Polar Microbiology: The Ecology, Biodiversity and Bioremediation Potential of Microorganisms in Extremely Cold Environments

424 Pages·2009·5.43 MB·English

by  Asim K. Bej

Polar
Microbiology
The Ecology, Biodiversity and
Bioremediation Potential of Microorganisms in
Extremely Cold Environments
Edited by
Asim K. Bej
Jackie Aislabie
Ronald M. Atlas
Boca Raton London New York
CRC Press is an imprint of the
Taylor & Francis Group, an informa business
Cover: Frozen lakes in Schirmacher Oasis and Lake Untersee in East Antarctica. Photo Courtesy: Asim Bej
from 2008 Tawani/NASA Antarctic Scientific Expedition.
CRC Press
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742
© 2010 by Taylor and Francis Group, LLC
CRC Press is an imprint of Taylor & Francis Group, an Informa business
No claim to original U.S. Government works
Printed in the United States of America on acid-free paper
10 9 8 7 6 5 4 3 2 1
International Standard Book Number: 978-1-4200-8384-2 (Hardback)
This book contains information obtained from authentic and highly regarded sources. Reasonable efforts
have been made to publish reliable data and information, but the author and publisher cannot assume
responsibility for the validity of all materials or the consequences of their use. The authors and publishers
have attempted to trace the copyright holders of all material reproduced in this publication and apologize to
copyright holders if permission to publish in this form has not been obtained. If any copyright material has
not been acknowledged please write and let us know so we may rectify in any future reprint.
Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmit-
ted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented,
including photocopying, microfilming, and recording, or in any information storage or retrieval system,
without written permission from the publishers.
For permission to photocopy or use material electronically from this work, please access www.copyright.
com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood
Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and
registration for a variety of users. For organizations that have been granted a photocopy license by the CCC,
a separate system of payment has been arranged.
Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used
only for identification and explanation without intent to infringe.
Library of Congress Cataloging-in-Publication Data
Polar microbiology : the ecology, biodiversity, and bioremediation potential of
microorganisms in extremely cold environments / editors, Asim K. Bej, Jackie
Aislabie, Ronald M. Atlas.
p. ; cm.
Includes bibliographical references and index.
ISBN 978-1-4200-8384-2 (hardcover : alk. paper)
1. Extreme environments--Microbiology. 2. Polar regions. I. Bej, Asim K. II. Aislabie,
Jackie. III. Atlas, Ronald M., 1946-
[DNLM: 1. Microbiological Phenomena--Antarctic Regions. 2. Microbiological
Phenomena--Arctic Regions. 3. Biodegradation, Environmental--Antarctic Regions. 4.
Biodegradation, Environmental--Arctic Regions. 5. Cold Climate--Antarctic Regions. 6.
Cold Climate--Arctic Regions. QW 4 P762 2010]
QR100.9.P65 2010
616.9’041--dc22 2009041209
Visit the Taylor & Francis Web site at
http://www.taylorandfrancis.com
and the CRC Press Web site at
http://www.crcpress.com
Contents
Preface........................................................................................................................v
Editors ......................................................................................................................vii
Contributors ..............................................................................................................ix
Chapter 1 Microbiology of Antarctic Terrestrial Soils and Rocks .......................1
Donald A. Cowan, Nuraan Khan, Caroline Heath, and
Moola Mutondo
Chapter 2 Archaeal Diversity in Antarctic Ecosystems .....................................31
Jackie Aislabie and John P. Bowman
Chapter 3 Bacterial Biodiversity of Antarctica: Conventional Polyphasic
and rRNA Approaches .......................................................................61
Sisinthy Shivaji and G.S.N. Reddy
Chapter 4 L.I.F.E. in Antarctic Lakes .................................................................95
Birgit Sattler and Michael C. Storrie-Lombardi
Chapter 5 Psychrophilic and Psychrotolerant Microbial Extremophiles in
Polar Environments ..........................................................................115
Richard B. Hoover and Elena V. Pikuta
Chapter 6 Cold Adaptation in Antarctic Biodegradative Microorganisms ......157
Asim K. Bej and Nazia Mojib
Chapter 7 Possible Role of Bacteriophage-Mediated Horizontal Gene
Transfer on Microbial Adaptation to Environmental
Stressors in Polar Ecosystems ..........................................................179
Michael C. Storrie-Lombardi and Shannon J. Williamson
Chapter 8 Sources of Organic Matter for the Archean Cryosphere .................201
Perry A. Gerakines and Michael C. Storrie-Lombardi
iii
iv Contents
Chapter 9 Response of Polar Soil Bacterial Communities to Fuel Spills .........215
Jackie Aislabie and Julia M. Foght
Chapter 10 Microbial Degradation of Petroleum Compounds in
Cold Marine Water and Ice ..............................................................231
Odd G. Brakstad, Andrew M. Booth, and Liv-Guri Faksness
Chapter 11 Potential for Microbial Biodegradation of Polychlorinated
Biphenyls in Polar Environments .....................................................255
Angelina Lo Giudice, Vivia Bruni, and Luigi Michaud
Chapter 12 Tolerance of Antarctic Soil Fungi to Hydrocarbons and Their
Potential Role in Soil Bioremediation ..............................................277
Kevin A. Hughes and Paul Bridge
Chapter 13 Do Fertilizers Help in Effective Bioremediation of Polycyclic
Aromatic Hydrocarbons in Polar Soils? ...........................................301
Daniel Delille, Emilien Pelletier, and Frédéric Coulon
Chapter 14 Bioremediation of Contaminated Sites in the Canadian Arctic:
Monitoring Performance and the Effects of Biostimulation
Using Molecular Methods ................................................................319
Charles W. Greer
Chapter 15 Occurrence, Distribution, and Nature of Hydrocarbon-
Degrading Genes in Biodegradative Microorganisms
from the Antarctic Environment ......................................................339
Adriana Philippi Luz, Emanuele Kuhn, and
Vivian Helena Pellizari
Chapter 16 Potential Use of Real-Time PCR to Assess Changes in
the Microbial Population Structure and Function during
Bioremediation of Polar Soils ..........................................................357
Shane M. Powell
Chapter 17 Microbial Bioremediation in Polar Environments: Current
Status and Future Directions ............................................................373
Ronald M. Atlas
Index ......................................................................................................................393
Preface
Polar Microbiology: The Ecology, Biodiversity, and Bioremediation Potential of
Microorganisms in Extremely Cold Environments explores the fi eld of polar microbiol-
ogy and, in particular, the environmental impact of hydrocarbon contamination and
the potential for microbial bioremediation. The polar regions of this planet include the
Antarctic continent and the area north of the tree line of the Arctic Circle. Ice domi-
nates much of the Antarctic continent and the Arctic Ocean. In fact, the polar environ-
ment is the coldest on Earth and poses signifi cant challenges to life in the Arctic and
the Antarctic. Yet, in this extremely cold environment, populations of microorganisms
thrive and carry out critical ecological functions. These microorganisms are adapted to
growing at low temperatures and have diverse and often unique metabolic capabilities.
Although they have had only limited exposure to pollutants, many microorgan-
isms that are indigenous to Arctic and Antarctic ecosystems are able to degrade
pollutants. It is this metabolic capacity that forms the basis for bioremediation as
a potential treatment for hydrocarbons that may contaminate polar environments.
Contamination may happen as a result of oil extraction and transport in the Arctic
and human activities in both the northern and southern polar regions.
Currently, much of the polar environment is relatively undisturbed by direct human
activities. However, global warming is causing the melting of ice, and the depletion
of the atmospheric ozone is exposing polar environments to increased ultraviolet
radiation. It is evident that the polar environment is changing, and increasing human
activities threaten to bring about signifi cant pollution in the polar terrestrial and
aquatic ecosystems. In particular, human activities pose serious risks of environmen-
tal contamination with petroleum hydrocarbons, especially in the Arctic due to oil
exploration, marine transportation, and human habitation, and in the Antarctic due
to tourism and scientifi c research activities.
It is critical that we exercise all prudent measures to prevent the environmental
contamination of polar regions. However, if we fail, we must have contingency plans
for abating pollution levels thereby restoring the ecosystem. It is within this con-
text that this book examines the diversity of polar microorganisms and their abili-
ties to degrade petroleum hydrocarbons that may contaminate ice, soil, and both
marine and freshwater aquatic environments in the Arctic and the Antarctic. In the
Antarctic, increased scientifi c knowledge about microbes is being generated as sci-
entifi c research activities have taken on a priority. In the Arctic, much is known
about the practical problems of dealing with pollutants.
Pollution with petroleum hydrocarbons has accompanied polar exploration from
its inception and now seems to be an unavoidable consequence of oil exploration and
extraction in the Arctic and scientifi c research activities in the Antarctic. Since the
fi rst landing on the Antarctic continent by Captain John Davis in 1821 (in the Cecilia
islands at Hughes Bay in the Antarctic Peninsula), numerous expeditions have been
completed resulting in the establishment of permanent research stations and bases
representing over 30 nations.
v
vi Preface
Even the earliest polar expeditions by Scott, Shackleton, and Amundsen polluted
the environment as they carried out their historic explorations. These early explor-
ers brought large quantities of supplies, including petroleum fuels, to support their
activities as they sought to reach the North and South Poles. When the expeditions
ended, materials that contaminated the environment—including stored fuels—were
left behind. Corrosion and weathering of wooden structures led to leakages into
the environment. Consequently, high concentrations of polyaromatic hydrocarbons,
such as anthracene, benzo[b]fl uoranthene, benzo[k]fl uoranthene, chrysene, fl uorene,
and pyrene, as well as benzo[a]anthracene, benzo[a]pyrene, and fl uoranthene, which
are recognized carcinogens, have contaminated Antarctic soils under and around the
historic fuel depots.* In the Arctic, many early exploration wells were not properly
capped and many are now surrounded by oozing oil, resulting in the contamination
of these historic sites, which need to be remediated.
Since 1960, human presence in the Antarctic continent has increased signifi cantly,
thereby requiring a greater need for energy to power the research stations and for
aviation and ground transportation refueling. It has therefore become necessary to
have year-round storage of hydrocarbon-based fuels, such as diesel and petroleum, at
bases and locations where temporary research stations have been established. Such
activities have all too frequently resulted in accidental oil spills causing the con-
tamination of ice, soil, lakes, and coastal sediments and waters. In the Arctic, the
development of oil wells and pipelines to transport oil southward has resulted in the
oil pollution of many previously pristine environments.
Petroleum hydrocarbon spills in the Antarctic and Arctic environments have cre-
ated pockets of microbial consortia in which biodegradative microorganisms have
been selected and have naturally become enriched over time with the hydrocarbon
and diesel fuels acting as the carbon source. This book is a compilation of the state
of scientifi c knowledge about the microbial populations that are present in polar eco-
systems and the diversity of their genes and physiological capabilities. It provides
an overview of the extremophilic microorganisms that inhabit polar ecosystems and
their potential for microbial bioremediation in the cold polar environments. All the
chapters have been written by leading investigators in the fi eld of polar m icrobiology.
This is the fi rst book to present a broad overview of the study of the ecology, the
diversity, and the bioremediation potential of microorganisms in extremely cold polar
environments. It should therefore serve as a very valuable resource for scientists and
those charged with environmental protection and the management of polar regions.
Asim K. Bej
Birmingham, Alabama
Jackie Aislabie
Hamilton, New Zealand
Ronald M. Atlas
Louisville, Kentucky
* For a discussion of the environmental pollution caused by early Antarctic expeditions see Blanchette,
R.A., B.W. Held, J.A. Jurgens, J. Aislabie, S. Duncan, and R.L. Farrell. 2004. Environmental pollutants
from the Scott and Shackleton expeditions during the “Heroic Age” of Antarctic exploration. Polar
Record 40: 143–151.
Editors
Asim K. Bej is currently a professor of biology at the University of Alabama at
Birmingham (UAB). He received his PhD in biology with research in microbial
molecular genetics from the University of Louisville at Kentucky, where he contin-
ued as a postdoctoral fellow in environmental molecular microbiology. He joined
UAB as an assistant professor in 1991 and was promoted to professor of biology in
2003. His research interests include the study of microbial extremophiles including
biodegradative microorganisms in cold environments, mechanisms of cold adapta-
tion, and the application of microbial metabolites in biomedical science and diagnos-
tics. He is a member of the editorial board of several microbiology journals and has
served as a guest journal editor. He has published nearly 100 manuscripts in scientifi c
journals and over 20 book chapters. He is an honorary member of the Golden Key
International Honor Society, a recipient of the NASA Faculty Fellowship program,
and a member of the Tawani International Antarctic Scientifi c Expedition.
Jackie Aislabie is a research leader within the Soils and Landscape Team at Landcare
Research in Hamilton, New Zealand. She received her BSc (Hons) and PhD from
the University of Otago, Dunedin, New Zealand. She was a postdoctoral fellow
at the University of Louisville, Kentucky, where she worked on the use of microbes
for the selective removal of nitrogen from shale oil. She has also worked as a lecturer
in microbiology at the University of Canterbury, Christchurch, New Zealand, and
has authored 70 manuscripts. She has been working in Antarctica since 1995 and has
added to the knowledge of microbial diversity of Antarctic soils and the potential of
bioremediation for hydrocarbon-contaminated Antarctic soils.
Ronald M. Atlas is a professor of biology and public health, and a codirector of the
Center for Health Hazards Preparedness at the University of Louisville, Kentucky.
He received his BS from the State University at Stony Brook, New York, his MS
and PhD from Rutgers University, and his DSc (honoris causa) from the University
of Guelph, Ontario, Canada. He was a postdoctoral fellow at the Jet Propulsion
Laboratory, Pasadena, California, where he worked on Mars life detection. He has
previously served as the president of the American Society for Microbiology; as a
member of the NIH Recombinant Advisory Committee; as a member of the DHS
Homeland Security Science and Technology Advisory Committee; as the chair of
NASA’s Planetary Protection Subcommittee; as the chair of the Wellcome Trust
Pathogens, Immunology and Population Health Strategy Committee; and as a
cochair of the American Society for Microbiology Biodefense Committee. He is a
fellow of the American Academy of Microbiology and has received the ASM Award
for Applied and Environmental Microbiology, the ASM Founders Award, and the
Edmund Youde Lectureship Award in Hong Kong. He has authored nearly 300 man-
uscripts and 20 books. He has helped pioneer the fi eld of bioremediation and has
published extensively on oil biodegradation in the Arctic and sub-Arctic regions.
vii

Contributors
Jackie Aislabie Vivia Bruni
Landcare Research Department of Animal Biology and
Hamilton, New Zealand Marine Ecology
Italian Collection of Antarctic Bacteria
University of Messina
Ronald M. Atlas
Messina, Italy
Department of Biology
University of Louisville
Louisville, Kentucky Frédéric Coulon
Sustainable Systems Department
Centre for Resource Management
Asim K. Bej
and Effi ciency
Department of Biology
School of Applied Sciences
University of Alabama at Birmingham
Cranfi eld University
Birmingham, Alabama
Cranfi eld, United Kingdom
Andrew M. Booth
Donald A. Cowan
Department of Marine Environmental
Department of Biotechnology
Technology
Institute for Microbial Biotechnology
SINTEF Materials and Chemistry
and Metagenomics
Trondheim, Norway
University of the Western Cape
Cape Town, South Africa
John P. Bowman
School of Agricultural Sciences
Daniel Delille
University of Tasmania
Observatoire Océanologique
Hobart, Tasmania, Australia
de Banyuls
Université Pierre et Marie Curie
Odd G. Brakstad Unité Mixte de Recherche-Centre
Department of Marine Environmental National de la Recherche
Technology Scientifi que
SINTEF Materials and Chemistry Banyuls sur mer, France
Trondheim, Norway
Liv-Guri Faksness
Paul Bridge Department of Marine Environmental
British Antarctic Survey Technology
Natural Environment Research Council SINTEF Materials and Chemistry
Cambridge, United Kingdom Trondheim, Norway
ix