DOCSLIB.ORG

Coexistance of Acetogens, Methanogens and Sulfate Reducing Bacteria in Enrichments from Trunk River

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Coexistance of Acetogens, Methanogens and Sulfate Reducing Bacteria in Enrichments from Trunk River Coexistance of acetogens, methanogens and sulfate reducing bacteria in enrichments from Trunk River María Consuelo Gazitúa Center for Genomics and Bioinformatics University Mayor - Chile [email protected] Introduction In the absence of oxygen, chemotrophic growth depends on alternative electron acceptors such as nitrate, iron, manganese, sulfate and CO2. In the presence of sulfate, such as in seawater, sulfate reduction is highly favorable, coupling the reduction of sulfate with the oxidation of H2 or simple organic compounds. In the absence of sulfate, methanogenic archaea are able to cleave acetate, producing CO2 and CH4, as well as reduce or disproportionate C1 compounds such as CO2, CO, formate and methanol, using H2 and formate as the main electron donor. Homoacetogenic bacteria use C-1 compounds as electron acceptors, catalyzing the reduction of two CO2 molecules to acetate. This is a highly variable group of strictly anaerobic bacteria, able to grow on a variety of substrates. In most anaerobic environments, hydrogen is present as an intermediate for which sulfate reducing bacteria (SRB), hydrogenotrophic methanogens and homoacetogens will compete. Under standard conditions, sulfate reduction and methanogenesis are thermodynamically more favorable than homoacetogenesis. However, Weijma et al. (2002) reported that when H2/CO2 is added as the sole substrate in sludge bioreactores, heterotrophic SRB and homoacetogens can coexist, suggesting the SRB growth depends on the growth kinetics of the homoacetogens. During the isolation of chemolithotrophic microorganisms during the course, specifically for SRB, homoacetogens and methanogens, the enrichment for SRB showed the coexistence of these three groups, based on measurements of methane, hydrogen sulfide and acetate. Some of the organisms growing in the enrichment formed aggregates, where the presence of methanogens could be inferred based on the blue autofluorescence, after excitation with AF430 (Doddema and Vogels 1978). Figure 1: aggregate formation in enrichments for sulfate reducing bacteria. Left: third transfer, right: second transfer. Scale bar 10 μm. The culture was transferred three times to fresh media, forming these kinds of aggregates every time. The main objective of this project is to follow up on the dynamics of this community during a 7 day time series, using the third transfer as an inoculum, determining the production of methane, acetate and hydrogen sulfide, as well as analyzing the community composition and distribution through fluorescent microscopy. Methods Enrichments: The initial inoculum for the enrichments used in this study comes from the sediments of Trunk River, in the first meters of the pond (after the river). Samples were stored in 50 mL falcon tubes, and used for inoculation during the same day. In the anaerobic chamber, a sample of approximately 0.5 cm3 was inoculated in 125 mL serum bottles, containing 25 ml of minimal media, specific for the enrichment of sulfate reducing bacteria. This media contained 342.2 mM NaCl, 14.8 mM MgCl2×6H2O, 1 mM CaCl2×2H2O, 6.71 mM KCl, 5mM NH4Cl, 1mM K phosphate, pH 7.2, 5mM MOPS buffer, pH 7.2, trace elements, 1% Resazurin, multivitamin solution, 28 mM NaHCO3 and 20 mM Na2SO4. The headspace gas is replaced with H2/CO2 (80%/20%) by five cycles of vacuum/pressurization. The bottle was incubated at 30ºC, and after 7 days, an inoculum of 1 mL was transferred to fresh media, using a sterile syringe. A total of four transfers were performed. For the last transfer, three conditions were evaluated: SRB media, incubated at 30ºC in the dark (4 bottles); SRB media at room temperature and 630 nm light (1 bottle) and methanogen enriching media (SRB media without sulfate) (1 bottle). The inoculum used for the fourth transfer was also used for the isolation of methanogens, acetogens and sulfate reducing bacteria in agar plates, using the same media described above. For the acetogens, the media was the same as for the methanogens, containing 0.01 M BES (inhibitor of methyl-coenzyme M reductase, a key enzyme in the methanogenic pathway). The plates were incubated at 30ºC in the Wolfe incubator, filled with N2/CO2/H2S gas. Methanogenesis, acetogenesis and sulfate reduction measurements The progress of the enrichments was monitored following the production of methane by gas chromatography, acetate by HPLC and sulfide by chemical assay. 1 mL samples were taken daily, and H2/CO2 was added every second day. Methane was measured taking 250 μl of the headspace and injecting it to the gas chromatograph (Shimadzu). The moles of methane present in the headspace were subsequently transformed to moles of methane per mL of culture, considering the variable volume of headspace/culture, due to daily sampling. These values were finally corrected to reflect accumulated methane, taking into account that after every H2/CO2 vacuum/pressurization event, the total methane was eliminated. The acetate was measured in the HPLC (Shimadzu), using 450 μl of culture fixed with 50 μl of 5N H2SO4. - 2- The concentration of dissolved hydrogen sulfide (H2S, HS , S ) was measured colorimetrically using the Cline assay (REF). Briefly, 300 μl of culture were fixed with 600 μl of Zinc Acetate 1M and stored at -20ºC. The Zinc Sulfide produced was diluted in MilliQ water (10 to 50 times) dissolved with 10 μl of the first reagent of the Hach kit, followed by the addition of 10 μl of the second reagent (N,N-dimethyl-p- phenylenediamine sulfate and ferric chloride). After 5 minutes the absorbance was determined spectrophotometrically at 670 nm. The concentration of H2S was corrected, considering a) the Cline assay measures only the aqueous forms of the dissolved hydrogen sulfide, excluding the gaseous H2S b) the pK value of the reaction H2S(aq) ! H2S(g) at 30ºC is -1.05, giving a ratio of H2S(g): H2S(aq) of 11.22 - + c) the pKa for the reaction H2S "! HS + H at 30ºC is 7.01 and the pH of the - media is 7.2, deriving ratio coefficients for H2S and HS of 0.39 and 0.61, respectively. d) After each H2/CO2 (80%/20%) vacuum/pressurization event, the H2S(g) is evacuated from the sample. The mmoles lost were added to the total dissolved hydrogen sulfide of the following two days. CARD-FISH Finally, 250 μl of culture was fixed with 250 μl of PFA 4%, and incubated at 4ºC overnight. The cells were washed with 10 mL of 1x PBS, filtered through a membrane filter (0.2 μm pore size, 47 mm diameter, polycarbonate (GTTP), Milipore). The cells were washed one more time, passing 15 mL of PBS through the filter. The filters from day 7 of the 6 bottles, and those from the first, second and third transfers, were used for CARD-FISH analysis. The filters were embedded with warm low gelling point agarose (0.2%) using a spray dispenser. The cells were permeabilized with lysozyme (100,000 U ml-1 in 0.05 M EDTA, pH 8.0; 0.1 M Tris-HCl, pH 8.0) for 30-60 minutes at 37ºC. After washing in excess MilliQ water, the cells were treated with proteinase K (15 μg ml-1 in 0.05 M EDTA, pH 8.0; 0.1 M Tris-HCl, pH 8.0, 0.5 M NaCl) for 2-5 minutes at room temperature. Next, endogenous peroxidases were inactivated with 0.01 M HCl for 10-20 minutes at room temperature, followed by a wash in excess MilliQ water and an additional incubation in 3% H2O2 in water for 10 minutes at room temperature. The filters were washed in excess MilliQ water and 96% ethanol, and dried at room temperature. Pieces of filters were incubated with the selected probes in hybridization solution at 46ºC for 3 hours, followed by a 10 minute incubation in washing buffer at 48º and a 15 minute incubation in 1x PBS at room temperature. The filters were subsequently incubated in amplification buffer with 0.15% H2O2 solution in a ratio 100:1 and fluorescently labeled tyramide in a ratio 1000:1, at 46ºC for 30 minutes in the dark. Finally, filters were incubated in 1x PBS at room temperature in the dark, and washed in excess MilliQ water and in 96% ethanol, letting them dry in the dark. Those filters that were subjected to only one CARD-FISH probe were counterstained with DAPI. Those who were subjected to a second hybridization followed the same protocol described above, beginning from the inactivation of peroxidases. The filters were analyzed through fluorescent microscopy (AXIO Imager A2, Zeiss), exciting the cells at 365 nm, 470 ± 20 nm and 550 ± 12,5 nm, for DAPI, Alexa Fluor 488 tyramide and Alexa Flour 594 tyramide signals, respectively. SEQUENCING Two clone libraries, one for bacteria and one for archaea, were prepared with DNA extracted from the culture used as an inoculum for the fourth transfer. A total of 8 clones were sequenced and aligned to the NCBI database. RESULTS The cultures from the six bottles showed consistent growth during the week of incubation. Cell density was qualitatively measured during day 2, 5 and 7 by microscopy, revealing cell growth and the formation of small aggregates. In this case, the size of the aggregates was between 3 and 5 μm (figure 2). Figure 2: DAPI staining of cells from day 5, present in the enrichment from a bottle in SRB media (left) and Metgen media (right), both incubated at 30º in the dark. Scale bar: 10 μm. The production of methane, acetate and hydrogen sulfide was measured daily. Figure 3 shows the moles of each compound, per ml of culture. Hydrogen sulfide increased consistently in those bottles that contained sulfate. The bottle that was incubated at room temperature and 630 nm produced approximately 1 mmole l-1 less than those grown at 30ºC in the dark.
Load more

Recommended publications
  • Representatives of a Novel Archaeal Phylum Or a Fast-Evolving
    Open Access Research2005BrochieretVolume al. 6, Issue 5, Article R42 Nanoarchaea: representatives of a novel archaeal phylum or a comment fast-evolving euryarchaeal lineage related to Thermococcales? Celine Brochier*, Simonetta Gribaldo†, Yvan Zivanovic‡, Fabrice Confalonieri‡ and Patrick Forterre†‡ Addresses: *EA EGEE (Evolution, Génomique, Environnement) Université Aix-Marseille I, Centre Saint-Charles, 3 Place Victor Hugo, 13331 Marseille, Cedex 3, France. †Unite Biologie Moléculaire du Gène chez les Extremophiles, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex ‡ 15, France. Institut de Génétique et Microbiologie, UMR CNRS 8621, Université Paris-Sud, 91405 Orsay, France. reviews Correspondence: Celine Brochier. E-mail: [email protected]. Simonetta Gribaldo. E-mail: [email protected] Published: 14 April 2005 Received: 3 December 2004 Revised: 10 February 2005 Genome Biology 2005, 6:R42 (doi:10.1186/gb-2005-6-5-r42) Accepted: 9 March 2005 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2005/6/5/R42 reports © 2005 Brochier et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Placement<p>Anteins from analysis 25of Nanoarcheumarchaeal of the positiongenomes equitans of suggests Nanoarcheum in the that archaeal N. equitans phylogeny inis likethe lyarchaeal to be the phylogeny representative using aof large a fast-evolving dataset of concatenatedeuryarchaeal ribosomalineage.</p>l pro- deposited research Abstract Background: Cultivable archaeal species are assigned to two phyla - the Crenarchaeota and the Euryarchaeota - by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis.
    [Show full text]
  • Open Dissertation 4-7-09.Pdf
    The Pennsylvania State University The Graduate School Department of Civil and Environmental Engineering IMPROVED ANAEROBIC DIGESTER STABILITY TO ORGANIC LOADING RATE SHOCKS WITH THE USE OF AN ENVIRONMENTALLY DERIVED INOCULUM A Dissertation in Environmental Engineering and Biogeochemistry by Lisa Marie Steinberg © 2009 Lisa Marie Steinberg Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2009 The dissertation of Lisa Marie Steinberg was reviewed and approved* by the following: John Regan Associate Professor of Environmental Engineering Dissertation Advisor Chair of Committee Christopher House Associate Professor of Geosciences Bruce Logan Kappe Professor of Environmental Engineering Jenn Macalady Assistant Professor of Geosciences Peggy Johnson Department Head and Professor of Civil Engineering *Signatures are on file in the Graduate School ABSTRACT Anaerobic digestion broadly describes technology that utilizes microorganisms to break down organic matter under anaerobic conditions through the coordinated efforts of several trophic groups of microorganisms. The last step is catalyzed by methanogens which produce primarily methane, carbon dioxide, and water as products of metabolism. Anaerobic digestion occurs naturally in a variety of water-saturated sediments, but is also used to treat waste in constructed reactors. There are a number of advantages to treating waste with anaerobic digestion, but perhaps the greatest is that waste treatment can be coupled to energy generation by the production of a methane-rich biogas. Despite the advantages, anaerobic digestion is severely under-utilized in waste treatment mainly due to the belief that anaerobic digesters are less stable than aerobic treatment processes. Anaerobic digesters are typically operated under warm temperatures and circumneutral pH, with operation outside of these conditions leading to instability and potential reactor failure.
    [Show full text]
  • A Web Tool for Hydrogenase Classification and Analysis
    bioRxiv preprint doi: https://doi.org/10.1101/061994; this version posted September 16, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 HydDB: A web tool for hydrogenase 2 classification and analysis 3 Dan Søndergaarda, Christian N. S. Pedersena, Chris Greeningb, c* 4 5 a Aarhus University, Bioinformatics Research Centre, C.F. Møllers Allé 8, Aarhus 6 DK-8000, Denmark 7 b The Commonwealth Scientific and Industrial Research Organisation, Land and 8 Water Flagship, Clunies Ross Street, Acton, ACT 2060, Australia 9 c Monash University, School of Biological Sciences, Clayton, VIC 2800, Australia 10 11 Correspondence: 12 Dr Chris Greening ([email protected]), Monash University, School of 13 Biological Sciences, Clayton, VIC 2800, Australia 14 Dan Søndergaard ([email protected]), Aarhus University, Bioinformatics Research 15 Centre, C.F. Møllers Allé 8, Aarhus DK-8000, Denmark 1 bioRxiv preprint doi: https://doi.org/10.1101/061994; this version posted September 16, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 16 Abstract 17 H2 metabolism is proposed to be the most ancient and diverse mechanism of 18 energy-conservation. The metalloenzymes mediating this metabolism, 19 hydrogenases, are encoded by over 60 microbial phyla and are present in all major 20 ecosystems.
    [Show full text]
  • (Gid ) Genes Coding for Putative Trna:M5u-54 Methyltransferases in 355 Bacterial and Archaeal Complete Genomes
    Table S1. Taxonomic distribution of the trmA and trmFO (gid ) genes coding for putative tRNA:m5U-54 methyltransferases in 355 bacterial and archaeal complete genomes. Asterisks indicate the presence and the number of putative genes found. Genomes Taxonomic position TrmA Gid Archaea Crenarchaea Aeropyrum pernix_K1 Crenarchaeota; Thermoprotei; Desulfurococcales; Desulfurococcaceae Cenarchaeum symbiosum Crenarchaeota; Thermoprotei; Cenarchaeales; Cenarchaeaceae Pyrobaculum aerophilum_str_IM2 Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae Sulfolobus acidocaldarius_DSM_639 Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus solfataricus Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus tokodaii Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Euryarchaea Archaeoglobus fulgidus Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae Haloarcula marismortui_ATCC_43049 Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Halobacterium sp Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Haloquadratum walsbyi Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloquadra Methanobacterium thermoautotrophicum Euryarchaeota; Methanobacteria; Methanobacteriales; Methanobacteriaceae Methanococcoides burtonii_DSM_6242 Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanococcus jannaschii Euryarchaeota; Methanococci; Methanococcales; Methanococcaceae Methanococcus maripaludis_S2 Euryarchaeota; Methanococci;
    [Show full text]
  • Microbial Extracellular Electron Transfer and Its Relevance to Iron Corrosion
    bs_bs_banner Minireview Microbial extracellular electron transfer and its relevance to iron corrosion Souichiro Kato1,2,3* acetogenic bacteria and nitrate-reducing bacteria. 1Bioproduction Research Institute, National Institute of Abilities of EET and EMIC are now regarded as micro- Advanced Industrial Science and Technology (AIST), bial traits more widespread among diverse microbial 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, clades than was thought previously. In this review, Hokkaido 062-8517,Japan. basic understandings of microbial EET and recent 2Research Center for Advanced Science and progresses in the EMIC research are introduced. Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan. 3Division of Applied Bioscience, Graduate School of Introduction Agriculture, Hokkaido University, Kita-9 Nishi-9,Kita-ku, Acquisition of energy is an indispensable activity for all Sapporo, Hokkaido 060-8589, Japan. living organisms. Most organisms, including human beings, conserve energy through respiration, with Summary organic compounds and oxygen gas as the electron donor and acceptor respectively. In contrast, many Extracellular electron transfer (EET) is a microbial microorganisms have the ability to utilize diverse inor- metabolism that enables efficient electron transfer ganic compounds as the substrates for respiration. Fur- between microbial cells and extracellular solid materi- thermore, some particular microorganisms have the als. Microorganisms harbouring EET abilities have ability to acquire energy through transferring electrons to received considerable attention for their various or from extracellular solid compounds. This microbial biotechnological applications, including bioleaching metabolism is specifically termed as ‘extracellular elec- and bioelectrochemical systems. On the other hand, tron transfer (EET)’ (Gralnick and Newman, 2007; Rich- recent research revealed that microbial EET poten- ter et al., 2012).
    [Show full text]
  • Methanogens: Pushing the Boundaries of Biology
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Biochemistry -- Faculty Publications Biochemistry, Department of 12-14-2018 Methanogens: pushing the boundaries of biology Nicole R. Buan Follow this and additional works at: https://digitalcommons.unl.edu/biochemfacpub Part of the Biochemistry Commons, Biotechnology Commons, and the Other Biochemistry, Biophysics, and Structural Biology Commons 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 Biochemistry -- Faculty Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Emerging Topics in Life Sciences (2018) 2 629–646 https://doi.org/10.1042/ETLS20180031 Review Article Methanogens: pushing the boundaries of biology Nicole R. Buan Department of Biochemistry, University of Nebraska-Lincoln, 1901 Vine St., Lincoln, NE 68588-0664, U.S.A. Correspondence: Nicole R. Buan ([email protected]) Downloaded from https://portlandpress.com/emergtoplifesci/article-pdf/2/4/629/484198/etls-2018-0031c.pdf by University of Nebraska Libraries user on 11 February 2020 Methanogens are anaerobic archaea that grow by producing methane gas. These microbes and their exotic metabolism have inspired decades of microbial physiology research that continues to push the boundary of what we know about how microbes conserve energy to grow. The study of methanogens has helped to elucidate the thermodynamic and bioener- getics basis of life, contributed our understanding of evolution and biodiversity, and has garnered an appreciation for the societal utility of studying trophic interactions between environmental microbes, as methanogens are important in microbial conversion of biogenic carbon into methane, a high-energy fuel.
    [Show full text]
  • Diversity of Methane-Cycling Microorganisms in Soils and Their Relation to Oxygen
    Diversity of Methane-cycling Microorganisms in Soils and Their Relation to Oxygen Claudia Knief* Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany. *Correspondence: [email protected] htps://doi.org/10.21775/cimb.033.023 Abstract Introduction Microorganisms are important players in the Methane cycling microorganisms are of interest global methane cycle. Anaerobic methanogenic for microbiologists since more than a century. archaea are largely responsible for methane pro- Research on these microorganisms was initially duction, while aerobic methanotrophic bacteria, largely driven by the curiosity to understand their as well as anaerobic methanotrophic bacteria particular physiology that leads to the production and archaea, are involved in methane oxidation. or consumption of methane. While this interest is In anoxic wetland soils, methanogens produce still a driver, the importance of methane as green- methane, while methanotrophs act as a flter house gas has become another important factor, and reduce methane emissions. In the predomi- promoting further research on methanogenic and nantly oxic upland soils, aerobic methanotrophs methanotrophic microorganisms. Tis leads to a oxidize atmospheric methane. Tis review gives continuously beter understanding of their physi- an overview of the diversity of methanogenic ology and ecology, and it becomes evident that and methanotrophic microorganisms, highlights the processes of microbial methane production recent discoveries and provides information and consumption are mediated by more com- concerning their occurrence in soils. Recent plex functional guilds than initially thought. Te fndings indicate that the methanogenic and improved understanding is not only due to the con- methanotrophic lifestyles are more widespread stantly increasing diversity of methanogenic and in microorganisms than previously thought, and methanotrophic microorganisms (e.g.
    [Show full text]
  • The Genome Sequence of Methanohalophilus Mahii SLPT
    Hindawi Publishing Corporation Archaea Volume 2010, Article ID 690737, 16 pages doi:10.1155/2010/690737 Research Article TheGenomeSequenceofMethanohalophilus mahii SLPT Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments Stefan Spring,1 Carmen Scheuner,1 Alla Lapidus,2 Susan Lucas,2 Tijana Glavina Del Rio,2 Hope Tice,2 Alex Copeland,2 Jan-Fang Cheng,2 Feng Chen,2 Matt Nolan,2 Elizabeth Saunders,2, 3 Sam Pitluck,2 Konstantinos Liolios,2 Natalia Ivanova,2 Konstantinos Mavromatis,2 Athanasios Lykidis,2 Amrita Pati,2 Amy Chen,4 Krishna Palaniappan,4 Miriam Land,2, 5 Loren Hauser,2, 5 Yun-Juan Chang,2, 5 Cynthia D. Jeffries,2, 5 Lynne Goodwin,2, 3 John C. Detter,3 Thomas Brettin,3 Manfred Rohde,6 Markus Goker,¨ 1 Tanja Woyke, 2 Jim Bristow,2 Jonathan A. Eisen,2, 7 Victor Markowitz,4 Philip Hugenholtz,2 Nikos C. Kyrpides,2 and Hans-Peter Klenk1 1 DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA 5 Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA 6 HZI—Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany 7 Davis Genome Center, University of California, Davis, CA 95817, USA Correspondence should be addressed to Stefan Spring, [email protected] and Hans-Peter Klenk, [email protected] Received 24 August 2010; Accepted 9 November 2010 Academic Editor: Valerie´ de Crecy-Lagard´ Copyright © 2010 Stefan Spring et al.
    [Show full text]
  • Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes
    GBE Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes Dennifier Costa Brandao~ Cruz1, Lenon Lima Santana1, Alexandre Siqueira Guedes2, Jorge Teodoro de Souza3,*, and Phellippe Arthur Santos Marbach1,* 1CCAAB, Biological Sciences, Recoˆ ncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil 2Agronomy School, Federal University of Goias, Goiania,^ Goias, Brazil 3 Department of Phytopathology, Federal University of Lavras, Minas Gerais, Brazil Downloaded from https://academic.oup.com/gbe/article/11/4/1235/5345563 by guest on 27 September 2021 *Corresponding authors: E-mails: [email protected]fla.br; [email protected]. Accepted: February 16, 2019 Abstract The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs.
    [Show full text]
  • Adaptations of Methanococcus Maripaludis to Its Unique Lifestyle
    ADAPTATIONS OF METHANOCOCCUS MARIPALUDIS TO ITS UNIQUE LIFESTYLE by YUCHEN LIU (Under the Direction of William B. Whitman) ABSTRACT Methanococcus maripaludis is an obligate anaerobic, methane-producing archaeon. In addition to the unique methanogenesis pathway, unconventional biochemistry is present in this organism in adaptation to its unique lifestyle. The Sac10b homolog in M. maripaludis, Mma10b, is not abundant and constitutes only ~ 0.01% of the total cellular protein. It binds to DNA with sequence-specificity. Disruption of mma10b resulted in poor growth of the mutant in minimal medium. These results suggested that the physiological role of Mma10b in the mesophilic methanococci is greatly diverged from the homologs in thermophiles, which are highly abundant and associate with DNA without sequence-specificity. M. maripaludis synthesizes lysine through the DapL pathway, which uses diaminopimelate aminotransferase (DapL) to catalyze the direct transfer of an amino group from L-glutamate to L-tetrahydrodipicolinate (THDPA), forming LL-diaminopimelate (LL-DAP). This is different from the conventional acylation pathway in many bacteria that convert THDPA to LL-DAP in three steps: succinylation or acetylation, transamination, and desuccinylation or deacetylation. The DapL pathway eliminates the expense of using succinyl-CoA or acetyl-CoA and may represent a thriftier mode for lysine biosynthesis. Methanogens synthesize cysteine primarily on tRNACys via the two-step SepRS/SepCysS pathway. In the first step, tRNACys is aminoacylated with O-phosphoserine (Sep) by O- phosphoseryl-tRNA synthetase (SepRS). In the second step, the Sep moiety on Sep-tRNACys is converted to cysteine with a sulfur source to form Cys-tRNACys by Sep-tRNA:Cys-tRNA synthase (SepCysS).
    [Show full text]
  • Bacterial Involvements in Ulcerative Colitis: Molecular and Microbiological Studies
    BACTERIAL INVOLVEMENTS IN ULCERATIVE COLITIS: MOLECULAR AND MICROBIOLOGICAL STUDIES Samia Alkhalil A thesis submitted in partial fulfilment of the requirements for the award of the degree of Doctor of Philosophy of the University of Portsmouth Institute of Biomedical and biomolecular Sciences School of Pharmacy and Biomedical Sciences October 2017 AUTHORS’ DECLARATION I declare that whilst registered as a candidate for the degree of Doctor of Philosophy at University of Portsmouth, I have not been registered as a candidate for any other research award. The results and conclusions embodied in this thesis are the work of the named candidate and have not been submitted for any other academic award. Samia Alkhalil I ABSTRACT Inflammatory bowel disease (IBD) is a series of disorders characterised by chronic intestinal inflammation, with the principal examples being Crohn’s Disease (CD) and ulcerative colitis (UC). A paradigm of these disorders is that the composition of the colon microbiota changes, with increases in bacterial numbers and a reduction in diversity, particularly within the Firmicutes. Sulfate reducing bacteria (SRB) are believed to be involved in the etiology of these disorders, because they produce hydrogen sulfide which may be a causative agent of epithelial inflammation, although little supportive evidence exists for this possibility. The purpose of this study was (1) to detect and compare the relative levels of gut bacterial populations among patients suffering from ulcerative colitis and healthy individuals using PCR-DGGE, sequence analysis and biochip technology; (2) develop a rapid detection method for SRBs and (3) determine the susceptibility of Desulfovibrio indonesiensis in biofilms to Manuka honey with and without antibiotic treatment.
    [Show full text]
  • Tour Pages by Clicking This Link
    STATION 1 (Welcome) WELCOME TO THE CBEC TINY THINGS TOUR (STATION 1) This tour is designed to acquaint CBEC visitors with the amazingly diverse array of organisms here that are not typically noticed, mainly because they’re too small to be seen without either very careful observation or the aid of a magnifier (either a handheld device or a microscope). The tour will discuss representatives of the six kingdoms of living things (Bacteria, Archaea, Fungi, Plants, Protists, and Animals), as well as viruses. In addition to brief discussions of the particular organisms themselves, we’ll consider the role that these organisms play in their immediate environment, their effect on the larger biosphere, and their ability to teach us about the past and the future. Taking the Tour: To take the tour, visitors may use the Tiny Things Tour map, where the 14 stations are indicated with red numbers. The map should be used in conjunction with the printable list of stations. The list has the GPS coordinates for each station, along with QR codes that provide links to the web pages that describe each station. The GPS coordinates, as well as a simple description of each location are included on each station’s web page. If visitors haven’t brought along a mobile device (to view the web pages), they can print a copy of the tour pages by clicking this link. A guided version of the Tiny Things Tour is scheduled on a regular basis. Check the CBEC schedule for upcoming guided tours. Each web page includes a photo of the representative organism, it’s common name and scientific name, a description of the station location (including its GPS location), and a description of the organism and its environment.
    [Show full text]