomonas palustris Although this mutualism centers on the bidirectional exchange of essential carbon and nitrogen, E. coli fitness was positively and negatively affected by genes involved in diverse cellular processes. Furthermore, we discovered an unexpected purine cross-feeding interaction. These results contribute knowledge on the genetic foundation of a microbial cross-feeding interaction and highlight that unanticipated interactions can occur even within engineered microbial communities.

The regulation of the disease resistance, mTOR and NF-kB signaling pathway of Aristichthys nobilis using Rhodopseudomonas wastewater treatment

The employment of traditional feed and medicament in freshwater aquaculture causes the frequent occurrence of environmental pollution and disease. Effluent collected after Rhodopseudomonas-mediated wastewater treatment could be re-utilized as microbial feeds, and aquaculture water to culture Aristichthys nobilis. Therefore, a novel integrated system of wastewater treatment using effluent containing Rhodopseudomonas that improves yield, increases disease resistance, and enhances the quality of aquaculture water for Aristichthys nobilis culture was proposed and investigated. Aristichthys nobilis can grow well in effluent containing Rhodopseudomonas (ER). The survival rate, yield, and whole body composition of the ER group were all increased compared to the control group (CK). The biochemical (B vitamin) and other substances in the effluent of Rhodopseudomonas enhanced the activity of AKP, ACP, phagocytic, SOD, and CAT by upregulating the expression of AKP, ACP, SOD, and CAT genes. Moreover, Rhodopseudomonas and biochemical substances improved mTOR and NF-kB signaling pathway. Furthermore, Rhodopseudomonas inhibited Aeromonas hydrophila that increases resistance against fish disease. Meanwhile, Rhodopseudomonas in the effluent also improved the aquaculture water quality. This technology would save the aquaculture water, reduce water pollution and wastewater discharge, and increase the output and disease resistance of Aristichthys nobilis, simultaneously.

Anaerobic Degradation of Syringic Acid by an Adapted Strain of Rhodopseudomonas palustris

Lignin is the most abundant aromatic polymer on Earth and a resource that could eventually substitute for fossil fuels as a source of aromatic compounds for industrial and biotechnological applications. Engineering microorganisms for the production of aromatic-based biochemicals requires detailed knowledge of the metabolic pathways for the degradation of aromatics that are present in lignin. Our isolation and analysis of a Rhodopseudomonas palustris strain capable of syringic acid degradation reveal a previously unknown metabolic route for aromatic degradation in R. palustris. This study highlights several key features of this pathway and sets the stage for a more complete understanding of the microbial metabolic repertoire required to metabolize aromatic compounds from lignin and other renewable sources.

While lignin represents a major fraction of the carbon in plant biomass, biological strategies to convert the components of this heterogeneous polymer into products of industrial and biotechnological value are lacking. Syringic acid (3,5-dimethoxy-4-hydroxybenzoic acid) is a by-product of lignin degradation, appearing in lignocellulosic hydrolysates, deconstructed lignin streams, and other agricultural products. Rhodopseudomonas palustris CGA009 is a known degrader of phenolic compounds under photoheterotrophic conditions via the benzoyl coenzyme A (CoA) degradation (BAD) pathway. However, R. palustris CGA009 is reported to be unable to metabolize meta-methoxylated phenolics, such as syringic acid. We isolated a strain of R. palustris (strain SA008.1.07), adapted from CGA009, which can grow on syringic acid under photoheterotrophic conditions, utilizing it as a sole source of organic carbon and reducing power. An SA008.1.07 mutant with an inactive benzoyl-CoA reductase structural gene was able to grow on syringic acid, demonstrating that the metabolism of this aromatic compound is not through the BAD pathway. Comparative gene expression analyses of SA008.1.07 implicated the involvement of products of the vanARB operon (rpa3619, rpa3620, rpa3621), which has been described as catalyzing aerobic aromatic ring demethylation in other bacteria, in anaerobic syringic acid degradation. In addition, experiments with a vanARB deletion mutant demonstrated the involvement of the vanARB operon in anaerobic syringic acid degradation. These observations provide new insights into the anaerobic degradation of meta-methoxylated and other aromatics by R. palustris.

IMPORTANCE Lignin is the most abundant aromatic polymer on Earth and a resource that could eventually substitute for fossil fuels as a source of aromatic compounds for industrial and biotechnological applications. Engineering microorganisms for the production of aromatic-based biochemicals requires detailed knowledge of the metabolic pathways for the degradation of aromatics that are present in lignin. Our isolation and analysis of a Rhodopseudomonas palustris strain capable of syringic acid degradation reveal a previously unknown metabolic route for aromatic degradation in R. palustris. This study highlights several key features of this pathway and sets the stage for a more complete understanding of the microbial metabolic repertoire required to metabolize aromatic compounds from lignin and other renewable sources.

Culture of attached and suspended Rhodopseudomonas faecalis in the presence of decomposing fish feed

An approach to culturing attached and suspended forms of Rhodopseudomonas faecalis by using compound fish feed with tap water in transparent containers is reported in this study. The ratio of fish feed to tap water was 14.3–50.8 g/L, and no other inoculum or substances were added during the culture process. When the ratio of fish feed to tap water was 14.3 g/L, the highest total nitrogen, total phosphorus, and total dissolved carbon content recorded in the water in the containers were approximately 730 mg/L, 356 mg/L, and 1,620 mg/L, respectively, during the process of feed decay. Comamonas, Rhodopseudomonas, and Clostridium successively dominated during the culture process. Rhodopseudomonas was the most common dominant genus in both the attached and suspended forms when the water was dark red, and the relative operational taxonomic unit abundance reached 80‒89% and 24.8%, respectively. The dominant species was R. faecalis. The maximum thickness of attached bacteria and the biomass of attached Rhodopseudomonas reached up to 0.56 mm and 7.5 mg/cm², respectively. This study provides a method for the mass culture of Rhodopseudomonas by using the fermentation of aquatic compound fish feed.

A Genomotaxonomy View of the Bradyrhizobium Genus

Whole genome analysis of the Bradyrhizobium genus using average nucleotide identity (ANI) and phylogenomics showed the genus to be essentially monophyletic with seven robust groups within this taxon that includes nitrogen-fixing nodule forming bacteria as well as free living strains. Despite the wide genetic diversity of these bacteria no indication was found to suggest that the Bradyrhizobium genus have to split in different taxa. Bradyrhizobia have larger genomes than other genera of the Bradyrhizobiaceae family, probably reflecting their metabolic diversity and different lifestyles. Few plasmids in the sequenced strains were revealed from rep gene analysis and a relatively low proportion of the genome is devoted to mobile genetic elements. Sequence diversity of recA and glnII gene metadata was used to theoretically estimate the number of existing species and to predict how many would exist. There may be many more species than those presently described with predictions of around 800 species in nature. Different arguments are presented suggesting that nodulation might have arose in the ancestral genus Bradyrhizobium.

Influence of Energy and Electron Availability on In Vivo Methane and Hydrogen Production by a Variant Molybdenum Nitrogenase

The anoxygenic phototrophic bacterium Rhodopseudomonas palustris produces methane (CH₄) from carbon dioxide (CO₂) and hydrogen (H₂) from protons (H⁺) when it expresses a variant form of molybdenum (Mo) nitrogenase that has two amino acid substitutions near its active site. We examined the influence of light energy and electron availability on in vivo production of these biofuels. Nitrogenase activity requires large amounts of ATP, and cells exposed to increasing light intensities produced increasing amounts of CH₄ and H₂ As expected for a phototroph, intracellular ATP increased with increasing light intensity, but there was only a loose correlation between ATP content and CH₄ and H₂ production. There was a much stronger correlation between decreased intracellular ADP and increased gas production with increased light intensity, suggesting that the rate-limiting step for CH₄ and H₂ production by R. palustris is inhibition of nitrogenase by ADP. Increasing the amounts of electrons available to nitrogenase by providing cells with organic alcohols, using nongrowing cells, blocking electrons from entering the Calvin cycle, or blocking H₂ uptake resulted in higher yields of H₂ and, in some cases, CH₄ Our results provide a more complete understanding of the constraints on nitrogenase-based production of biofuels.IMPORTANCE A variant form of Mo nitrogenase catalyzes the conversion of CO₂ and protons to the biofuels CH₄ and H₂ A constant supply of electrons and ATP is needed to drive these reduction reactions. The bacterium R. palustris generates ATP from light and has a versatile metabolism that makes it ideal for manipulating electron availability intracellularly. We therefore explored its potential as a biocatalyst for CH₄ and H₂ production. We found that intracellular ADP had a major effect on biofuel production, more pronounced than the effect caused by ATP. This is probably due to inhibition of nitrogenase activity by ADP. In general, the amount of CH₄ produced by the variant nitrogenase in vivo was affected by electron availability much less than was the amount of H₂ produced. This study shows the nature of constraints on in vivo biofuel production by variant Mo nitrogenase.

An Escherichia coli Nitrogen Starvation Response Is Important for Mutualistic Coexistence with Rhodopseudomonas palustris

Microbial mutualistic cross-feeding interactions are ubiquitous and can drive important community functions. Engaging in cross-feeding undoubtedly affects the physiology and metabolism of individual species involved. However, the nature in which an individual species' physiology is influenced by cross-feeding and the importance of those physiological changes for the mutualism have received little attention. We previously developed a genetically tractable coculture to study bacterial mutualisms. The coculture consists of fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris In this coculture, E. coli anaerobically ferments sugars into excreted organic acids as a carbon source for R. palustris In return, a genetically engineered R. palustris strain constitutively converts N₂ into NH₄⁺, providing E. coli with essential nitrogen. Using transcriptome sequencing (RNA-seq) and proteomics, we identified transcript and protein levels that differ in each partner when grown in coculture versus monoculture. When in coculture with R. palustris, E. coli gene expression changes resembled a nitrogen starvation response under the control of the transcriptional regulator NtrC. By genetically disrupting E. coli NtrC, we determined that a nitrogen starvation response is important for a stable coexistence, especially at low R. palustris NH₄⁺ excretion levels. Destabilization of the nitrogen starvation regulatory network resulted in variable growth trends and, in some cases, extinction. Our results highlight that alternative physiological states can be important for survival within cooperative cross-feeding relationships.IMPORTANCE Mutualistic cross-feeding between microbes within multispecies communities is widespread. Studying how mutualistic interactions influence the physiology of each species involved is important for understanding how mutualisms function and persist in both natural and applied settings. Using a bacterial mutualism consisting of Rhodopseudomonas palustris and Escherichia coli growing cooperatively through bidirectional nutrient exchange, we determined that an E. coli nitrogen starvation response is important for maintaining a stable coexistence. The lack of an E. coli nitrogen starvation response ultimately destabilized the mutualism and, in some cases, led to community collapse after serial transfers. Our findings thus inform on the potential necessity of an alternative physiological state for mutualistic coexistence with another species compared to the physiology of species grown in isolation.

Bacteremia caused by the photosynthetic environmental bacterium Rhodopseudomonas

We report a case of persistent Rhodopseudomonas bacteremia in a patient two months after an allogeneic bone marrow transplant for acute myeloid leukemia. The bacteremia persisted until IV catheter removal. To our knowledge, this is the first report of Rhodopseudomonas causing infection in humans.

A Rhizobiales-Specific Unipolar Polysaccharide Adhesin Contributes to Rhodopseudomonas palustris Biofilm Formation across Diverse Photoheterotrophic Conditions

Bacteria predominantly exist as members of surfaced-attached communities known as biofilms. Many bacterial species initiate biofilms and adhere to each other using cell surface adhesins. This is the case for numerous ecologically diverse Alphaprotebacteria, which use polar exopolysaccharide adhesins for cell-cell adhesion and surface attachment. Here, we show that Rhodopseudomonas palustris, a metabolically versatile member of the alphaproteobacterial order Rhizobiales, contains a functional unipolar polysaccharide (UPP) biosynthesis gene cluster. Deletion of genes predicted to be critical for UPP biosynthesis and export abolished UPP production. We also found that R. palustris uses UPP to mediate biofilm formation across diverse photoheterotrophic growth conditions, wherein light and organic substrates are used to support growth. However, UPP was less important for biofilm formation during photoautotrophy, where light and CO₂ support growth, and during aerobic respiration with organic compounds. Expanding our analysis beyond R. palustris, we examined the phylogenetic distribution and genomic organization of UPP gene clusters among Rhizobiales species that inhabit diverse niches. Our analysis suggests that UPP is a conserved ancestral trait of the Rhizobiales but that it has been independently lost multiple times during the evolution of this clade, twice coinciding with adaptation to intracellular lifestyles within animal hosts.

IMPORTANCE

Bacteria are ubiquitously found as surface-attached communities and cellular aggregates in nature. Here, we address how bacterial adhesion is coordinated in response to diverse environments using two complementary approaches. First, we examined how Rhodopseudomonas palustris, one of the most metabolically versatile organisms ever described, varies its adhesion to surfaces in response to different environmental conditions. We identified critical genes for the production of a unipolar polysaccharide (UPP) and showed that UPP is important for adhesion when light and organic substrates are used for growth. Looking beyond R. palustris, we performed the most comprehensive survey to date on the conservation of UPP biosynthesis genes among a group of closely related bacteria that occupy diverse niches. Our findings suggest that UPP is important for free-living and plant-associated lifestyles but dispensable for animal pathogens. Additionally, we propose guidelines for classifying the adhesins produced by various Alphaprotebacteria, facilitating future functional and comparative studies.

Light-driven carbon dioxide reduction to methane by nitrogenase in a photosynthetic bacterium

Nitrogenase is an ATP-requiring enzyme capable of carrying out multielectron reductions of inert molecules. A purified remodeled nitrogenase containing two amino acid substitutions near the site of its FeMo cofactor was recently described as having the capacity to reduce carbon dioxide (CO2) to methane (CH4). Here, we developed the anoxygenic phototroph, Rhodopseudomonas palustris, as a biocatalyst capable of light-driven CO2 reduction to CH4 in vivo using this remodeled nitrogenase. Conversion of CO2 to CH4 by R. palustris required constitutive expression of nitrogenase, which was achieved by using a variant of the transcription factor NifA that is able to activate expression of nitrogenase under all growth conditions. Also, light was required for generation of ATP by cyclic photophosphorylation. CH4 production by R. palustris could be controlled by manipulating the distribution of electrons and energy available to nitrogenase. This work shows the feasibility of using microbes to generate hydrocarbons from CO2 in one enzymatic step using light energy.

A polymorphism in the oxygen-responsive repressor PpsR2 confers a growth advantage to Rhodopseudomonas palustris under low light

The purple nonsulfur bacterium Rhodopseudomonas palustris grows aerobically using oxidative phosphorylation or anaerobically using photophosphorylation. The oxygen-responsive transcription regulator, PpsR2, regulates the transition to a phototrophic lifestyle by repressing transcription of photosynthesis genes during aerobic growth. Whereas most R. palustris strains have an arginine (Arg) at position 439 in the helix-turn-helix DNA-binding domain of this protein, some strains, including the well-studied strain CGA009, have a cysteine (Cys) at this position. Using allelic exchange, we found that the Cys439 in PpsR2 resulted in increased pigmentation and photosynthetic gene expression under both aerobic and anaerobic conditions. The Cys439 substitution also conferred a growth advantage to R. palustris at low light intensities. This indicates that variation in the PpsR2 protein results in R. palustris strains that have two different thresholds for derepressing photosynthesis genes in response to oxygen and light.

Skatole remediation potential of Rhodopseudomonas palustris WKU-KDNS3 isolated from an animal waste lagoon

Skatole (3MI) is a major contributor to the malodor emission resulting from ruminant and human faeces. The remediation of malodor has been a major challenge for the animal production industry. In this investigation, a pure culture of purple nonsulphur bacterium capable of degrading 3MI was isolated from a swine waste lagoon using an enrichment technique and identified as Rhodopseudomonas palustris WKU-KDNS3 based on 16S rRNA analysis and UV-visible spectroscopy. The cell structure of the organism was confirmed by transmission electron microscopy. Growth profile and 3MI removal pattern were determined using media supplemented with 0.1 μmol 3MI under short-term and long-term aerobic growth conditions. The organism grew on 3MI media as luxuriantly as control (without 3MI). Growth of R. palustris WKU-KDNS3 demonstrated a significant reduction in the level of 3MI (>48%) in 72 h. The level of 3MI dropped further by >93% of the total concentration present in the medium in 21 days. Skatole remediation potential of R. palustris WKU-KDNS3 can be judiciously utilized in various animal and industrial waste treatment systems.

SIGNIFICANCE AND IMPACT OF THE STUDY

Odour pollution is a serious environmental problem, particularly in the agriculture industry, and technologies based on chemical remediation are less effective and cost prohibitive. In this study, the newly isolated Rhodopseudomonas palustris strain WKU-KDNS3 causes biodegradation of 3-methylindole (skatole), which is one of the most offensive odorants present in wastewater lagoons. Aerobic degradation of this widely spread aromatic pollutant by Rhodopseudomonas strain is a significant finding that enhances the present understanding about metabolic versatility of purple photosynthetic nonsulphur bacteria. The remediation potential of R. palustris WKU-KDNS3 can also be gainfully utilized in various waste treatment facilities.