Coupled carbon, sulfur and nitrogen cycles of mixotrophic growth of Pseudomonas sp. C27 under denitrifying sulfide removal conditions

Mixotrophic bacteria for environmental detoxification of contaminated waste and wastewater

Mixotrophic bacteria provide a desirable alternative to the use of classical heterotrophic or chemolithoautotrophic bacteria in environmental technology, particularly under limiting nutrients conditions. Their bi-modal ability of adapting to inorganic or organic carbon feed and sulfur, nitrogen, or even heavy metal stress conditions are attractive features to achieve efficient bacterial activity and favorable operation conditions for the environmental detoxification or remediation of contaminated waste and wastewater. This review provides an overview on the state of the art and summarizes the metabolic traits of the most promising and emerging non-model mixotrophic bacteria for the environmental detoxification of contaminated wastewater and waste containing excess amounts of limiting nutrients. Although mixotrophic bacteria usually function with low organic carbon sources, the unusual capabilities of mixotrophic electroactive exoelectrogens and electrotrophs in bioelectrochemical systems and in microbial electrosynthesis for accelerating simultaneous metabolism of inorganic or organic C and N, S or heavy metals are reviewed. The identification of the mixotrophic properties of electroactive bacteria and their capability to drive mono- or bidirectional electron transfer processes are highly exciting and promising aspects. These aspects provide an appealing potential for unearthing new mixotrophic exoelectrogens and electrotrophs, and thus inspire the next generation of microbial electrochemical technology and mixotrophic bacterial metabolic engineering. KEY POINTS: • Mixotrophic bacteria efficiently and simultaneously remove C and N, S or heavy metals. • Exoelectrogens and electrotrophs accelerate metabolism of C and N, S or heavy metals. • New mixotrophic exoelectrogens and electrotrophs should be discovered and exploited.

Nitrate removal from low C/N wastewater at low temperature by immobilized Pseudomonas sp. Y39-6 with versatile nitrate metabolism pathways

For solving the challenge in nitrate removal from low C/N wastewater at low temperature, Pseudomonas sp. Y39-6 was isolated and used in nitrate removal. It showed aerobic-heterotrophic denitrification with rate of 1.77 ± 0.31 mg/L·h and unusual aerobic-autotrophic nitrate removal (rate of 0.324 mg/L·h). The aerobic-autotrophic nitrate removal mechanisms were deep investigated by analyzing the nitrate removal process and genomic information. At aerobic-autotrophic condition, the strain Y39-6 could assimilate nitrate to amino acid (NO₃^- + PHA + CO₂ → C₅H₇O₂N) with the carbon source from Polyhydroxyalkanoic acid (PHA) degradation and CO₂ fixation. Flagella motivation, swarming activity and extracellular polymeric substances (EPS) production regulated Pseudomonas sp. Y39-6 forming biofilm. Carriers immobilized with Pseudomonas sp. Y39-6 were used in moving bed biofilm reactor (MBBR) and achieved 24.83% nitrate removal at C/N < 1 and 4 °C. Results of this study provided a practical way for nitrogen removal from low C/N wastewater in cold region.

Manipulating denitrifying sulfide removal of Pseudomonas sp. C27 with nitrite as sole nitrogen source: Shotgun proteomics analysis

Pseudomonas sp. C27 can effectively conduct denitrifying sulfide removal (DSR) reactions via autotrophic denitrification, heterotrophic denitrification and coupled-cycle pathway. This study is the first to cultivate strain C27 using nitrite as the sole nitrogen source, and to conduct shotgun proteomics analysis and investigate the characteristics of DSR growth of strain C27 with nitrate or nitrite as sole nitrogen source. Shotgun proteomics analysis identified a total of 42 specially expressed proteins of C27 in the nitrite medium, based on which, together with chemical analysis data, a supplementary pathway of sulfur metabolism for C27 from sulfate to thiosulfate via intermediate adenosine-5'-phosphosulfate and 3'-phosphoadenosine-5'-phosphosulfate was proposed. Based on the newly revised scheme, the use of nitrite as sole nitrogen source expands the assessible regime of DSR reactions by C27 and provides the potential to recover renewable chemicals such as pyruvate and succinate from the coupled-cycle pathway.

Different maturities drive proteomic and metabolomic changes in Chinese black truffle

Chinese black truffle (Tuber indicum) is rich in nutrition. However, commercial interests lead to the aroma components and nutrients of T. indicum being greatly affected by overexploitation without consideration of their maturity. This study investigated the proteomic and metabolomic profiles of truffle fruiting bodies at different maturities using a meta-proteomic approach. Among the 3007 identified proteins, the most up-expressed protein in the mature ascocarps was involved in the peptidyl-diphthamide biosynthetic process, while thiamine metabolism was the most differentially expressed pathway. Furthermore, a total of 54 metabolites identified upon LC-MS differed significantly, with 30 being up-expressed in the mature ascocarps, including organic acids, carnitine substances and polysaccharides. Additionally, the ash, protein, fat, crude fiber and total sugar contents were all higher in the mature ascocarps. Overall, our findings reveal that mature truffles have a higher nutritional value, providing a basis for further exploring protein functionality of T. indicum at different maturities.

Application of activated sludge for odor control in wastewater treatment plants: Approaches, advances and outlooks

Odors from wastewater treatment plants (WWTPs) have attracted extensive attention and stringent environmental standards are more widely adopted to reduce odor emissions. Biological odor treatment methods have broader applications than the physical and chemical counterparts as they are environment-friendly, cost-effective and generate low secondary wastes. The aqueous activated sludge (AS) processes are among the most promising approaches for the prevention or end-of-pipe removal of odor emissions and have the potential to simultaneously treat odor and wastewater. However, AS deodorization biotechnologies in WWTPs still need to be further systematically summarized and categorized while in-depth discussions on the characteristics and underlying mechanisms of AS deodorization process are still lacking. Recently, considerable studies have been reported to elucidate the microbial metabolisms in odor control and wastewater treatment. This paper reviews the fundamentals, characteristics, advances and field experiences of three AS biotechnologies for odor treatment in WWTPs, i.e., AS recycling, microaeration in AS digester and AS diffusion. The underlying deodorization mechanisms of typical odors have been revealed through the summary of recent advances on multi-element conversions, metabolic interactions of bacteria, microscopic characterization and identification of functional microorganisms. Future research aspects to advance the emerging deodorization AS process, such as deodorization mechanisms, simultaneous odor and water treatment, synergistic treatment with other air emissions, are discussed.

Structural and metabolic performance of p-cresol producing microbiota in different carbon sources

p-Cresol (PC) is a potential off-flavor and carcinogenic compound that affects food flavor and safety. However, controlling the production of PC when making fermented food is hindered by a lack of knowledge of the microbial diversity and the growth requirements of the microbiota that produce PC. To address this, the present study used three media with selected carbon sources (glucose, ethanol and lactic acid) to explore the microbial origin of PC and to determine the preferred carbon source for the PC-producing microbiota in the pit mud of the strong-aroma type Baijiu. The results showed that the different carbon sources affected the microbial structure, especially of the PC-producing microbiota. Glucose led to the highest production of PC and lactic acid to the lowest. The production of PC was significantly correlated (p < 0.05, |ρ| > 0.6) with Dorea, Sporanaerobacter, Tepidimicrobium, Tissierella Soehngenia, Clostridium and Sedimentibacter in the glucose medium; with Proteiniborus, Ruminococcus and Sporanaerobacter in the ethanol medium; and with Lutispora and Tepidimicrobium in the lactic acid medium. Multiphasic metabolite target analysis further indicated that the PC-producing microbiota could also metabolize flavor compounds. Lactic acid could inhibit the production of PC and ensure that the microbiota produced the appropriate flavor compounds during culture. Collectively, Dorea, Sporanaerobacter, Tepidimicrobium, Tissierella_Soehngenia, Clostridium, Sedimentibacter, Proteiniborus, Ruminococcus and Lutispora were identified as potential PC producers in three media with glucose preferred as the carbon source. These findings provide a perspective on the microbiota and carbon source preference for ultimately improving the quality of distilled alcoholic beverage.

Co-metabolic substrates enhanced biological nitrogen removal from cellulosic ethanol biorefinery wastewater using aerobic granular sludges

The effect of different co-metabolic substrates (glucose, acetic acid and ethanol) on aerobic granular sludge treating cellulose ethanol wastewater was investigated using sequencing batch reactors. The efficiencies of the three substrates in removing chemical oxygen demand were respectively 18.87%, 28.88% and 27.99%, all of which were remarkably higher than without co-metabolic substrates, indicating that co-metabolic substrates can promote the degradation of the refractory substances. With acetic acid as the co-metabolic substrate, the removal amount of ammonium nitrogen and nitrate nitrogen was greater than glucose and ethanol used. The nitrogen removals by the three co-metabolic substrates were 53.18%, 72.15%, 69.36%, respectively, which were 1.4, 1.8, and 1.6 times the removal without co-metabolic substrates. Fluorescence in situ hybridization results showed that the proportion of ammonium-oxidizing bacteria in the granular sludge was greater than that of nitrite-oxidizing bacteria after adding co-metabolic substrates, and the order was acetic acid > ethanol > glucose.

Nitrogen and sulfur metabolisms of Pseudomonas sp. C27 under mixotrophic growth condition

Pseudomonas sp. C27 is a facultative autotrophic bacterium that can grow mixotrophically to undergo denitrifying sulfide removal (DSR) reactions with both organic matters and sulfide as electron donors. A detailed understanding of how the C27 strain simultaneously removes nitrogen, sulfur and carbon from water is critical for optimal DSR process design and implementation. This study is the first to reveal the pathways of nitrogen and sulfur metabolisms, identifying a total of 47 proteins that are related to the nitrogen metabolism and seven proteins to the sulfur metabolism of strain C27 using iTRAQ and LC-MS/MS techniques. The proposed pathway of nitrogen metabolism for strain C27 from external nitrate to nitrogen gas and phosphate with a coupled ammonia cycle is based on the identified proteins, and suggests that nitrate was not essential for nitrogen metabolism and could be replaced by nitrite as the sole nitrogen source for C27.

Dissecting the proteome dynamics of the salt stress induced changes in the leaf of diploid and autotetraploid Paulownia fortunei

Exposure to high salinity can trigger acclimation in many plants. Such an adaptative response is greatly advantageous for plants and involves extensive reprogramming at the molecular level. Acclimation allows plants to survive in environments that are prone to increasing salinity. In this study, diploid and autotetraploid Paulownia fortunei seedlings were used to detect alterations in leaf proteins in plants under salt stress. Up to 152 differentially abundant proteins were identified by Multiplex run iTRAQ-based quantitative proteomic and LC-MS/MS methods. Bioinformatics analysis suggested that P. fortunei leaves reacted to salt stress through a combination of common responses, such as induced metabolism, signal transduction, and regulation of transcription. This study offers a better understanding of the mechanisms of salt tolerance in P. fortunei and provides a list of potential target genes that could be engineered for salt acclimation in plants, especially trees.

Effect of aspartic acid and glutamate on metabolism and acid stress resistance of Acetobacter pasteurianus

Background

Acetic acid bacteria (AAB) are widely applied in food, bioengineering and medicine fields. However, the acid stress at low pH conditions limits acetic acid fermentation efficiency and high concentration of vinegar production with AAB. Therefore, how to enhance resistance ability of the AAB remains as the major challenge. Amino acids play an important role in cell growth and cell survival under severe environment. However, until now the effects of amino acids on acetic fermentation and acid stress resistance of AAB have not been fully studied.

Results

In the present work the effects of amino acids on metabolism and acid stress resistance of Acetobacter pasteurianus were investigated. Cell growth, culturable cell counts, acetic acid production, acetic acid production rate and specific production rate of acetic acid of A. pasteurianus revealed an increase of 1.04, 5.43, 1.45, 3.30 and 0.79-folds by adding aspartic acid (Asp), and cell growth, culturable cell counts, acetic acid production and acetic acid production rate revealed an increase of 0.51, 0.72, 0.60 and 0.94-folds by adding glutamate (Glu), respectively. For a fully understanding of the biological mechanism, proteomic technology was carried out. The results showed that the strengthening mechanism mainly came from the following four aspects: (1) Enhancing the generation of pentose phosphates and NADPH for the synthesis of nucleic acid, fatty acids and glutathione (GSH) throughout pentose phosphate pathway. And GSH could protect bacteria from low pH, halide, oxidative stress and osmotic stress by maintaining the viability of cells through intracellular redox equilibrium; (2) Reinforcing deamination of amino acids to increase intracellular ammonia concentration to maintain stability of intracellular pH; (3) Enhancing nucleic acid synthesis and reparation of impaired DNA caused by acid stress damage; (4) Promoting unsaturated fatty acids synthesis and lipid transport, which resulted in the improvement of cytomembrane fluidity, stability and integrity.

Conclusions

The present work is the study to show the effectiveness of Asp and Glu on metabolism and acid stress resistance of A. pasteurianus as well as their working mechanism. The research results will be helpful for development of nutrient salts, the optimization and regulation of high concentration of cider vinegar production process.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0717-6) contains supplementary material, which is available to authorized users.

Genome of Paulownia (Paulownia fortunei) illuminates the related transcripts, miRNA and proteins for salt resistance

Polyploidy in plants can bestow long-term evolutionary flexibility and resistance to biotic and abiotic stresses. The upstream activation mechanisms of salt response remain unknown. Here we integrated transcriptome, miRNA and proteome data to describe the link between abscisic acid (ABA)-effectors and salt resistance against the background of Paulownia genome. Combing GO and KEGG pathway annotation of differentially expressed genes and proteins, as well as differentially expressed miRNA, these results reflect endogenous signal ABA activate the downstream effectors, such as ion channel effectors and oxido-reduction effectors, to maintain the homeostasis of Paulownia’s growth. The cascaded metabolic network involved ABA biosynthesis, signaling transduction and the response of effectors. Our results will contribute to a comprehensive understanding of the genetic basis of salt tolerance, which may help to expand the available arable land for P. fortunei cultivation.

Influence of perfluorooctanoic acid on proteomic expression and cell membrane fatty acid of Escherichia coli

Perfluorooctanoic acid (PFOA) has received an increasing attention in the agricultural and food industries due to its risk to human health. To facilitate the development of novel biomarkers of Escherichia coli against PFOA through multi-omics technologies, and to reveal the resistance mechanism of E. coli against PFOA at protein levels, the interactions among pollutant stress, protein expression and cell metabolism was investigated by using iTRAQ-based quantitative proteomic analysis. The results revealed that the 63 up-regulated proteins mainly involved in tricarboxylic acid cycle, glyoxylate and dicarboxylate metabolism and fatty acid biosynthesis, whereas, the 69 down-regulated proteins related to oxidative phosphorylation, pyruvate metabolism and the cell cycle-caulobacter pathway, were also associated with the increase of membrane permeability, excessive expenditure of ATP, disruption of fatty acid biosynthesis under PFOA stress. The results provide novel insights into the influence mechanisms of PFOA on fatty acid and protein networks.

iTRAQ-Based Proteomics Identification of Serum Biomarkers of Two Chronic Hepatitis B Subtypes Diagnosed by Traditional Chinese Medicine

Background. Chronic infection with hepatitis B virus (HBV) is a leading cause of cirrhosis and hepatocellular carcinoma. By traditional Chinese medicine (TCM) pattern classification, damp heat stasis in the middle-jiao (DHSM) and liver Qi stagnation and spleen deficiency (LSSD) are two most common subtypes of CHB. Results. In this study, we employed iTRAQ proteomics technology to identify potential serum protein biomarkers in 30 LSSD-CHB and 30 DHSM-CHB patients. Of the total 842 detected proteins, 273 and 345 were differentially expressed in LSSD-CHB and DHSM-CHB patients compared to healthy controls, respectively. LSSD-CHB and DHSM-CHB shared 142 upregulated and 84 downregulated proteins, of which several proteins have been reported to be candidate biomarkers, including immunoglobulin (Ig) related proteins, complement components, apolipoproteins, heat shock proteins, insulin-like growth factor binding protein, and alpha-2-macroglobulin. In addition, we identified that proteins might be potential biomarkers to distinguish LSSD-CHB from DHSM-CHB, such as A0A0A0MS51_HUMAN (gelsolin), PON3_HUMAN, Q96K68_HUMAN, and TRPM8_HUMAN that were differentially expressed exclusively in LSSD-CHB patients and A0A087WT59_HUMAN (transthyretin), ITIH1_HUMAN, TSP1_HUMAN, CO5_HUMAN, and ALBU_HUMAN that were differentially expressed specifically in DHSM-CHB patients. Conclusion. This is the first time to report serum proteins in CHB subtype patients. Our findings provide potential biomarkers can be used for LSSD-CHB and DHSM-CHB.

Metagenomic analysis of microbiota structure evolution in phytoremediation of a swine lagoon wastewater

Pytoremediation was studied in this project to treat swine manure lagoon wastewater characteristic of high concentrations of organic carbon, ammonium (N) and phosphorus (P). The impacts of introducing exogenous microalgae Chlorella into the lagoon wastewater on the removal of major nutrients and the transformation of the native wastewater microbiota structure were explored under two phytoremediation modes (shake flask and CO2-air bubbling). The results showed that the inoculation of microalgae could significantly enhance N and P removal. Metagenomic analysis of the native microbiota composition in the wastewater affected by algae inoculation revealed that a substantial population of algicidal bacteria was developed in the shake flask system, while in the CO2-air bubbling system, a niche for more mutualistic bacteria was created, which benefited the maximal algal growth with the simultaneous optimal N and P removal. To our knowledge, this study presents, the first reported case of applying metagenomic approach to a phytoremediation system treating real swine lagoon wastewater.

Quantitative Proteomic and Transcriptomic Study on Autotetraploid Paulownia and Its Diploid Parent Reveal Key Metabolic Processes Associated with Paulownia Autotetraploidization

Polyploidy plays a very important role in speciation and plant evolution by way of genomic merging and doubling. In the process of polyploidy, rapid genomic, and transcriptomic changes have been observed and researched. However, proteomic divergence caused by the effects of polyploidization is still poorly understood. In the present study, we used iTRAQ coupled with mass spectrometry to quantitatively analyze proteomic changes in the leaves of autotetraploid Paulownia and its diploid parent. A total of 2963 proteins were identified and quantified. Among them, 463 differentially abundant proteins were detected between autotetraploid Paulownia and its diploid parent, and 198 proteins were found to be non-additively abundant in autotetraploid Paulownia, suggesting the presence of non-additive protein regulation during genomic merger and doubling. We also detected 1808 protein-encoding genes in previously published RNA sequencing data. We found that 59 of the genes that showed remarkable changes at mRNA level encoded proteins with consistant changes in their abundance levels, while a further 48 genes that showed noteworthy changes in their expression levels encoded proteins with opposite changes in their abundance levels. Proteins involved in posttranslational modification, protein turnover, and response to stimulus, were significantly enriched among the non-additive proteins, which may provide some of the driving power for variation and adaptation in autopolyploids. Quantitative real-time PCR analysis verified the expression patterns of related protein-coding genes. In addition, we found that the percentage of differentially abundant proteins that matched previously reported differentially expressed genes was relatively low.

Denitrifying sulfide removal process on high-tetracycline wastewater

Antibiotics wastewater from tetracycline (TC) production unit can have high levels of chemical oxygen demand, ammonium and sulfate and up to a few hundreds of milligrams per liter of TC. Denitrifying sulfide removal (DSR) process is set up for simultaneously removal of sulfur, carbon and nitrogen from waters. The DSR process was for the first time studied for treating TC wastewaters. The TC stress has no adverse effects on removal rates of nitrate and acetate; however, it moderately deteriorated sulfide removal rates and S(0) accumulation rates when the concentration is higher than 100mgL(-1) TC. The Thauera sp., and Pseudomonas sp. present the heterotrophs and Sulfurovum sp. presented the autotroph for the present DSR reactions. The high tolerance of TC stress by the tested consortium was explained by the excess production of extracellular polymeric substances at high TC concentration, which can bind with TC for minimizing its inhibition effects.

Integration of the proteome and transcriptome reveals multiple levels of gene regulation in the rice dl2 mutant

Leaf vascular system differentiation and venation patterns play a key role in transporting nutrients and maintaining the plant shape, which is an important agronomic trait for improving photosynthetic efficiency. However, there is little knowledge about the regulation of leaf vascular specification and development. Here we utilized the rice midribless mutant (dl2) to investigate the molecular changes in transcriptome and proteome profiles during leaf vascular specification and differentiation. Using isobaric tags for relative and absolute quantification (iTRAQ) with digital gene expression (DGE) techniques, a nearly complete catalog of expressed protein and mRNA was acquired. From the catalog, we reliably identified 3172 proteins and 9,865,230 tags mapped to genes, and subsets of 141 proteins and 98 mRNAs, which were differentially expressed between the dl2 mutant and wild type. The correlation analysis between the abundance of differentially expressed mRNA and DEPs (differentially expressed proteins) revealed numerous discordant changes in mRNA/protein pairs and only a modest correlation was observed, indicative of divergent regulation of transcription and translational processes. The DEPs were analyzed for their involvement in biological processes and metabolic pathways. Up- or down- regulation of some key proteins confirmed that the physiological process of vascular differentiation is an active process. These key proteins included those not previously reported to be associated with vascular differentiation processes, and included proteins that are involved in the spliceosome pathway. Together, our results show that the developmental and physiological process of the leaf vascular system is a thoroughly regulated and complicated process and this work has identified potential targets for genetic modification that could be used to regulate the development of the leaf vasculature.

Accessible mixotrophic growth of denitrifying sulfide removal consortium

Nitrate, sulfide and organic matters in wastewaters can be removed simultaneously by denitrifying sulfide removal (DSR) process. Complicated interactions between different microbial groups in the DSR medium render the process design and control difficult to implement. A consortium with DSR activity was grown mixotrophically at varying concentrations of nitrate, acetate or ammonium. The kinetic diagram previously proposed was adopted to quantitatively represent DSR performance with accessible regimes of the diagram being identified. Example on the use of the so-yielded accessible regime was provided.

Denitrifying sulfide removal by Pseudomonas sp. C27 at excess carbon supply: mechanisms

Pseudomonas sp. C27 can effectively conduct mixotrophic denitrifying sulfide removal (DSR) reactions using both organic matters and sulfide as electron donors. This study conducted DSR tests using C27 and quantitatively analyzed the protein abundances at C/N=1.26, 1.63 and 3.0. At C/N=1.26, C27 principally adopted autotrophic denitrification pathway in DSR reaction. As C/N ratio was increased to 1.63, C27 enhanced heterotrophic denitrification pathway for removing nitrous compounds. As the C/N ratio was further increased to 3.0, C27 accelerated metabolism via coupled-cycles pathway. The C/N ratio for coupled-cycles pathway was estimated ranging 2.0-2.3 in the studied medium. Optimal C/N ratio of traditional DSR processes ranged 1.05-1.26. With the coupled-cycles pathway, the accessible C/N/S regime for C27 on DSR reactions is enlarged. Minor revision of the coupled-cycles pathway considering production of ammonium step was made.