DOCSLIB.ORG

Experimental Validation of in Silico Modelpredicted Isocitrate

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Experimental Validation of in Silico Modelpredicted Isocitrate Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Islam, M. Ahsanul, Anatoli Tchigvintsev, Veronica Yim, Alexei Savchenko, Alexander F. Yakunin, Radhakrishnan Mahadevan, and Elizabeth A. Edwards. “Experimental Validation of in Silico Model-Predicted Isocitrate Dehydrogenase and Phosphomannose Isomerase from Dehalococcoides Mccartyi.” Microbial Biotechnology (September 16, 2015): n/a–n/a. As Published http://dx.doi.org/10.1111/1751-7915.12315 Publisher Wiley Blackwell Version Final published version Citable link http://hdl.handle.net/1721.1/99704 Terms of Use Creative Commons Attribution Detailed Terms http://creativecommons.org/licenses/by/4.0/ bs_bs_banner Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi M. Ahsanul Islam,† Anatoli Tchigvintsev, Veronica and confirmed experimentally. Further bioinformatics Yim, Alexei Savchenko, Alexander F. Yakunin, analyses of these two protein sequences suggest Radhakrishnan Mahadevan and Elizabeth A. their affiliation to potentially novel enzyme families Edwards* within their respective larger enzyme super families. Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Introduction Canada As one of the smallest free-living organisms, Dehalococcoides mccartyi are important for their ability to Summary detoxify ubiquitous and stable groundwater pollutants Gene sequences annotated as proteins of unknown such as chlorinated ethenes and benzenes into benign or or non-specific function and hypothetical proteins less toxic compounds (Maymó-Gatell et al., 1997; Adrian account for a large fraction of most genomes. In et al., 2000; 2007a; He et al., 2003; Löffler et al., 2012). the strictly anaerobic and organohalide respiring Only these strictly anaerobic niche specialists are capable Dehalococcoides mccartyi, this lack of annotation of harnessing energy for growth from the complete detoxi- plagues almost half the genome. Using a combination fication of known human carcinogens, trichloroethene of bioinformatics analyses and genome-wide meta- (TCE) and vinyl chloride (VC) (EPA, 2011, Guha bolic modelling, new or more specific annotations et al., 2012) to benign ethene. This energy-conserving were proposed for about 80 of these poorly annotated metabolic process, termed reductive dechlorination, is genes in previous investigations of D. mccartyi catalysed by reductive dehalogenases, the respiratory metabolism. Herein, we report the experimental vali- enzyme system of D. mccartyi. Reductive dechlorination, dation of the proposed reannotations for two such also known as organohalide respiration, is useful not only genes (KB1_0495 and KB1_0553) from D. mccartyi for the bioremediation of toxic chlorinated solvents, but strains in the KB-1 community. KB1_0495 or DmIDH also a key component to comprehend the recycling of + was originally annotated as an NAD -dependent naturally occurring organohalides (Gribble, 2010; 2012). isocitrate dehydrogenase, but biochemical assays As such, the fundamental understanding of D. mccartyi + revealed its activity primarily with NADP as a metabolism, including the genes and enzymes involved in cofactor. KB1_0553, also denoted as DmPMI, was metabolic processes, has wide-ranging implications for originally annotated as a hypothetical protein/ the remediation of toxic compounds and global element sugar isomerase domain protein. We previously pro- cycling (Gribble, 2012). So far, numerous systems-level posed that it was a bifunctional phosphoglucose studies on D. mccartyi metabolism, including the con- isomerase/phosphomannose isomerase, but only struction of a pan-genome-scale metabolic model phosphomannose isomerase activity was identified (Ahsanul Islam et al., 2010), and various transcriptomic and proteomic analyses (Morris et al., 2006; 2007; Received 11 November, 2014; revised 12 July, 2015; accepted 7 August, 2015. *For correspondence. E-mail elizabeth.edwards@ Johnson et al., 2008; 2009; Lee et al., 2012), have begun utoronto.ca; Tel. 416 946 3506; Fax 416 978 8605. to shed light on key metabolic processes and associated doi:10.1111/1751-7915.12315 genes. †Present address: Department of Chemical Engineering, Massachu- setts Institute of Technology, Cambridge, Massachusetts, USA. Although D. mccartyi metabolism is well studied, the Funding Information This research was funded by the University of activities of only a handful of metabolic genes have Toronto, the Natural Sciences and Engineering Research Council of been experimentally validated. These include an Canada (NSERC), the Government of Canada through Genome Canada and Ontario Genomics Institute (2009-OGI-ABC-1405) and Re-citrate synthase (Marco-Urrea et al., 2011) involved in the United States Department of Defense Strategic Environmental the tricarboxylic acid (TCA)-cycle, a bifunctional Research and Development Program (SERDP). MAI was funded by mannosylglycerate (MG) synthase/phosphatase with a the Ontario Graduate Scholarship (OGS), the SERDP and Genome Canada funds to EAE and the departmental faculty start-up funds to potential role in osmotic stress adaptation (Empadinhas RM. et al., 2004), 12 reductive dehalogenases involved in res- © 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. 2 M. A. Islam et al. piration and energy conservation (Magnuson et al., 1998; btf_472, dcmb_518, GY50_0435) are 98–100% similar at 2000; Krajmalnik-Brown et al., 2004; Müller et al., 2004; the amino acid level (Markowitz et al., 2012). Although Adrian et al., 2007b; Tang et al., 2013; Wang et al., 2014), IDH is an important TCA-cycle enzyme catalysing the + + and two hydrogenases (Jayachandran et al., 2004; formation of 2-oxoglutarate and CO2 with NAD or NADP Nijenhuis and Zinder, 2005) potentially involved in the as a cofactor (Nelson and Cox, 2006; Madigan et al., electron transport chain of D. mccartyi. Genome 2010; Kanehisa et al., 2011), the physiological role of a sequences of several strains of these bacteria (Kube bifunctional PGI/PMI in D. mccartyi is unclear. PGI, in et al., 2005; Seshadri et al., 2005) revealed the presence general, plays a central role in sugar metabolism via of ∼ 50% hypothetical proteins and proteins with unknown glycolysis and gluconeogenesis in all life forms (Hansen or non-specific functions in their genomes. The primary et al., 2004a,b; Nelson and Cox, 2006), whereas PMI gene annotations, including the annotations for more helps to produce precursors for cell wall components, than 80 metabolic genes, were reviewed, and in some glycoproteins, glycolipids and storage polysaccharides instances corrected during the construction and manual (Hansen et al., 2004a; Quevillon et al., 2005; Rajesh curation of the genome-wide D. mccartyi metabolic model et al., 2012). However, glycolysis is inactive in D. mccartyi (Ahsanul Islam et al., 2010). Also, a recent systems-level (Kube et al., 2005; Seshadri et al., 2005; Ahsanul Islam study (Ahsanul Islam et al., 2014) on D. mccartyi et al., 2010), and cells of these bacteria also lack a typical transcriptomes provided additional confidence to some of bacterial cell wall (Löffler et al., 2012). The genes the proposed gene reannotations used in the metabolic (KB1_0495 and KB1_0553) were, thus, heterologously model and helped predict putative functions for five hypo- expressed in E. coli, and the purified proteins were experi- thetical proteins. One such hypothetical protein was mentally tested for activities with enzymatic assays to proposed to be a putative bifunctional phosphoglucose confirm or refute the proposed annotations. Further isomerase (PGI; EC 5.3.1.8)/ phosphomannose bioinformatics analyses of their sequences suggested isomerase (PMI; EC 5.3.1.9) from the gene-expression their affiliation to potentially new enzyme families within analysis (Ahsanul Islam et al., 2014) and metabolic mod- their respective larger enzyme super families. elling studies on D. mccartyi (Ahsanul Islam et al., 2010). Another metabolic gene that was primarily annotated Results and discussion as a putative NAD+-isocitrate dehydrogenase (IDH) (EC Biochemical activities of KB1_0495 and KB1_0553 1.1.1.41) was reannotated as a putative NADP+- dependent IDH (EC 1.1.1.42) during the modelling study. The heterologously expressed and purified protein from However, these proposed reannotations were not sup- KB1_0495 was tested for the IDH activity using a stand- ported by any experimental data. ard assay (Experimental procedures) to measure the con- In this study, we report the heterologous expression and version of D-isocitric acid to 2-oxoglutarate and CO2 using biochemical characterization of the aforementioned puta- NADP+ or NAD+ as a cofactor. The pH range and activity tive IDH (KB1_0495) and PGI/PMI (KB1_0553) from of the enzyme (Table 1) were measured using D-isocitric D. mccartyi in KB-1 (Hug, 2012; Ahsanul Islam et al., acid as substrate. The enzyme showed IDH activity using 2014). KB-1 is a mixed enrichment culture containing both NADP+ and NAD+ as the cofactor, but several
Load more

Recommended publications
  • Microbial Community and Geochemical Analyses of Trans-Trench Sediments for Understanding the Roles of Hadal Environments
    The ISME Journal (2020) 14:740–756 https://doi.org/10.1038/s41396-019-0564-z ARTICLE Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments 1 2 3,4,9 2 2,10 2 Satoshi Hiraoka ● Miho Hirai ● Yohei Matsui ● Akiko Makabe ● Hiroaki Minegishi ● Miwako Tsuda ● 3 5 5,6 7 8 2 Juliarni ● Eugenio Rastelli ● Roberto Danovaro ● Cinzia Corinaldesi ● Tomo Kitahashi ● Eiji Tasumi ● 2 2 2 1 Manabu Nishizawa ● Ken Takai ● Hidetaka Nomaki ● Takuro Nunoura Received: 9 August 2019 / Revised: 20 November 2019 / Accepted: 28 November 2019 / Published online: 11 December 2019 © The Author(s) 2019. This article is published with open access Abstract Hadal trench bottom (>6000 m below sea level) sediments harbor higher microbial cell abundance compared with adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been well explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and fi 1234567890();,: 1234567890();,: Mariana Trenches. Tag-sequencing analyses showed speci c distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortia that covaried across regions. Our results further support that the OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean.
    [Show full text]
  • Evolution of the 3-Hydroxypropionate Bicycle and Recent Transfer of Anoxygenic Photosynthesis Into the Chloroflexi
    Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi Patrick M. Shiha,b,1, Lewis M. Wardc, and Woodward W. Fischerc,1 aFeedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608; bEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; and cDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125 Edited by Bob B. Buchanan, University of California, Berkeley, CA, and approved August 21, 2017 (received for review June 14, 2017) Various lines of evidence from both comparative biology and the provide a hard geological constraint on these analyses, the timing geologic record make it clear that the biochemical machinery for of these evolutionary events remains relative, thus highlighting anoxygenic photosynthesis was present on early Earth and provided the uncertainty in our understanding of when and how anoxy- the evolutionary stock from which oxygenic photosynthesis evolved genic photosynthesis may have originated. ca. 2.3 billion years ago. However, the taxonomic identity of these A less recognized alternative is that anoxygenic photosynthesis early anoxygenic phototrophs is uncertain, including whether or not might have been acquired in modern bacterial clades relatively they remain extant. Several phototrophic bacterial clades are thought recently. This possibility is supported by the observation that to have evolved before oxygenic photosynthesis emerged, including anoxygenic photosynthesis often sits within a derived position in the Chloroflexi, a phylum common across a wide range of modern the phyla in which it is found (3). Moreover, it is increasingly environments. Although Chloroflexi have traditionally been thought being recognized that horizontal gene transfer (HGT) has likely to be an ancient phototrophic lineage, genomics has revealed a much played a major role in the distribution of phototrophy (8–10).
    [Show full text]
  • Anaerobic Bacteria Confirmed Plenary Speakers
    OFFICIALOFFICIAL JOURNALJOURNAL OFOF THETHE AUSTRALIAN SOCIETY FOR MICROBIOLOGY INC.INC. VolumeVolume 3636 NumberNumber 33 SeptemberSeptember 20152015 Anaerobic bacteria Confirmed Plenary speakers Professor Peter Professor Dan Assoc Prof Susan Lynch Dr Brian Conlon Professor Anna Hawkey Andersson University of California Northeastern Durbin University of Upsalla University San Francisco University, Boston Johns Hopkins Birmingham Environmental pollution Colitis, Crohn's Disease Drug discovery in Dengue and vaccines Nosocomial by antibiotics and its and Microbiome soil bacteria infection control and role in the evolution of Research antibiotic resistance resistance As with previous years, ASM 2016 will be co-run with NOW CONFIRMED! EduCon 2016: Microbiology Educators’ Conference 2016 Rubbo Oration Watch this space for more details on the scientific and Professor Anne Kelso social program, speakers, ASM Public Lecture, workshops, CEO NHMRC ASM awards, student events, travel awards, abstract deadlines and much more.. Perth, WA A vibrant and beautiful city located on the banks of the majestic Swan river. Come stay with us in WA and experience our world class wineries and restaurants, stunning national parks, beaches and much more.. www.theasm.org.au www.westernaustralia.theasm.org.au Annual Scientific Meeting and Trade Exhibition The Australian Society for Microbiology Inc. OFFICIAL JOURNAL OF THE AUSTRALIAN SOCIETY FOR MICROBIOLOGY INC. 9/397 Smith Street Fitzroy, Vic. 3065 Tel: 1300 656 423 Volume 36 Number 3 September 2015 Fax: 03 9329 1777 Email: [email protected] www.theasm.org.au Contents ABN 24 065 463 274 Vertical For Microbiology Australia Transmission 102 correspondence, see address below. Jonathan Iredell Editorial team Guest Prof. Ian Macreadie, Mrs Jo Macreadie Editorial 103 and Mrs Hayley Macreadie Anaerobic bacteria 103 Editorial Board Dena Lyras and Julian I Rood Dr Chris Burke (Chair) Dr Gary Lum Under the Prof.
    [Show full text]
  • Evolution of the 3-Hydroxypropionate Bicycle and Recent Transfer of Anoxygenic Photosynthesis Into the Chloroflexi
    Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi Patrick M. Shiha,b,1, Lewis M. Wardc, and Woodward W. Fischerc,1 aFeedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608; bEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; and cDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125 Edited by Bob B. Buchanan, University of California, Berkeley, CA, and approved August 21, 2017 (received for review June 14, 2017) Various lines of evidence from both comparative biology and the provide a hard geological constraint on these analyses, the timing geologic record make it clear that the biochemical machinery for of these evolutionary events remains relative, thus highlighting anoxygenic photosynthesis was present on early Earth and provided the uncertainty in our understanding of when and how anoxy- the evolutionary stock from which oxygenic photosynthesis evolved genic photosynthesis may have originated. ca. 2.3 billion years ago. However, the taxonomic identity of these A less recognized alternative is that anoxygenic photosynthesis early anoxygenic phototrophs is uncertain, including whether or not might have been acquired in modern bacterial clades relatively they remain extant. Several phototrophic bacterial clades are thought recently. This possibility is supported by the observation that to have evolved before oxygenic photosynthesis emerged, including anoxygenic photosynthesis often sits within a derived position in the Chloroflexi, a phylum common across a wide range of modern the phyla in which it is found (3). Moreover, it is increasingly environments. Although Chloroflexi have traditionally been thought being recognized that horizontal gene transfer (HGT) has likely to be an ancient phototrophic lineage, genomics has revealed a much played a major role in the distribution of phototrophy (8–10).
    [Show full text]
  • Research Project Summary
    Division of Science, Research and Environmental Health Research Project Summary August 2016 Applying Innovative Diagnostic Tools at New Jersey Publicly Funded Sites Authors Donna E. Fennell, Ph.D.1 and Max Häggblom, Ph.D.2 Prepared By Robert Mueller, M.S. (Project Manager) 3 Abstract This project demonstrated the use of Environmental Molecular Diagnostic Tools (EMDs) for detecting microbial biodegradation of contaminants and identifying bacteria responsible for contaminant biodegradation or biotransformation at three contaminated sites in New Jersey. These sites were unique based on the contamination present, and EMDs were selected to address a particular issue at each site. EMDs is a collective term that describes a group of advanced and emerging techniques used to analyze biological and chemical characteristics of soils, sediments, groundwater, and surface water. Many of these tools were originally developed for applications in medicine, defense, and industry. Over the last decade, great advances have been made in adapting and applying EMDs for site characterization, remediation, monitoring, and closure. EMDs are important and valuable because they can provide key information not available using traditional analytical methods (e.g., groundwater analysis for volatile organic compounds). While they are intended to complement these traditional methods, EMDs can bring a new perspective to all stages in the environmental management decision-making process. As a result of this work, a bio-augmentation/bio-stimulation design was developed for an organic solvent plume at one site. At a second site, Stable Isotope Probing (SIP) was used to confirm the presence of dehalogenating organisms and bio-stimulation demonstrated rapid reductive dechlorination. Finally, aniline degrading organisms were studied using SIP.
    [Show full text]
  • Multiple Interaction Domains in Ftsl, a Protein Component of the Widely Conserved Bacterial Ftslbq Cell Division Complex Mark D
    Washington University School of Medicine Digital Commons@Becker Open Access Publications 2010 Multiple interaction domains in FtsL, a protein component of the widely conserved bacterial FtsLBQ cell division complex Mark D. Gonzalez Washington University School of Medicine in St. Louis Esra A. Akbay University of Texas Southwestern Medical Center at Dallas Dana Boyd Harvard Medical School Jon Beckwith Harvard Medical School Follow this and additional works at: http://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Gonzalez, Mark D.; Akbay, Esra A.; Boyd, Dana; and Beckwith, Jon, ,"Multiple interaction domains in FtsL, a protein component of the widely conserved bacterial FtsLBQ cell division complex." Journal of Bacteriology.192,11. 2757-2768. (2010). http://digitalcommons.wustl.edu/open_access_pubs/2422 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. JOURNAL OF BACTERIOLOGY, June 2010, p. 2757–2768 Vol. 192, No. 11 0021-9193/10/$12.00 doi:10.1128/JB.01609-09 Copyright © 2010, American Society for Microbiology. All Rights Reserved. Multiple Interaction Domains in FtsL, a Protein Component of the Widely Conserved Bacterial FtsLBQ Cell Division Complexᰔ† Mark D. Gonzalez,1,2 Esra A. Akbay,3 Dana Boyd,1 and Jon Beckwith1* Department of Microbiology and Molecular Genetics, Harvard Medical School, 200
    [Show full text]
  • The Oral Metagenome in Health and Disease
    The ISME Journal (2012) 6, 46–56 & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 www.nature.com/ismej ORIGINAL ARTICLE The oral metagenome in health and disease Pedro Belda-Ferre1, Luis David Alcaraz1, Rau´ l Cabrera-Rubio1,He´ctor Romero2, Aurea Simo´n-Soro1, Miguel Pignatelli1 and Alex Mira1 1Department of Genomics and Health, Center for Advanced Research in Public Health, Valencia, Spain and 2Laboratorio de Organizacio´n y Evolucio´n del Genoma, Facultad de Ciencias/C.U.R.E., Universidad de la Repu´blica, Montevideo, Uruguay The oral cavity of humans is inhabited by hundreds of bacterial species and some of them have a key role in the development of oral diseases, mainly dental caries and periodontitis. We describe for the first time the metagenome of the human oral cavity under health and diseased conditions, with a focus on supragingival dental plaque and cavities. Direct pyrosequencing of eight samples with different oral-health status produced 1 Gbp of sequence without the biases imposed by PCR or cloning. These data show that cavities are not dominated by Streptococcus mutans (the species originally identified as the ethiological agent of dental caries) but are in fact a complex community formed by tens of bacterial species, in agreement with the view that caries is a polymicrobial disease. The analysis of the reads indicated that the oral cavity is functionally a different environment from the gut, with many functional categories enriched in one of the two environments and depleted in the other. Individuals who had never suffered from dental caries showed an over- representation of several functional categories, like genes for antimicrobial peptides and quorum sensing.
    [Show full text]
  • Perfluoroalkyl Acids and Microorganisms: Implications For
    PERFLUOROALKYL ACIDS AND MICROORGANISMS: IMPLICATIONS FOR SUBSURFACE TRANSPORT AND MICROBIAL PROCESSES by Tess Suzanne Weathers A thesis submitted to the Faculty and the Board of Trustees of the Colorado School of Mines in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Hydrology). Golden, Colorado Date: ______________________________ Signed: ______________________________ Tess S. Weathers Signed: ______________________________ Jonathan O. Sharp Thesis Advisor Golden, Colorado Date: ______________________________ Signed: ______________________________ John E. McCray Professor and Head Department of Civil and Environmental Engineering Signed: ______________________________ Terri S. Hogue Professor and Director Hydrologic Science and Engineering Program ii TABLE OF CONTENTS ABSTRACT ...................................................................................................................... vii LIST OF FIGURES ....................................................................................................................... ix LIST OF TABLES ....................................................................................................................... xi ACKNOWLEDGMENTS ............................................................................................................ xii CHAPTER 1 INTRODUCTORY REMARKS .................................................................... 1 CHAPTER 2 PERFLUOROALKYL ACIDS INHIBIT REDUCTIVE DECHLORINATION OF TRICHLOROETHENE BY REPRESSING DEHALOCOCCOIDES
    [Show full text]
  • Systema Naturae. the Classification of Living Organisms
    Systema Naturae. The classification of living organisms. c Alexey B. Shipunov v. 5.601 (June 26, 2007) Preface Most of researches agree that kingdom-level classification of living things needs the special rules and principles. Two approaches are possible: (a) tree- based, Hennigian approach will look for main dichotomies inside so-called “Tree of Life”; and (b) space-based, Linnaean approach will look for the key differences inside “Natural System” multidimensional “cloud”. Despite of clear advantages of tree-like approach (easy to develop rules and algorithms; trees are self-explaining), in many cases the space-based approach is still prefer- able, because it let us to summarize any kinds of taxonomically related da- ta and to compare different classifications quite easily. This approach also lead us to four-kingdom classification, but with different groups: Monera, Protista, Vegetabilia and Animalia, which represent different steps of in- creased complexity of living things, from simple prokaryotic cell to compound Nature Precedings : doi:10.1038/npre.2007.241.2 Posted 16 Aug 2007 eukaryotic cell and further to tissue/organ cell systems. The classification Only recent taxa. Viruses are not included. Abbreviations: incertae sedis (i.s.); pro parte (p.p.); sensu lato (s.l.); sedis mutabilis (sed.m.); sedis possi- bilis (sed.poss.); sensu stricto (s.str.); status mutabilis (stat.m.); quotes for “environmental” groups; asterisk for paraphyletic* taxa. 1 Regnum Monera Superphylum Archebacteria Phylum 1. Archebacteria Classis 1(1). Euryarcheota 1 2(2). Nanoarchaeota 3(3). Crenarchaeota 2 Superphylum Bacteria 3 Phylum 2. Firmicutes 4 Classis 1(4). Thermotogae sed.m. 2(5).
    [Show full text]
  • Metabolic Potential and Survival Strategies of Microbial Communities
    Metabolic potential and survival strategies of microbial communities across extreme temperature gradients on Deception Island volcano, Antarctica AMANDA BENDIA1, Leandro Nascimento Lemos2, Lucas Mendes1, Camila Signori1, Brendan Bohannan3, and Vivian Pellizari1 1University of Sao Paulo 2USP 3University of Oregon August 11, 2020 Abstract Active volcanoes in Antarctica, in contrast to the rest of the icy landscape, have remarkable temperature and geochemical gradients that could select for a wide variety of microbial adaptive mechanisms and metabolic pathways. Deception Island is a stratovolcano flooded by the sea, resulting in contrasting ecosystems such as permanent glaciers (<0 oC) and active fumaroles (up to 100 oC). Steep gradients in temperature, salinity and geochemistry over very short distances have been reported for Deception Island, and have been shown to effect microbial community structure and diversity. However, little is known regarding how these gradients affect ecosystem functioning, for example due to inhibition of key metabolic enzymes or pathways. In this study, we used shotgun metagenomics and metagenome-assembled genomes to explore how microbial functional diversity is shaped by extreme geochemical, salinity and temperature gradients in fumarole and glacier sediments. We observed that microbial communities from a 98 oC fumarole harbor specific hyperthermophilic molecular strategies, as well as reductive and autotrophic pathways, while those from <80 oC fumaroles possess more diverse metabolic and survival strategies capable of responding to fluctuating redox and temperature conditions. In contrast, glacier communities showed less diverse metabolic potentials, comprising mainly heterotrophic and carbon pathways. Through the reconstruction of genomes, we were able to clarify putative novel lifestyles of underrepresented taxonomic groups, especially those related to Nanoarchaeota and thermophilic ammonia-oxidizing archaeal lineages.
    [Show full text]
  • And Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments
    Originally published as: Genderjahn, S., Alawi, M., Mangelsdorf, K., Horn, F., Wagner, D. (2018): Desiccation- and Saline- Tolerant Bacteria and Archaea in Kalahari Pan Sediments. - Frontiers in Microbiology, 9. DOI: http://doi.org/10.3389/fmicb.2018.02082 fmicb-09-02082 September 19, 2018 Time: 14:22 # 1 ORIGINAL RESEARCH published: 20 September 2018 doi: 10.3389/fmicb.2018.02082 Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments Steffi Genderjahn1,2*, Mashal Alawi1, Kai Mangelsdorf2, Fabian Horn1 and Dirk Wagner1,3 1 GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam, Germany, 2 GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, Potsdam, Germany, 3 Institute of Earth and Environmental Science, University of Potsdam, Potsdam, Germany More than 41% of the Earth’s land area is covered by permanent or seasonally arid dryland ecosystems. Global development and human activity have led to an increase in aridity, resulting in ecosystem degradation and desertification around the world. The objective of the present work was to investigate and compare the microbial community structure and geochemical characteristics of two geographically distinct saline pan sediments in the Kalahari Desert of southern Africa. Our data suggest that these microbial communities have been shaped by geochemical drivers, including water content, salinity, and the supply of organic matter. Using Illumina 16S rRNA gene sequencing, this study provides new insights into the diversity of bacteria and archaea Edited by: Jesse G. Dillon, in semi-arid, saline, and low-carbon environments. Many of the observed taxa are California State University, Long halophilic and adapted to water-limiting conditions.
    [Show full text]
  • Anaerobic Microbial Processes for Energy Conservation and Biotransformation of Pollutants
    Anaerobic processes for energy conservation and biotransformation of pollutans Lara M. Paulo M. Lara of pollutans and biotransformation conservation energy for processes Anaerobic Anaerobic microbial processes for energy conservation and biotransformation of pollutants Lara da Luz Ferreira Martins Paulo Propositions 1. Metal supplementation can be used as a strategy to enhance environmental biotechnological processes. (this thesis) 2. Microbial community analysis provides crucial information to understand a particular biological system (this thesis) 3. Scientists are often unsure how to use statistical tools correctly. 4. With their statement ”Life is a net exergonic chemical reaction, it releases energy to go forward.”, Sousa et al. (Phil. Trans. R. Soc. B. 368: 20130088, 2013) ignored that a small input of energy is always required. 5. Besides scientific skills, good scientific collaborations are also necessary to finish a PhD. 6. The deprivation of sunlight has great impact on a person’s happiness and mood. Propositions belonging to the thesis, entitled ‘’Anaerobic microbial processes for energy conservation and biotransformation of pollutants’’ Lara da Luz Ferreira Martins Paulo Wageningen, 8 May 2017 Anaerobic microbial processes for energy conservation and biotransformation of pollutants Lara da Luz Ferreira Martins Paulo Anaerobic microbial processes for energy conservation and Thesis committee biotransformation of pollutants Promotor Prof. Dr Alfons J. M. Stams Personal chair at the Laboratory of Microbiology Wageningen University & Research Lara da Luz Ferreira Martins Paulo Co-promotor Dr Diana Z. Sousa Assistant Professor, Laboratory of Microbiology Wageningen University & Research Thesis Other members submitted in fulfilment of the requirements for the degree of doctor Prof. Dr Grietje Zeeman, Wageningen University & Research at Wageningen University Prof.
    [Show full text]