DOCSLIB.ORG

Effect of the Environment on Horizontal Gene Transfer Between Bacteria and Archaea C

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Effect of the Environment on Horizontal Gene Transfer between Bacteria and Archaea C. A. Fuchsman, R.E. Collins1, W.J. Brazelton2 and G. Rocap [email protected] 1. Present address: University of Alaska Fairbanks School of Oceanography, University of Washington 2. Present address: University of Utah Who Shares Unusually Large #s of Genes? What Genes are Horizontally Transferred? Where is the Transfer Happening? Abstract Difference between Bacteria over the 95% CI Functional Gene Categories Isolation environment for bacteria > 95% CI from Horizontal gene transfer, the transfer and incorporation of & the bacterial dataset genetic material between different species is important in average for horizontally transferred genes Whole Dataset Bacteria with many the evolution and adaption of microbes to their environment. shared genes 448 bacterial and 57 archaeal genomes were compared using Lifestyle reciprocal BLAST hits. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. The DarkHorse algorithm, a probability based lineage-weighted method (Podell and Gaasterland, 2007), identified potential horizontally transferred genes between archaea and bacteria. Archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. This is mainly due Environment of Culture Isolation Horizontally tranferred genes are enriched in inorganic ion transfer to horizontal gene transfer of genes from the archaea to the and energy metabolism. Enriched: hot springs, sediment, soil bacteria. Horizontally transferred genes are enriched in the Shared genes are enriched in translation and nucleotide metabolism, functional gene categories inorganic ion and amino acid transport These two categories are likely shared due to vertical descent. 0 from marine water, freshwater or the gut. and metabolism as well as energy conversion. Potential hotspots of horizontal gene transfer between archaea and bacteria include Bacteria Who Donated the Transferred Genes? hotsprings, sediments, and oil wells. Cold spots for horizontal Hyperthermo Effect of Environment on Gene Transfer Aerobic Meso transfer included dilute aerobic mesophilic environments: marine Bacteria: Sediments Marine Anaerobic Meso Transfer from archaea to bacteria drives high shared gene #s Soil Salt Sludge Hot Spring Facultative Meso Food/Gut Oil Well Freshwater Hydrothermal and freshwater water column. 80 >95% CI Aerobic Thermo The DarkHorse algorithm indicates the direction of transfer. >95% CI Anaerobic Thermo Hot springs archaea Sediment archaea Facultative Thermo Bacteria and Archaea Share Genes Example: Desulfurococcus kamchatkensis 60 hyperthermophilic anaerobic HOTSPRINGS archaea Examine genes between 1 archaea and 1 bacteria 80 80 Bacteria 40 at a time Bacteria with unusually large numbers of shared genes Normal >95% CI Over 95% CI w/this archaea ( >95% CI) are preferentially ANAEROBIC THERMOPHILES Over 95% CI w/other archaea or ANAEROBIC MESOPHILES. 60 60 20 Bacteria Archaea They are also enriched in hotsprings, sediments and oil wells. Genes Transferred Horizontally Total 0 40 40 -150 -100 -50 0 50 -150 -100 -50 0 50 Shared Genes (genome size corrected) Lifestyles of archaea that share unusually large #s of 20 20 genes with bacteria Hotsprings microbes preferentially transfer genes with Archaea other hotsprings microbes. Sediment microbes preferentially transfer genes with other -10 0 0 Use BLAST (<e ) to determine similarity Genes Tranferred Horizontally Total sediment microbes. -200 -100 0 100 0 10 20 30 40 Counting these Reciprocal Best Hits avoids database bias Shared Genes (Genome Size Corrected) HGT from archaea to bacteria Repeat for 57 archaea and 450 bacteria Horizontally transferred genes correlate with shared genes. Transfer in the Marine Environment The bacteria with the most transferred genes with this anaerobic thermophilic Removing the effect of bacterial genome size archaea were also anaerobic and thermophilic. A 4 parameter log-logistic function & Example: Methanosarcina acetivorans Gradient Very little transfer 95% CI were fit for each archaeon 108 cells/g with R. Residuals were calculated. Anaerobic mesophilic MARINE SEDIMENT archaea oxic Marine 80 hot upper 95% CI 80 >95% CI anoxic cold Water column 5 line 10 106 cells/g lower 95% CI cells/g Very Little 60 60 Horizontal Gene Transfer Anaerobic Hyperthermophilic archaea 5 Lots of transfer cell counts = 10 cells/ml 40 40 Anaerobic bacteria share genes with anaerobic archaea. Thermophilic bacteria share genes with thermophilic archaea. Hydrothermal 9 Anoxic Sediment cell counts =10 cells/ml Anaerobic Mesophile Bacteria and archaea with similar lifestyles share genes. 20 20 Vent Supported by two-way ANOSIM p=0.001. Lots of Horizontal Gene Transfer High cell abundances increases transfer rates in biofilms. Total Horizontally Tranferred Genes Tranferred Horizontally Total 0 0 Attached microbes secrete polysaccharides that localize free DNA -200 -100 0 100 0 20 40 60 80 Which archaea share the most or least genes with bacteria? (Molin and Tolker-Nielsen, 2003; Aminov, 2011) Shared Genes (Genome Size Corrected) HGT from archaea to bacteria High Salt (aerobic) Lifestyle Archaea Isolation Archaea There is high virus production and abundance in sediments Anaerobic Thermophile Marine Hot Springs Horizontal transfer from archaea dominates in bacteria with large # of shared genes (Danovaro et al., 2008) Anaerobic Mesophile High Salt Hydrothermal 30 Aerobic Thermophile Freshwater Sediment The bacteria with the most transferred genes with this anaerobic mesophilic ∴Not surprisingly horizontal gene transfer between archaea and Aerobic Mesophile Other Soil I Gut archaea were also anaerobic and mesophilic bacteria is lower in the aerobic dilute environments like the A small genome is an adaptive strategy that allows a C 25 marine water column. microbe to use fewer nutrients & replicate faster. Microbes % 5 Transfer by both domains-- Example: Aeropyrum pernix 9 with small genomes expel unused genes (Giovannoni et al., e h t 20 Aerobic hyperthermophilic HYDROTHERMAL VENT archaea 2005). r 80 Aerobic e v Thermophiles Conclusions: A large genome is an adaptive strategy that allows more o Increasing a 15 i • Anaerobic and thermophilic bacteria share unusually versatility. Microbes with large genomes may keep excess r Oxygen e t 60 genes (Chang et al., 2011). c large numbers of genes with archaea. a 10 High Salt B # To include a range of adaptations, we remove the 40 Marine watercolumn • Gene transfer from archaea to bacteria that live in affect of genome size. 5 10 20 30 40 50 10 20 30 40 50 similar oxygen concentration and temperature Average # shared genes over the 95% CI Average # shared genes over the 95% CI 20 conditions may explain these large #s of shared genes. Many Bacteria over the 95% CI are at the base of the Anaerobic archaea share unusual #s of genes with the most bacteria. Total Horizontally Tranferred Genes Tranferred Horizontally Total 0 phylogenetic tree Aerobic Mesophilic archaea share unusual #s of genes with the fewest bacteria. -200 -100 0 100 0 10 20 30 400 20 40 60 80 •Horizontally transferred genes between archaea and These include high salt and marine archaea. Shared Genes (Genome Size Corrected) HGT from archaea to bacteria HGT from bacteria to archaea bacteria are enriched in the categories inorganic ion Here many of the bacteria with unusual #s of shared genes had transferred genes transfer and energy metabolism. from archaea to bacteria BUT some were transferred from the bacteria to archaea Note: the bacteria transferring genes TO archaea were aerobic thermophiles Where do the Shared Genes Come From? • Potential hotspots of horizontal gene transfer between Example: Nitrosopumilus maritimus 80 archaea and bacteria include hotsprings, sediments, 1) Vertical Descent-- a common ancestor had this gene Aerobic mesophilic and oil wells. Of course some genes are shared due to vertical descent: >95% CI MARINE archaea Mantel test indicates similarily between shared genes & 16S rDNA 60 distances but the R value is small (R=0.176 p=0.0000) • Cold spots for horizontal transfer included dilute 40 aerobic mesophilic environments: marine and 2) Horizontal Gene Transfer-- genes transferred between domains of life freshwater water column. a) Bacteria or archaea can pick up free DNA from the environment b) Viruses can transfer DNA between domains of life 20 Bacteria over the 95% CI (Prangishvili et al., 2006) with Nitrosopumilus were References not aerobic mesophiles. Aminov (2011) Frontiers in Microbiology 2: 158. Horizontally transferred genes were identified using DarkHorse, a statistical 0 Chang et al. (2011) Stand. Genomic Sci. 5: 97–111 Total Horizontally Tranferred Genes Tranferred Horizontally Total Danovaro et al. (2008) Nature 454: 1084-1088. method which calculates phylogenetic distance between the query and its closest -200 -100 0 1000 10 20 30 Giovannoni et al. (2005) Science 309: 1242–5. database match (Podell &Gaasterland, 2007). Shared Genes (Genome Size Corrected) HGT from archaea to bacteria Molin &Tolker-Nielsen (2003) Curr. Opin. Biotechnol. 14: 255–261 Bacterial Dataset Podell &Gaasterland (2007) Genome Biol. 8: R16 In general, transfer from archaea drive unusually large #s of shared genes in bacteria Prangishvili et al. (2006) Nat. Rev. Microbiol. 4: 837–848 Thanks to Michael Carlson..
Recommended publications
  • Horizontal Gene Transfer

    Horizontal Gene Transfer

    Genetic Variation: The genetic substrate for natural selection Horizontal Gene Transfer Dr. Carol E. Lee, University of Wisconsin Copyright ©2020; Do not upload without permission What about organisms that do not have sexual reproduction? In prokaryotes: Horizontal gene transfer (HGT): Also termed Lateral Gene Transfer - the lateral transmission of genes between individual cells, either directly or indirectly. Could include transformation, transduction, and conjugation. This transfer of genes between organisms occurs in a manner distinct from the vertical transmission of genes from parent to offspring via sexual reproduction. These mechanisms not only generate new gene assortments, they also help move genes throughout populations and from species to species. HGT has been shown to be an important factor in the evolution of many organisms. From some basic background on prokaryotic genome architecture Smaller Population Size • Differences in genome architecture (noncoding, nonfunctional) (regulatory sequence) (transcribed sequence) General Principles • Most conserved feature of Prokaryotes is the operon • Gene Order: Prokaryotic gene order is not conserved (aside from order within the operon), whereas in Eukaryotes gene order tends to be conserved across taxa • Intron-exon genomic organization: The distinctive feature of eukaryotic genomes that sharply separates them from prokaryotic genomes is the presence of spliceosomal introns that interrupt protein-coding genes Small vs. Large Genomes 1. Compact, relatively small genomes of viruses, archaea, bacteria (typically, <10Mb), and many unicellular eukaryotes (typically, <20 Mb). In these genomes, protein-coding and RNA-coding sequences occupy most of the genomic sequence. 2. Expansive, large genomes of multicellular and some unicellular eukaryotes (typically, >100 Mb). In these genomes, the majority of the nucleotide sequence is non-coding.
  • Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation

    Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation

    City University of New York (CUNY) CUNY Academic Works Open Educational Resources Queensborough Community College 2016 Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation Joan Petersen CUNY Queensborough Community College Susan McLaughlin CUNY Queensborough Community College How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/qb_oers/16 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation By Dr. Susan McLaughlin & Dr. Joan Petersen Queensborough Community College Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation Table of Contents Preface………………………………………………………………………………………i Acknowledgments…………………………………………………………………………..ii Microbiology Lab Safety Instructions…………………………………………………...... iii Lab 1. Introduction to Microscopy and Diversity of Cell Types……………………......... 1 Lab 2. Introduction to Aseptic Techniques and Growth Media………………………...... 19 Lab 3. Preparation of Bacterial Smears and Introduction to Staining…………………...... 37 Lab 4. Acid fast and Endospore Staining……………………………………………......... 49 Lab 5. Metabolic Activities of Bacteria…………………………………………….…....... 59 Lab 6. Dichotomous Keys……………………………………………………………......... 77 Lab 7. The Effect of Physical Factors on Microbial Growth……………………………... 85 Lab 8. Chemical Control of Microbial Growth—Disinfectants and Antibiotics…………. 99 Lab 9. The Microbiology of Milk and Food………………………………………………. 111 Lab 10. The Eukaryotes………………………………………………………………........ 123 Lab 11. Clinical Microbiology I; Anaerobic pathogens; Vectors of Infectious Disease….. 141 Lab 12. Clinical Microbiology II—Immunology and the Biolog System………………… 153 Lab 13. Putting it all Together: Case Studies in Microbiology…………………………… 163 Appendix I.
  • Horizontal Gene Transfer Elements: Plasmids in Antarctic Microorganisms

    Horizontal Gene Transfer Elements: Plasmids in Antarctic Microorganisms

    Chapter 5 Horizontal Gene Transfer Elements: Plasmids in Antarctic Microorganisms Matías Giménez, Gastón Azziz, Paul R. Gill, and Silvia Batista Abstract Plasmids play an important role in the evolution of microbial communi- ties. These mobile genetic elements can improve host survival and may also be involved in horizontal gene transfer (HGT) events between individuals. Diverse culture-dependent and culture-independent approaches have been used to character- ize these mobile elements. Culture-dependent methods are usually associated with classical microbiological techniques. In the second approach, development of spe- cific protocols for analysis of metagenomes involves many challenges, including assembly of sequences and availability of a reliable database, which are crucial. In addition, alternative strategies have been developed for the characterization of plas- mid DNA in a sample, generically referred to as plasmidome. The Antarctic continent has environments with diverse characteristics, including some with very low temperatures, humidity levels, and nutrients. The presence of microorganisms and genetic elements capable of being transferred horizontally has been confirmed in these environments, and it is generally accepted that some of these elements, such as plasmids, actively participate in adaptation mechanisms of host microorganisms. Information related to structure and function of HGT elements in Antarctic bac- teria is very limited compared to what is known about HGT in bacteria from temper- ate/tropical environments. Some studies are done with biotechnological objectives. The search for mobile elements, such as plasmids, may be related to improve the expression of heterologous genes in host organisms growing at very low tempera- tures. More recently, however, additional studies have been done to detect plasmids in isolates, associated or not with specific phenotypes such as drug resistance.
  • Comprehensive Analysis of Mobile Genetic Elements in the Gut Microbiome Reveals Phylum-Level Niche-Adaptive Gene Pools

    Comprehensive Analysis of Mobile Genetic Elements in the Gut Microbiome Reveals Phylum-Level Niche-Adaptive Gene Pools

    bioRxiv preprint doi: https://doi.org/10.1101/214213; this version posted December 22, 2017. 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. 1 Comprehensive analysis of mobile genetic elements in the gut microbiome 2 reveals phylum-level niche-adaptive gene pools 3 Xiaofang Jiang1,2,†, Andrew Brantley Hall2,3,†, Ramnik J. Xavier1,2,3,4, and Eric Alm1,2,5,* 4 1 Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, 5 Cambridge, MA 02139, USA 6 2 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA 7 3 Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard 8 Medical School, Boston, MA 02114, USA 9 4 Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General 10 Hospital and Harvard Medical School, Boston, MA 02114, USA 11 5 MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 12 02142, USA 13 † Co-first Authors 14 * Corresponding Author bioRxiv preprint doi: https://doi.org/10.1101/214213; this version posted December 22, 2017. 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. 15 Abstract 16 Mobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer 17 could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could 18 threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological 19 importance and medical relevance, MGEs from the gut microbiome have not been systematically 20 characterized.
  • A New Biological Definition of Life

    A New Biological Definition of Life

    BioMol Concepts 2020; 11: 1–6 Research Article Open Access Victor V. Tetz, George V. Tetz* A new biological definition of life https://doi.org/10.1515/bmc-2020-0001 received August 17, 2019; accepted November 22, 2019. new avenues for drug development and prediction of the results of genetic interventions. Abstract: Here we have proposed a new biological Defining life is important to understand the definition of life based on the function and reproduction development and maintenance of living organisms of existing genes and creation of new ones, which is and to answer questions on the origin of life. Several applicable to both unicellular and multicellular organisms. definitions of the term “life” have been proposed (1-14). First, we coined a new term “genetic information Although many of them are highly controversial, they are metabolism” comprising functioning, reproduction, and predominantly based on important biological properties creation of genes and their distribution among living and of living organisms such as reproduction, metabolism, non-living carriers of genetic information. Encompassing growth, adaptation, stimulus responsiveness, genetic this concept, life is defined as organized matter that information inheritance, evolution, and Darwinian provides genetic information metabolism. Additionally, approach (1-5, 15). we have articulated the general biological function of As suggested by the Nobel Prize-winning physicist, life as Tetz biological law: “General biological function Erwin Schrödinger, in his influential essay What Is of life is to provide genetic information metabolism” and Life ?, the purpose of life relies on creating an entropy, formulated novel definition of life: “Life is an organized and therefore defined living things as not just a “self- matter that provides genetic information metabolism”.
  • Section 4. Guidance Document on Horizontal Gene Transfer Between Bacteria

    Section 4. Guidance Document on Horizontal Gene Transfer Between Bacteria

    306 - PART 2. DOCUMENTS ON MICRO-ORGANISMS Section 4. Guidance document on horizontal gene transfer between bacteria 1. Introduction Horizontal gene transfer (HGT) 1 refers to the stable transfer of genetic material from one organism to another without reproduction. The significance of horizontal gene transfer was first recognised when evidence was found for ‘infectious heredity’ of multiple antibiotic resistance to pathogens (Watanabe, 1963). The assumed importance of HGT has changed several times (Doolittle et al., 2003) but there is general agreement now that HGT is a major, if not the dominant, force in bacterial evolution. Massive gene exchanges in completely sequenced genomes were discovered by deviant composition, anomalous phylogenetic distribution, great similarity of genes from distantly related species, and incongruent phylogenetic trees (Ochman et al., 2000; Koonin et al., 2001; Jain et al., 2002; Doolittle et al., 2003; Kurland et al., 2003; Philippe and Douady, 2003). There is also much evidence now for HGT by mobile genetic elements (MGEs) being an ongoing process that plays a primary role in the ecological adaptation of prokaryotes. Well documented is the example of the dissemination of antibiotic resistance genes by HGT that allowed bacterial populations to rapidly adapt to a strong selective pressure by agronomically and medically used antibiotics (Tschäpe, 1994; Witte, 1998; Mazel and Davies, 1999). MGEs shape bacterial genomes, promote intra-species variability and distribute genes between distantly related bacterial genera. Horizontal gene transfer (HGT) between bacteria is driven by three major processes: transformation (the uptake of free DNA), transduction (gene transfer mediated by bacteriophages) and conjugation (gene transfer by means of plasmids or conjugative and integrated elements).
  • Horizontal Gene Transfer and Recombination Analysis of SARS-Cov-2 Genes Helps Discover Its Close Relatives and Shed Light on Its Origin

    Horizontal Gene Transfer and Recombination Analysis of SARS-Cov-2 Genes Helps Discover Its Close Relatives and Shed Light on Its Origin

    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.03.410233; this version posted December 3, 2020. 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 4.0 International license. Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin Vladimir Makarenkov1*, Bogdan Mazoure2*, Guillaume Rabusseau2,3 and Pierre Legendre4 1. Département d’informatique, Université du Québec à Montréal, Montréal, QC, Canada 2. Montreal Institute for Learning Algorithms (Mila), Montréal, QC, Canada 3. Département d'informatique et de recherche opérationnelle, Université de Montréal, Montréal, QC, Canada 4. Département de sciences biologiques, Université de Montréal, C. P. 6128, succursale Centre-ville, Montréal, QC, H3C 3J7 Canada *Both authors contributed equally to this manuscript. Vladimir Makarenkov is the corresponding author of this manuscript (email: [email protected]) Abstract Background The SARS-CoV-2 pandemic is among the most dangerous infectious diseases that have emerged in recent history. Human CoV strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2.
  • EXTREMOPHILES – Vol

    EXTREMOPHILES – Vol

    EXTREMOPHILES – Vol. I - Extremophiles: Basic Concepts - Charles Gerday EXTREMOPHILES: BASIC CONCEPTS Charles Gerday Laboratory of Biochemistry, University of Liège, Belgium Keywords: extremophiles, thermophiles, halophiles, alkaliphiles, acidophiles, metallophiles, barophiles, psychrophiles, piezophiles, extreme conditions Contents 1. Introduction 2. Effects of Extreme Conditions on Cellular Components 2.1. Membrane Structure 2.2. Nucleic Acids 2.2.1. Introduction 2.2.2. Desoxyribonucleic Acids 2.2.3. Ribonucleic Acids 2.3. Proteins 2.3.1. Introduction 2.3.2. Thermophilic Proteins 2.3.3. Psychrophilic Proteins 2.3.4. Halophilic Proteins 2.3.5. Piezophilic Proteins 2.3.6. Alkaliphilic Proteins 2.3.7. Acidophilic Proteins 3. Conclusions Acknowledgments Glossary Bibliography Biographical Sketch Summary Extremophiles are organisms which permanently experience environmental conditions which mayUNESCO be considered as extreme –in comparisonEOLSS to the physico-chemical characteristics of the normal environment of human cells: the latter belonging to the mesophile or temperate world. Some eukaryotic organisms such as fishes, invertebrates, yeasts, fungi, and plants have partially colonized extreme habitats characterized by low temperature and/orSAMPLE of elevated hydrostatic pressure. CHAPTERS In general, however, the organisms capable of thriving at the limits of temperature, pH, salt concentration and hydrostatic pressure, are prokaryotic. In fact, some organisms depend on these extreme conditions for survival and have therefore developed unique adaptations, especially at the level of their membranes and macromolecules, and affecting proteins and nucleic acids in particular. The molecular bases of the various adaptations are beginning to be understood and are briefly described. The study of the extremophile world has contributed greatly to defining, in more precise terms, fundamental concepts such as macromolecule stability and protein folding.
  • Microbial Diversity Course 2005 Attempt to Cultivate Mesophile

    Microbial Diversity Course 2005 Attempt to Cultivate Mesophile

    Microbial Diversity course 2005 Attempt to cultivate mesophile Archaea from marine sediments Lois MAIGNIEN Ghent University Introduction The diversity and ecology of the Archaea domain remains a very intriguing question and a promising field of research. Indeed, it has fisrt been observed that Archaea were thriving in very limited ecological niches, often associated with extreme temperature, salt concentration, or low pH. Methanogens, though very successful in mesophilic anaerobic environments, don’t display the same variety of energy metabolisms as most bacteria. Their growth is restricted to strict anaerobic environments; their substrate range is limited to CO2/H2, acetate and a few methylated compounds. Alternative energy metabolism such as anaerobic respiration (some halophiles and crenarchaeota) using a wide range of terminal electron acceptor such as nitrate (pyrobaculum, pyrococcus), iron III (pyrodictium), sulphate (Archaeoglobus), elemental sulfur (Ignicoccus) or aerobic respiration on sulfur or oxygen are all present in this domain. Some archaea are also able to carry fermentation and even thrive on light energy through the use of bacteriorhodopsin (Halobacterium). Thus, archaea possess in theory high diversity of energy metabolism. So why archaeal cells would display and use this metabolic diversity only in extreme environments? However, several clue from molecular surveys, especially in marine environment, such as 16s clone library and fosmid cloning and sequencing show that Archaea are much more widespread than previously thought, even in mesophilic environments. The main problem that prevent further understanding of their metabolism and environmental contribution have been the inability to cultivate them. An increasing interest for this environmental microbiology mystery, growing number of cultivation attempts, new cultivation methods, and valuable information from metagenomics should progressively reveal the environmental diversity of mesophilic Archaea and provide a better understanding of their contribution to various environments.
  • Microbiologically Contaminated and Over-Preserved Cosmetic Products According Rapex 2008–2014

    Microbiologically Contaminated and Over-Preserved Cosmetic Products According Rapex 2008–2014

    cosmetics Article Microbiologically Contaminated and Over-Preserved Cosmetic Products According Rapex 2008–2014 Edlira Neza * and Marisanna Centini Department of Biotechnologies, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, Siena 53100, Italy; [email protected] * Correspondence: [email protected]; Tel.: +355-685-038-408 Academic Editors: Lidia Sautebin and Immacolata Caputo Received: 25 December 2015; Accepted: 25 January 2016; Published: 30 January 2016 Abstract: We investigated the Rapid Alert System (RAPEX) database from January 2008 until week 26 of 2014 to give information to consumers about microbiologically contaminated cosmetics and over-preserved cosmetic products. Chemical risk was the leading cause of the recalls (87.47%). Sixty-two cosmetic products (11.76%) were recalled because they were contaminated with pathogenic or potentially pathogenic microorganisms. Pseudomonas aeruginosa was the most frequently found microorganism. Other microorganisms found were: Mesophilic aerobic microorganisms, Staphylococcus aureus, Candida albicans, Enterococcus spp., Enterobacter cloacae, Enterococcus faecium, Enterobacter gergoviae, Rhizobium radiobacter, Burkholderia cepacia, Serratia marcescens, Achromabacter xylosoxidans, Klebsiella oxytoca, Bacillus firmus, Pantoea agglomerans, Pseudomonas putida, Klebsiella pneumoniae and Citrobacter freundii. Nine cosmetic products were recalled because they contained methylisothiazolinone (0.025%–0.36%), benzalkonium chloride (1%), triclosan (0.4%) in concentrations higher than the limits allowed by European Regulation 1223/2009. Fifteen products were recalled for the presence of methyldibromo glutaronitrile, a preservative banned for use in cosmetics. Thirty-two hair treatment products were recalled because they contained high concentrations of formaldehyde (0.3%–25%). Keywords: microbiologically contaminated; over-preserved cosmetics; formaldehyde; RAPEX 1. Introduction The European Commission (EC) has an early warning system for safety management called the Rapid Alert System (RAPEX).
  • Managing Risks Associated with Outdoor Use of Genetically Modified Organisms

    Managing Risks Associated with Outdoor Use of Genetically Modified Organisms

    July 2012 Commissioned Review | July 2014 Managing Risks Associated with Outdoor Use of Genetically Modified Organisms Professor Barry Scott FRSNZ Professor Clive Ronson FRSNZ Foreword In February 2014 the Council of the Royal Society of New Zealand considered a request from Federated Farmers to review the validity of scientific conclusions underpinning Auckland Council, Far North District Council, Kaipara District Council and Whangarei District Council Draft Proposed Plan Change to the District /Unitary Plan for Managing Risks Associated with Outdoor Use of Genetically Modified Organisms (GMO) Draft Section 32 Report (January 2013). Professor Barry Scott FRSNZ and Professor Clive Ronson FRSNZ are the authors of this focused review of scientific and technical assertions in that Report, on behalf of the Royal Society of New Zealand. Economic and cultural aspects relating to the outdoor use of GMOs were outside the scope of this review. We thank the authors and peer reviewer Dr Tony Conner FRSNZ for undertaking this work. Sir David Skegg FRSNZ, President, Royal Society of New Zealand Benefits and risks In assessing benefits and risks, both the magnitude and the likelihood of each need to be taken into account; this is the approach taken in New Zealand by agencies such as the Environmental Protection Authority1 and Food Standards Australia New Zealand2. There is an element of risk associated with most human activities but it is the weighing up of magnitude and likelihood that is important in the decision making process. The Report’s section on benefits and risks, however, does not include these considerations in the issues it raises. In considering the risks, the Report highlights the impact of rare events and uses the emergence of bovine spongiform encephalopathy (BSE) in United Kingdom cattle as the example.
  • Horizontal Gene Transfer Is More Frequent with Increased Heterotrophy and Contributes to Parasite Adaptation

    Horizontal Gene Transfer Is More Frequent with Increased Heterotrophy and Contributes to Parasite Adaptation

    Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation Zhenzhen Yanga,b,c,1, Yeting Zhangb,c,d,1,2, Eric K. Wafulab,c, Loren A. Honaasa,b,c,3, Paula E. Ralphb, Sam Jonesa,b, Christopher R. Clarkee, Siming Liuf, Chun Sug, Huiting Zhanga,b, Naomi S. Altmanh,i, Stephan C. Schusteri,j, Michael P. Timkog, John I. Yoderf, James H. Westwoode, and Claude W. dePamphilisa,b,c,d,i,4 aIntercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802; bDepartment of Biology, The Pennsylvania State University, University Park, PA 16802; cInstitute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802; dIntercollege Graduate Program in Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802; eDepartment of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061; fDepartment of Plant Sciences, University of California, Davis, CA 95616; gDepartment of Biology, University of Virginia, Charlottesville, VA 22904; hDepartment of Statistics, The Pennsylvania State University, University Park, PA 16802; iHuck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802; and jDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 Edited by David M. Hillis, The University of Texas at Austin, Austin, TX, and approved September 20, 2016 (received for review June 7, 2016) Horizontal gene transfer (HGT) is the transfer of genetic material diverse angiosperm lineages (13, 14) and widespread incorpo- across species boundaries and has been a driving force in prokaryotic ration of fragments or entire mitochondrial genomes from algae evolution.