Syntrophic Propionate Degradation in Anaerobic Digestion: a Review

Total Page:16

File Type:pdf, Size:1020Kb

Syntrophic Propionate Degradation in Anaerobic Digestion: a Review INTERNATIONAL JOURNAL OF AGRICULTURE & BIOLOGY ISSN Print: 1560–8530; ISSN Online: 1814–9596 12–315/MFA/2012/14–5–843–850 http://www.fspublishers.org Review Article Syntrophic Propionate Degradation in Anaerobic Digestion: A Review JIANZHENG LI1, QIAOYING BAN, LIGUO ZHANG AND AJAY KUMAR JHA State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, China 1Corresponding author’s e-mail: [email protected] ABSTRACT Degradation of propionate is a central issue for improving performance of an anaerobic digestion system, because propionate is an intermediate product, which is generally accumulated in anaerobic digesters. Many factors containing pH, temperature, volatile fatty acids, hydrogen partial pressure, and toxins would inhibit the biodegradation of propionate under anaerobic conditions. Propionate can be oxidized only if a syntrophic association is carried out by propionate-oxidizing bacteria and hydrogen-consumming bacteria. As propionate degraders, syntrophic propionate-oxidizing bacteria (SPOB) play an important role in anaerobic food chain and anaerobic global carbon cycles. However, these microorganisms are often difficult to be isolated and cultured as result of extremely fastidious metabolism type. To date, only ten species were identified as SPOB, which belonged to class Deltaproteobacteria or Firmicutes. Most identified SPOB degrade propionate through methylmalonyl coenzyme A pathway (MMC) pathway and genomic information indicated the catabolic pathways are controlled by ecological factors and/or global cellular conditions. Further investigation is needed on the response mechanism of SPOB to the environmental factors. To prevent anaerobic digestor from propionate accumulation, it is important to detect SPOB in time and forecast the accumulation of propionate with mathematical models. © 2012 Friends Science Publishers Key Words: Anaerobic digestion; Propionate degradation; Syntrophic propionate-oxidizing bacteria; Ecophysiology; Phylogeny INTRODUCTION (Kaspar & Wuhrmann, 1978; Van Lier et al., 1996; Shah et al., 2009; Ghasimi et al., 2009; Liu et al., 2010). Anaerobic Anaerobic digestion technology was paid attention by oxidation of propionate is affected by many factors, more researchers, because of the removal of organic including pH, temperature, hydrogen partial pressure, pollutants in solid waste and wastewater and simultaneously volatile fatty acids (VFAs), reactor configuration and produces methane as an energy resource (Wang et al., 2004; organic compounds (Kim et al., 2002; Dhaked et al., 2003; Mahmood et al., 2011). It is complex with a number of Siegert & Banks, 2005; Liu et al., 2006). sequential and parallel steps that are carried out by mainly The biodegradation of propionate depends on four groups of microorganisms including primary syntrophy between propionate-oxidizing bacteria and fermenting bacteria, syntrophic acetogens, homoacetogens hydrogenotrophic methanogenic archaea in methanogenic and methanogenic archaea (Kosaka et al., 2006; Jha et al., environments (Worm et al., 2011). The syntrophic 2011). Each group of microbes have specific metabolic metabolism with other bacteria result in the pure cultivation functions (Fig. 1). Propionate is an important intermediate of syntrophic propionate-oxidizing bacteria (SPOB) is very during anaerobic digestion of organic polymers. Its difficult. To date, only ten SPOB species have been isolated degradation into acetate and H2/CO2 (and then to CH4) and identified (Table II). The analysis of propionate- accounts for 6% ~ 35% in the total methanogenesis oxidizing pathways provides information about these (Glissmann & Conrad, 2000). However, the oxidation of microorganisms in depth, including intermediates, enzymes propionate is energetically unfavorable with a standard and energy conservation. Furthermore, the genomes of change in Gibbs free energy (ΔG°′) of +76 kJ per mol several representative bacteria present the prospects to reaction as illustrated in Table I (Müller et al., 2010). assess their unexplored functions (McInerney et al., 2007; Thermodynamically, propionate is more difficult to be Kosaka et al., 2008). anaerobically oxidized than butyrate, lactate and ethanol. So, Propionate is always produced in anaerobic digestion it is usually accumulated in an anaerobic digester, even and oxidized only if a syntrophic association is carried out resulting in failure of the anaerobic digestion process by propionate-oxidizing bacteria and hydrogen- To cite this paper: Li, J., Q. Ban, L. Zhang and Jha, A.K. 2012. Syntrophic propionate degradation in anaerobic digestion: a review. Int. J. Agric. Biol., 14: 843–850 LI et al. / Int. J. Agric. Biol., Vol. 14, No. 5, 2012 consumming bacteria (Chen et al., 2005; de Bok et al., 2005; Table I: Reactions involved in syntrophic propionate Ghasimi et al., 2009). It is accumulated in anaerobic metabolism digestion process whenever, there is a change in organic loading rate, influent pH and temperature, etc., because the Reaction ΔG°′ syntrophic propionate-oxidizing is more difficult than other (kJ mol-1) Proton-reducing bacteria intermediate products such as butyrate and ethanol (Müller – – Propionate + 2 H2O → acetate + CO2 + 3 H2 +76.0 et al., 2010). Thus, degradation of propionate is very - + Propionate- + 2 H2O + 2 CO2 →Acetate- + 3 HCOO + 3 H +65.3 important for improving performance of anaerobic digestion Methanogens process. However, only a few species have been obtained by 4 H2 + CO2 → CH4 + 2 H2O –131.7 - + 4 HCOO + 4 H → CH4 + 3 CO2 + 2 H2O –144.5 now, leading to a lack in deep understanding of syntrophic – Acetate + H+ → CO2 + CH4 –36.0 propionate degradation. Based on the analysis of effect of ΔG°′ (Standard Gibbs free energy change): concentration of 1 M, pH 7.0 propionate accumulation on the performance of anaerobic and T = 25°C (Müller et al., 2010) digestion, main factors affecting its biodegradation were discussed in this work. The currently isolated SPOB and Fig. 1: Anaerobic food chain of the conversion of their ecophysiological, phylogenetic and genomics were organic matter to methane. The major microbial focused on as well. This summary should help to isolate groups catalyzing the reactions are in oval. SPOB: more SPOB and reveal the biochemical mechanism in Syntrophic propionate-oxidizing bacteria, SBOB: propionate oxidation process. syntrophic butyrate-oxidizing bacteria (Modified from Effect of propionate accunulation on anaerobic digestion: Liu and Whitman, 2008) Under high operational performance, the conversion rate is proportional to the generation rate of the intermediate Organic polymers products, so these compounds are hardly accumulated. However, overloading, toxicity and process parameters fluctuation disturb the process and consequently cause Heterotrophic anaerobes process instable. The process imbalance generally results in accumulation of VFAs including propionate (Pullammanppallil et al., 2001). The degradation of Monomers or oligomers propionate into acetate is considered as one rate limiting step in anaerobic digestion system (Amani et al., 2011a). Furthermore, its high concentration (> 3000 mg L-1) may Heterotrophic anaerobes cease the fermentation process (Boone & Xun, 1987). An increase of propionate has been observed before the failure Acetogens of anaerobic digesters in treating swine, municipal sludge, Short fatty acids, Alcohols and food processing water (Kaspar & Wuhrmann, 1978). Several researchers presented that propionate Syntrophs (SPOB, SBOB) accumulation affect growth, diversity and activity of the methanogens. One previous research suggested that a lot of methanogens was influenced when the propionate -1 concentration is as low as 1500-2220 mg L and 2 orders of H +CO magnitude of methanogens were decreased at the 2 2 Homoacetogenic Formate Acetate concentration of propionate above 5920 mg L-1 (Barredo & bacteria Evison, 1991). Another research also indicated that methane Aceticlastic generation was decreased by 62~78% compared with the Hydrogentrophic -1 methanogens control at neutral pH when propionate was 5000 mg L methanogens (Hajarnis & Ranade, 1994). The inhibition extent CH +CO dramatically increased when the pH was decreased, 4 2 indicating that undissociated propionate is the most toxic. In addition, Dhaked et al. (2003) found a two-log reduction in microbial growth and metabolism. Dhaked et al. (2003) methanogenic counts in the slurry fermentation at pH 6.0 or reported that the propionate anaerobic conversion is much 7.0 after propionate of 15000 mg L-1 was added into slurry. faster at neutral or weak alkaline pH (7 to 8) than at weak They also found that methane content of biogas decreased acid (pH 6). Pure culture of SPOB or co-culture of SPOB with the increase in propionate concentration (Dhaked et al., and methanogens grow in a neutral environment with the 2003). pH ranged from 6 to 8.8 (Table II). We found that Factors Affecting Syntrophic Propionate Degradation propionate degradation was much faster at pH 7.0 to 8.5 pH: The pH is the most important operational parameter for than that of pH 6.5 or below; the propionate anaerobic anaerobic digestion processes. It has direct influence on oxidation hardly occurred at pH 5.5 (unpublished data). 844 SYNTROPHIC DEGRADATION OF PROPIONATE / Int. J. Agric. Biol., Vol. 14, No. 5, 2012 Table II: Characteristics of syntrophic propionate-oxidizing bacteria Organism Cell morphology pH Tempe G+C Substrates Reference
Recommended publications
  • Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens
    microorganisms Article Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens Maryam Rezadehbashi and Susan A. Baldwin * Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC V6T 1Z3, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-604-822-1973 Received: 2 January 2018; Accepted: 17 February 2018; Published: 23 February 2018 Abstract: Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations.
    [Show full text]
  • From Sporulation to Intracellular Offspring Production: Evolution
    FROM SPORULATION TO INTRACELLULAR OFFSPRING PRODUCTION: EVOLUTION OF THE DEVELOPMENTAL PROGRAM OF EPULOPISCIUM A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by David Alan Miller January 2012 © 2012 David Alan Miller FROM SPORULATION TO INTRACELLULAR OFFSPRING PRODUCTION: EVOLUTION OF THE DEVELOPMENTAL PROGRAM OF EPULOPISCIUM David Alan Miller, Ph. D. Cornell University 2012 Epulopiscium sp. type B is an unusually large intestinal symbiont of the surgeonfish Naso tonganus. Unlike most other bacteria, Epulopiscium sp. type B has never been observed to undergo binary fission. Instead, to reproduce, it forms multiple intracellular offspring. We believe this process is related to endospore formation, an ancient and complex developmental process performed by certain members of the Firmicutes. Endospore formation has been studied for over 50 years and is best characterized in Bacillus subtilis. To study the evolution of endospore formation in the Firmicutes and the relatedness of this process to intracellular offspring formation in Epulopiscium, we have searched for sporulation genes from the B. subtilis model in all of the completed genomes of members of the Firmicutes, in addition to Epulopiscium sp. type B and its closest relative, the spore-forming Cellulosilyticum lentocellum. By determining the presence or absence of spore genes, we see the evolution of endospore formation in closely related bacteria within the Firmicutes and begin to predict if 19 previously characterized non-spore-formers have the genetic capacity to form a spore. We can also map out sporulation-specific mechanisms likely being used by Epulopiscium for offspring formation.
    [Show full text]
  • Gene Conservation Among Endospore-Forming Bacteria Reveals Additional Sporulation Genes in Bacillus Subtilis
    Gene Conservation among Endospore-Forming Bacteria Reveals Additional Sporulation Genes in Bacillus subtilis Bjorn A. Traag,a Antonia Pugliese,a Jonathan A. Eisen,b Richard Losicka Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USAa; Department of Evolution and Ecology, University of California Davis Genome Center, Davis, California, USAb The capacity to form endospores is unique to certain members of the low-G؉C group of Gram-positive bacteria (Firmicutes) and requires signature sporulation genes that are highly conserved across members of distantly related genera, such as Clostridium and Bacillus. Using gene conservation among endospore-forming bacteria, we identified eight previously uncharacterized genes that are enriched among endospore-forming species. The expression of five of these genes was dependent on sporulation-specific transcription factors. Mutants of none of the genes exhibited a conspicuous defect in sporulation, but mutants of two, ylxY and ylyA, were outcompeted by a wild-type strain under sporulation-inducing conditions, but not during growth. In contrast, a ylmC mutant displayed a slight competitive advantage over the wild type specific to sporulation-inducing conditions. The phenotype of a ylyA mutant was ascribed to a defect in spore germination efficiency. This work demonstrates the power of combining phy- logenetic profiling with reverse genetics and gene-regulatory studies to identify unrecognized genes that contribute to a con- served developmental process. he formation of endospores is a distinctive developmental the successive actions of four compartment-specific sigma factors Tprocess wherein a dormant cell type (the endospore) is formed (appearing in the order ␴F, ␴E, ␴G, and ␴K), whose activities are inside another cell (the mother cell) and ultimately released into confined to the forespore (␴F and ␴G) or the mother cell (␴E and the environment by lysis of the mother cell (1, 2).
    [Show full text]
  • A Metagenomic Window Into the 2-Km-Deep Terrestrial Subsurface Aquifer Revealed Multiple Pathways of Organic Matter Decomposition Vitaly V
    FEMS Microbiology Ecology, 94, 2018, fiy152 doi: 10.1093/femsec/fiy152 Advance Access Publication Date: 7 August 2018 Research Article RESEARCH ARTICLE A metagenomic window into the 2-km-deep terrestrial subsurface aquifer revealed multiple pathways of organic matter decomposition Vitaly V. Kadnikov1, Andrey V. Mardanov1, Alexey V. Beletsky1, David Banks3, Nikolay V. Pimenov4, Yulia A. Frank2,OlgaV.Karnachuk2 and Nikolai V. Ravin1,* 1Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33-2, Moscow, 119071, Russia, 2Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenina prosp. 35, Tomsk, 634050, Russia, 3School of Engineering, Systems Power & Energy, Glasgow University, Glasgow G12 8QQ, and Holymoor Consultancy Ltd., 360 Ashgate Road, Chesterfield, Derbyshire S40 4BW, UK and 4Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp 33-2, Moscow, 119071, Russia ∗Corresponding author: Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33-2, Moscow, 119071, Russia. Tel: +74997833264; Fax: +74991353051; E-mail: [email protected] One sentence summary: metagenome-assembled genomes of microorganisms from the deep subsurface thermal aquifer revealed functional diversity of the community and novel uncultured bacterial lineages Editor: Tillmann Lueders ABSTRACT We have sequenced metagenome of the microbial community of a deep subsurface thermal aquifer in the Tomsk Region of the Western Siberia, Russia. Our goal was the recovery of near-complete genomes of the community members to enable accurate reconstruction of metabolism and ecological roles of the microbial majority, including previously unstudied lineages. The water, obtained via a 2.6 km deep borehole 1-R, was anoxic, with a slightly alkaline pH, and a temperature around 45◦C.
    [Show full text]
  • Desulfovirga Adipica Gen. Nov., Sp. Nov., an Adipate-Degrading, Gram-Negative, Sulfate-Reducing Bacterium
    International Journal of Systematic and Evolutionary Microbiology (2000), 50, 639–644 Printed in Great Britain Desulfovirga adipica gen. nov., sp. nov., an adipate-degrading, Gram-negative, sulfate-reducing bacterium Kazuhiro Tanaka,1 Erko Stackebrandt,2 Shigehiro Tohyama3 and Tadashi Eguchi3 Author for correspondence: Kazuhiro Tanaka. Tel\Fax: j81 298 61 6083. e-mail: ktanaka!nibh.go.jp 1 Applied Microbiology A novel, mesophilic, Gram-negative bacterium was isolated from an anaerobic Department, National digestor for municipal wastewater. The bacterium degraded adipate in the Institute of Bioscience and Human-Technology, presence of sulfate, sulfite, thiosulfate and elemental sulfur. (E)-2- Higashi 1-1, Tsukuba, Hexenedioate accumulated transiently in the degradation of adipate. (E)-2- Ibaraki 305-8566, Japan Hexenedioate, (E)-3-hexenedioate, pyruvate, lactate, C1–C12 straight-chain fatty 2 Deutsche Sammlung von acids and C2–C10 straight-chain primary alcohols were also utilized as electron Mikroorganismen und donors. 3-Phenylpropionate was oxidized to benzoate. The GMC content of the Zellkulturen GmbH, Mascheroder Weg 1b, DNA was 60 mol%. 16S rDNA sequence analysis revealed that the new isolate D-38124 Braunschweig, clustered with species of the genus Syntrophobacter and Desulforhabdus Germany amnigenus. Strain TsuAS1T resembles Desulforhabdus amnigenus DSM 10338T 3 Department of Chemistry with respect to the ability to utilize acetate as an electron donor and the and Materials Science, inability to utilize propionate without sulfate in co-culture with Tokyo Institute of T T Technology, O-okayama, Methanospirillum hungatei DSM 864. Strains TsuAS1 and DSM 10338 form a Meguro-ku, Tokyo ‘non-syntrophic subcluster’ within the genus Syntrophobacter. Desulfovirga 152-8551, Japan adipica gen.
    [Show full text]
  • Sp. Nov., New Syntrophically Propionate-Oxidizing Anaerobe Growing in Pure Culture with Propionate and Sulfate
    Arch Microbiol (1995) 164:346-352 Springer-Verlag 1995 Christina Wallrabenstein Elisabeth Hauschild Bernhard Schink Syntrophobacter pfennigii sp. nov., new syntrophically propionate-oxidizing anaerobe growing in pure culture with propionate and sulfate Received: 3 July 1995 / Accepted: 16 August 1995 Abstract A new strain of syntrophically propionate-oxi- teria (Zehnder 1978). Fermentation of propionate to ac- dizing fermenting bacteria, strain KoPropl, was isolated etate, CO2, and hydrogen is a highly endergonic process from anoxic sludge of a municipal sewage plant. It oxi- (calculations of free energies after Thauer et al. 1977): dized propionate or lactate in cooperation with the hydro- CH3CH2COO + 2 H20----)CH3COO -t-CO2 + 3 H 2 (1) gen- and formate-utilizing Methanospirillum hungatei AG 0" = +76.0 kJ/mol propionate and grew as well in pure culture without a syntrophic part- ner with propionate or lactate plus sulfate as energy The hydrogen partial pressure has to be kept low by the source. In all cases, the substrates were oxidized stoichio- partner organism to make the reaction energetically feasi- metrically to acetate and CO2, with concomitant forma- ble, e.g., in syntrophic methanogenic propionate degrada- tion of methane or sulfide. Cells formed gas vesicles in tion: the late growth phase and contained cytochromes b and c, 4 CH3CH2COO- + 2 H20--M CH3COO- + CO2+3 CH 4 (2) a menaquinone-7, and desulforubidin, but no desul- AG 0" = -26.5 kJ/mol propionate foviridin. Enzyme measurements in cell-free extracts indi- cated that propionate was oxidized through the methyl- However, the amount of free energy liberated during syn- malonyl CoA pathway.
    [Show full text]
  • 'Candidatus Desulfonatronobulbus Propionicus': a First Haloalkaliphilic
    Delft University of Technology ‘Candidatus Desulfonatronobulbus propionicus’ a first haloalkaliphilic member of the order Syntrophobacterales from soda lakes Sorokin, D. Y.; Chernyh, N. A. DOI 10.1007/s00792-016-0881-3 Publication date 2016 Document Version Accepted author manuscript Published in Extremophiles: life under extreme conditions Citation (APA) Sorokin, D. Y., & Chernyh, N. A. (2016). ‘Candidatus Desulfonatronobulbus propionicus’: a first haloalkaliphilic member of the order Syntrophobacterales from soda lakes. Extremophiles: life under extreme conditions, 20(6), 895-901. https://doi.org/10.1007/s00792-016-0881-3 Important note To cite this publication, please use the final published version (if applicable). Please check the document version above. Copyright Other than for strictly personal use, it is not permitted to download, forward or distribute the text or part of it, without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license such as Creative Commons. Takedown policy Please contact us and provide details if you believe this document breaches copyrights. We will remove access to the work immediately and investigate your claim. This work is downloaded from Delft University of Technology. For technical reasons the number of authors shown on this cover page is limited to a maximum of 10. Extremophiles DOI 10.1007/s00792-016-0881-3 ORIGINAL PAPER ‘Candidatus Desulfonatronobulbus propionicus’: a first haloalkaliphilic member of the order Syntrophobacterales from soda lakes D. Y. Sorokin1,2 · N. A. Chernyh1 Received: 23 August 2016 / Accepted: 4 October 2016 © Springer Japan 2016 Abstract Propionate can be directly oxidized anaerobi- from its members at the genus level.
    [Show full text]
  • Tropical Soil Metagenome Library Reveals Complex Microbial Assemblage
    bioRxiv preprint doi: https://doi.org/10.1101/018895; this version posted May 3, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Tropical Soil Metagenome Library Reveals Complex Microbial Assemblage Kok-Gan Chan 1# and Zahidah Ismail 1 1 Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia # Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +603-7967-5162; Fax: +603-7967-4509. 1 1 bioRxiv preprint doi: https://doi.org/10.1101/018895; this version posted May 3, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 2 Abstract 3 In this work, we characterized the metagenome of a Malaysian mangrove soil sample via next 4 generation sequencing (NGS). Shotgun NGS data analysis revealed high diversity of microbes 5 from Bacteria and Archaea domains. The metabolic potential of the metagenome was 6 reconstructed using the NGS data and the SEED classification in MEGAN shows abundance of 7 virulence factor genes, implying that mangrove soil is potential reservoirs of pathogens. 8 9 Keywords: Metagenomics, Mangrove, Soil, Proteobacteria 10 2 bioRxiv preprint doi: https://doi.org/10.1101/018895; this version posted May 3, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
    [Show full text]
  • Phylogenetic Profile of Copper Homeostasis in Deltaproteobacteria
    Phylogenetic Profile of Copper Homeostasis in Deltaproteobacteria A Major Qualifying Report Submitted to the Faculty of Worcester Polytechnic Institute In Partial Fulfillment of the Requirements for the Degree of Bachelor of Science By: __________________________ Courtney McCann Date Approved: _______________________ Professor José M. Argüello Biochemistry WPI Project Advisor 1 Abstract Copper homeostasis is achieved in bacteria through a combination of copper chaperones and transporting and chelating proteins. Bioinformatic analyses were used to identify which of these proteins are present in Deltaproteobacteria. The genetic environment of the bacteria is affected by its lifestyle, as those that live in higher concentrations of copper have more of these proteins. Two major transport proteins, CopA and CusC, were found to cluster together frequently in the genomes and appear integral to copper homeostasis in Deltaproteobacteria. 2 Acknowledgements I would like to thank Professor José Argüello for giving me the opportunity to work in his lab and do some incredible research with some equally incredible scientists. I need to give all of my thanks to my supervisor, Dr. Teresita Padilla-Benavides, for having me as her student and teaching me not only lab techniques, but also how to be scientist. I would also like to thank Dr. Georgina Hernández-Montes and Dr. Brenda Valderrama from the Insituto de Biotecnología at Universidad Nacional Autónoma de México (IBT-UNAM), Campus Morelos for hosting me and giving me the opportunity to work in their lab. I would like to thank Sarju Patel, Evren Kocabas, and Jessica Collins, whom I’ve worked alongside in the lab. I owe so much to these people, and their support and guidance has and will be invaluable to me as I move forward in my education and career.
    [Show full text]
  • DNA-SIP Identifies Sulfate-Reducing Clostridia As Important Toluene Degraders in Tar-Oil-Contaminated Aquifer Sediment
    The ISME Journal (2010) 4, 1314–1325 & 2010 International Society for Microbial Ecology All rights reserved 1751-7362/10 www.nature.com/ismej ORIGINAL ARTICLE DNA-SIP identifies sulfate-reducing Clostridia as important toluene degraders in tar-oil-contaminated aquifer sediment Christian Winderl, Holger Penning, Frederick von Netzer, Rainer U Meckenstock and Tillmann Lueders Institute of Groundwater Ecology, Helmholtz Zentrum Mu¨nchen—German Research Centre for Environmental Health, Neuherberg, Germany Global groundwater resources are constantly challenged by a multitude of contaminants such as aromatic hydrocarbons. Especially in anaerobic habitats, a large diversity of unrecognized microbial populations may be responsible for their degradation. Still, our present understanding of the respective microbiota and their ecophysiology is almost exclusively based on a small number of cultured organisms, mostly within the Proteobacteria. Here, by DNA-based stable isotope probing (SIP), we directly identified the most active sulfate-reducing toluene degraders in a diverse sedimentary microbial community originating from a tar-oil-contaminated aquifer at a former coal gasification plant. 13 13 On incubation of fresh sediments with C7-toluene, the production of both sulfide and CO2 was clearly coupled to the 13C-labeling of DNA of microbes related to Desulfosporosinus spp. within the Peptococcaceae (Clostridia). The screening of labeled DNA fractions also suggested a novel benzylsuccinate synthase alpha-subunit (bssA) sequence type previously only detected in the environment to be tentatively affiliated with these degraders. However, carbon flow from the contaminant into degrader DNA was only B50%, pointing toward high ratios of heterotrophic CO2-fixation during assimilation of acetyl-CoA originating from the contaminant by these degraders.
    [Show full text]
  • Dynamic Evolution of Selenocysteine Utilization in Bacteria: a Balance Between Selenoprotein Loss and Evolution of Selenocysteine from Redox Active Cysteine Residues
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Vadim Gladyshev Publications Biochemistry, Department of October 2006 Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues Yan Zhang University of Nebraska-Lincoln, [email protected] Hector Romero Instituto de Biología, Facultad de Ciencias, Uruguay Gustavo Salinas Instituto de Higiene, Avda A Navarro 3051, Montevideo, CP 11600, Uruguay Vadim Gladyshev University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/biochemgladyshev Part of the Biochemistry, Biophysics, and Structural Biology Commons Zhang, Yan; Romero, Hector; Salinas, Gustavo; and Gladyshev, Vadim, "Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues" (2006). Vadim Gladyshev Publications. 6. https://digitalcommons.unl.edu/biochemgladyshev/6 This Article is brought to you for free and open access by the Biochemistry, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Vadim Gladyshev Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Open Access Research2006ZhangetVolume al. 7, Issue 10, Article R94 Dynamic evolution of selenocysteine utilization in bacteria: a comment balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues Yan Zhang*, Hector Romero†, Gustavo Salinas‡ and Vadim N Gladyshev* Addresses: *Department of Biochemistry, University of Nebraska, 1901 Vine street, Lincoln, NE 68588-0664, USA. †Laboratorio de Organización y Evolución del Genoma, Laboratorio de Organización y Evolución del Genoma, Dpto de Biología Celular y Molecular, Instituto ‡ de Biología, Facultad de Ciencias, Iguá 4225, Montevideo, CP 11400, Uruguay.
    [Show full text]
  • Ecophysiology of Sulfate-Reducing Bacteria and Syntrophic Communities in Marine Anoxic Sediments” Derya Özüölmez Wageningen, 12 September 2017
    Propositions 1. Prolonged incubation is a key strategy toward the enrichment of marine syntrophs. (this thesis) 2. Hydrogen-consuming methanogens can effectively compete with hydrogen- consuming sulfate reducers even at high sulfate concentration. (this thesis) 3. The plastic-eating wax worm, Galleria mellonella, can help cleaning up existing plastic mass (Bombelli et al. 2017, Current Biology 27(8): 292-293), but the real solution to environmental pollution still relies on shifting from disposable plastics to reusable and biodegradable materials. 4. With the discovery of abundant molecular hydrogen in Enceladus’ salty ocean (Waite et al. (2017) Science 356:6334, 155-159) extraterrestrial life in our solar system has become highly probable, and should shift our life-hunting focus from distant stars to our nearby neighbors. 5. With the "Help me to do it myself" motto, the Montessori education leads children to grow into mature, creative and self-confident adults. 6. Nothing is impossible as long as the dream is held close to the heart and patience and persistence are applied for the accomplishment. Propositions belonging to the PhD thesis entitled: “Ecophysiology of sulfate-reducing bacteria and syntrophic communities in marine anoxic sediments” Derya Özüölmez Wageningen, 12 September 2017 Ecophysiology of sulfate-reducing bacteria and syntrophic communities in marine anoxic sediments Derya Özüölmez Thesis committee Promotor Prof. Dr Alfons J.M. Stams Personal chair at the Laboratory of Microbiology Wageningen University & Research Co-promotor Dr Caroline M. Plugge Associate professor, Laboratory of Microbiology Wageningen University & Research Other members Prof. Dr Tinka Murk, Wageningen University & Research Prof. Dr Gerard Muyzer, University of Amsterdam, The Netherlands Prof.
    [Show full text]