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New Opportunities Revealed by Biotechnological Explorations of Extremophiles - Mircea Podar and Anna-Louise Reysenbach
BIOTECHNOLOGY – Vol .III – New Opportunities Revealed by Biotechnological Explorations of Extremophiles - Mircea Podar and Anna-Louise Reysenbach NEW OPPORTUNITIES REVEALED BY BIOTECHNOLOGICAL EXPLORATIONS OF EXTREMOPHILES Mircea Podar and Anna-Louise Reysenbach Department of Biology, Portland State University, Portland, OR 97201, USA. Keywords: extremophiles, genomics, biotechnology, enzymes, metagenomics. Contents 1. Introduction 2. Extremophiles and Biomolecules 3. Extremophile Genomics Exposing the Biotechnological Potential 4. Tapping into the Hidden Biotechnological Potential through Metagenomics 5. Unexplored Frontiers and Future Prospects Acknowledgements Glossary Bibliography Biographical Sketches Summary Over the past few decades the extremes at which life thrives has continued to challenge our understanding of biochemistry, biology and evolution. As more new extremophiles are brought into laboratory culture, they have provided a multitude of new potential applications for biotechnology. Furthermore, more recently, innovative culturing approaches, environmental genome sequencing and whole genome sequencing have provided new opportunities for biotechnological exploration of extremophiles. 1. Introduction Organisms that live at the extremes of pH (>pH 8.5,< pH 5.0), temperature (>45°C, <15°C), pressure (>500 atm), salinity (>1.0M NaCl) and in high concentrations of recalcitrant substances or heavy metals (extremophiles) represent one of the last frontiers for biotechnological and industrial discovery. As we learn more about the -
Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co. -
Molecular Detection of Tick-Borne Pathogens in Ticks Collected from Hainan Island, China
Molecular Detection of Tick-Borne Pathogens in Ticks Collected From Hainan Island, China Miao Lu National Institute for Communicable Disease Control and Prevention Guangpeng Tang PHLIC: Centers for Disease Control and Prevention Xiaosong Bai Congjiang CDC Xincheng Qin National Institute for Communicable Disease Control and Prevention Wenping Guo Chengde Medical University Kun Li ( [email protected] ) National Institute for Communicable Disease Control and Prevention Research Keywords: Ticks, Rickettsiales bacteria, Protozoa, Coxiellaceae bacteria, Tick-borne disease, China Posted Date: December 1st, 2020 DOI: https://doi.org/10.21203/rs.3.rs-114641/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/29 Abstract Background Kinds of pathogens such as viruses, bacteria and protozoa are transmitted by ticks as vectors, and they have deeply impact on human and animal health worldwide. Methods To better understand the genetic diversity of bacteria and protozoans carried by ticks in Chengmai county of Hainan province, China, 285 adult hard ticks belonging to two species (Rhipicephalus sanguineus: 183, 64.21% and R. microplus: 102, 35.79%) from dogs, cattle, and goats were colleted. Rickettsiales bacteria, Coxiellaceae bacteria, Babesiidae, and Hepatozoidae were identied in these ticks by amplifying the 18S rRNA, 16S rRNA (rrs), citrate synthase (gltA), and heat shock protein (groEL) genes. Results Our data revealed the presence of four recognized species and two Candidatus spp. of Anaplasmataceae and Coxiellaceae in locality. Conclusions In sum, these data reveal an extensive diversity of Anaplasmataceae bacteria, Coxiellaceae bacteria, Babesiidae, and Hepatozoidae in ticks from Chengmai county, highlighting the need to understand the tick-borne pathogen infection in local animals and humans. -
DDDC 2019 Organizing Committee
Conference Sponsors 2 Drug Discovery and Development Colloquium 2018 VI Annual Conference June 13 - 15, 2019 DDDC 2019 Organizing Committee Skylar Connor, Conference Co-chair, SHraddHa THakkar, PH.D., Conference Co-chair, UAMS AAPS Student CHapter President, Student UAMS AAPS Student CHapter Sponsor, Faculty University of Arkansas for Medical Sciences • FDA National Center for Toxicological Research University of Arkansas Little Rock Ujwani Nukala, Organizing Committee, UAMS Cesar M. Compadre, PH.D., Conference Co-chair, AAPS Student CHapter Past-President, Student UAMS AAPS Student CHapter Co-Sponsor, University of Arkansas for Medical Sciences Faculty University of Arkansas Little Rock University of Arkansas for Medical Sciences Ting Lee, Organizing Committee, UAMS AAPS David Mery, Organizing Committee, UAMS Student CHapter Treasurer, Student AAPS Student CHapter CHair Elect, Student University of Arkansas for Medical Sciences. University of Arkansas for Medical Sciences University of Arkansas Little Rock Cord Carter, Organizing Committee, UAMS AAPS Pankaj Patyal, Organizing Committee, UAMS Student CHapter Secretary, Student AAPS Student CHapter Vice President, Student University of Arkansas for Medical Sciences University of Arkansas for Medical Sciences Taylor Connor, Organizing Committee, UAMS Nemu Saumyadip, Organizing Committee, AAPS Student Chapter Member, Student UAMS AAPS Student CHapter Member, Student University of Arkansas for Medical Sciences University of Arkansas for Medical Sciences PHuc Tran, Organizing Committee, UAMS AAPS Edward Selvik, Organizing Committee, UAMS Student CHapter Member, Student AAPS Student CHapter Member, Student University of Arkansas for Medical Sciences University of Arkansas for Medical Sciences University of Arkansas Little Rock Table of Contents DDDC 2019 Agenda 5 List of Poster Presenters 10 Speakers and Organizers Bios 11 Abstracts 23 3 Drug Discovery and Development Colloquium 2019 University of Arkansas for Medical Sciences I. -
General Introduction
Physiological Characteristics and Genomic Properties of Nitrosomonas mobilis Isolated from Nitrifying Granule of Wastewater Treatment Bioreactor December 2016 Soe Myat Thandar ソー ミャット サンダー Physiological Characteristics and Genomic Properties of Nitrosomonas mobilis Isolated from Nitrifying Granule of Wastewater Treatment Bioreactor December 2016 Waseda University Graduate School of Advanced Science and Engineering Department of Life Science and Medical Bioscience Research on Environmental Biotechnology Soe Myat Thandar ソー ミャット サンダー Contents Abbreviations ................................................................................................................... i Chapter 1-General introduction .................................................................................... 1 1.1. Nitrification and wastewater treatment system .......................................................... 3 1.2. Important of Nitrosomonas mobilis ........................................................................... 8 1.3. Objectives and outlines of this study ....................................................................... 12 1.4. Reference.................................................................................................................. 12 Chapter 2- Physiological characteristics of Nitrosomonas mobilis Ms1 ................... 17 2.1. Introduction .............................................................................................................. 19 2.2. Material and methods .............................................................................................. -
APP201895 APP201895__Appli
APPLICATION FORM DETERMINATION Determine if an organism is a new organism under the Hazardous Substances and New Organisms Act 1996 Send by post to: Environmental Protection Authority, Private Bag 63002, Wellington 6140 OR email to: [email protected] Application number APP201895 Applicant Neil Pritchard Key contact NPN Ltd www.epa.govt.nz 2 Application to determine if an organism is a new organism Important This application form is used to determine if an organism is a new organism. If you need help to complete this form, please look at our website (www.epa.govt.nz) or email us at [email protected]. This application form will be made publicly available so any confidential information must be collated in a separate labelled appendix. The fee for this application can be found on our website at www.epa.govt.nz. This form was approved on 1 May 2012. May 2012 EPA0159 3 Application to determine if an organism is a new organism 1. Information about the new organism What is the name of the new organism? Briefly describe the biology of the organism. Is it a genetically modified organism? Pseudomonas monteilii Kingdom: Bacteria Phylum: Proteobacteria Class: Gamma Proteobacteria Order: Pseudomonadales Family: Pseudomonadaceae Genus: Pseudomonas Species: Pseudomonas monteilii Elomari et al., 1997 Binomial name: Pseudomonas monteilii Elomari et al., 1997. Pseudomonas monteilii is a Gram-negative, rod- shaped, motile bacterium isolated from human bronchial aspirate (Elomari et al 1997). They are incapable of liquefing gelatin. They grow at 10°C but not at 41°C, produce fluorescent pigments, catalase, and cytochrome oxidase, and possesse the arginine dihydrolase system. -
Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg -
Differential Depth Distribution of Microbial Function and Putative Symbionts Through Sediment-Hosted Aquifers in the Deep Terrestrial Subsurface
ARTICLES https://doi.org/10.1038/s41564-017-0098-y Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface Alexander J. Probst1,5,7, Bethany Ladd2,7, Jessica K. Jarett3, David E. Geller-McGrath1, Christian M. K. Sieber1,3, Joanne B. Emerson1,6, Karthik Anantharaman1, Brian C. Thomas1, Rex R. Malmstrom3, Michaela Stieglmeier4, Andreas Klingl4, Tanja Woyke 3, M. Cathryn Ryan 2* and Jillian F. Banfield 1* An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome- resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep- branching nanoarchaea dominate the deepest groundwater. A nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface. -
The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment
life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment. -
Evolution and Design Governing Signal Precision and Amplification
Evolution and Design Governing Signal Precision and Amplification in a Bacterial Chemosensory Pathway Mathilde Guzzo, Rym Agrebi, Leon Espinosa, Gregory Baronian, Virginie Molle, Emilia M. F. Mauriello, Céline Brochier-Armanet, Tam Mignot To cite this version: Mathilde Guzzo, Rym Agrebi, Leon Espinosa, Gregory Baronian, Virginie Molle, et al.. Evolution and Design Governing Signal Precision and Amplification in a Bacterial Chemosensory Pathway. PLoS Genetics, Public Library of Science, 2015, 11 (8), pp.e1005460. 10.1371/journal.pgen.1005460. hal- 01452074 HAL Id: hal-01452074 https://hal.archives-ouvertes.fr/hal-01452074 Submitted on 27 Sep 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License RESEARCH ARTICLE Evolution and Design Governing Signal Precision and Amplification in a Bacterial Chemosensory Pathway Mathilde Guzzo1☯, Rym Agrebi1☯¤, Leon Espinosa1, Grégory Baronian2, Virginie Molle2, Emilia M. F. Mauriello1, Céline Brochier-Armanet3, Tâm Mignot1* 1 Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS Aix-Marseille University UMR 7283, Marseille, France, 2 Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, CNRS Universités de Montpellier II et I, UMR 5235, case 107, Montpellier, France, 3 Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France ☯ These authors contributed equally to this work. -
Revealing the Full Biosphere Structure and Versatile Metabolic Functions In
Chen et al. Genome Biology (2021) 22:207 https://doi.org/10.1186/s13059-021-02408-w RESEARCH Open Access Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep Ping Chen1†, Hui Zhou1,2†, Yanyan Huang3,4†, Zhe Xie5†, Mengjie Zhang1,2†, Yuli Wei5, Jia Li1,2, Yuewei Ma3, Min Luo5, Wenmian Ding3, Junwei Cao5, Tao Jiang1,2, Peng Nan3*, Jiasong Fang5* and Xuan Li1,2* * Correspondence: nanpeng@fudan. edu.cn; [email protected]; lixuan@ Abstract sippe.ac.cn †Ping Chen, Hui Zhou, Yanyan Background: The full biosphere structure and functional exploration of the microbial Huang, Zhe Xie and Mengjie Zhang communities of the Challenger Deep of the Mariana Trench, the deepest known contributed equally to this work. hadal zone on Earth, lag far behind that of other marine realms. 3Ministry of Education Key Laboratory for Biodiversity Science Results: We adopt a deep metagenomics approach to investigate the microbiome and Ecological Engineering, School in the sediment of Challenger Deep, Mariana Trench. We construct 178 of Life Sciences, Fudan University, Shanghai, China metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are 5Shanghai Engineering Research reported from hadal sediment for the first time. Based on the MAGs, we find the Center of Hadal Science and microbial community functions are marked by enrichment and prevalence of Technology, College of Marine Sciences, Shanghai Ocean mixotrophy and facultative anaerobic metabolism. The microeukaryotic community is University, Shanghai, China found to be dominated by six fungal groups that are characterized for the first time 1CAS-Key Laboratory of Synthetic in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute reduction, and hydrogen sulfide oxidation pathways. -
Thermophilic Carboxydotrophs and Their Applications in Biotechnology Springerbriefs in Microbiology
SPRINGER BRIEFS IN MICROBIOLOGY EXTREMOPHILIC BACTERIA Sonia M. Tiquia-Arashiro Thermophilic Carboxydotrophs and their Applications in Biotechnology SpringerBriefs in Microbiology Extremophilic Bacteria Series editors Sonia M. Tiquia-Arashiro, Dearborn, MI, USA Melanie Mormile, Rolla, MO, USA More information about this series at http://www.springer.com/series/11917 Sonia M. Tiquia-Arashiro Thermophilic Carboxydotrophs and their Applications in Biotechnology 123 Sonia M. Tiquia-Arashiro Department of Natural Sciences University of Michigan Dearborn, MI USA ISSN 2191-5385 ISSN 2191-5393 (electronic) ISBN 978-3-319-11872-7 ISBN 978-3-319-11873-4 (eBook) DOI 10.1007/978-3-319-11873-4 Library of Congress Control Number: 2014951696 Springer Cham Heidelberg New York Dordrecht London © The Author(s) 2014 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer.