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 HYDROCARBON
BIOTECHNOLOGY
Challenges and Future Trends

Edited by
Wael Ahmed Ismail, PhD
Jonathan Van Hamme, PhD
First edition published 2023
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Library and Archives Canada Cataloguing in Publication

Title: Hydrocarbon biotechnology : challenges and future trends / edited by Wael Ahmed Ismail, PhD, Jonathan Van Hamme,
PhD.
Names: Ismail, Wael Ahmed, editor. | Van Hamme, Jonathan, editor.
Description: First edition. | Includes bibliographical references and index.
Identifiers: Canadiana (print) 20220213690 | Canadiana (ebook) 20220213747 | ISBN 9781774639894 (hardcover) |
ISBN 9781774639900 (softcover) | ISBN 9781003277354 (ebook)
Subjects: LCSH: Hydrocarbons—Biotechnology. | LCSH: Microbiology. | LCSH: Bioremediation. | LCSH: Fossil fuels.
Classification: LCC QD305.H5 H93 2023 | DDC 547/.01—dc23
Library of Congress Cataloging-in-Publication Data

CIP data on file with US Library of Congress

ISBN: 978-1-77463-989-4 (hbk)

ISBN: 978-1-77463-990-0 (pbk)
ISBN: 978-1-00327-735-4 (ebk)
About the Editors

Wael Ahmed Ismail, PhD

Environmental Biotechnology Program,
Life Sciences Dept., College of Graduate Studies,
Arabian Gulf University, Manama, Bahrain

Wael Ahmed Ismail, PhD, is a Professor of Micro­

biology and Environmental Biotechnology, and the
former director of the Biotechnology Program at the
Arabian Gulf University. Having more than 25 years of research experience
in the field of microbial biodegradation of hydrocarbons (HCs), Dr. Ismail
received his BSc in Microbiology and Chemistry from Ain Shams Univer­
sity (Cairo-Egypt) and joined the Egyptian Petroleum Research Institute in
1994 to pursue his MSc in Petroleum Microbiology. He then moved to the
Department of Microbiology at Freiburg University, Germany, to earn his
PhD (funded by the German Research Foundation) under the supervision of
Prof. Georg Fuchs. His PhD research was dedicated to the biochemistry and
molecular biology of microbial degradation of aromatic compounds, with
particular focus on the elucidation of unprecedented catabolic pathways (the
hybrid pathways) for aromatic compounds degradation. During his post­
doctoral training in the same group, he continued research on the aerobic
and anaerobic degradation of aromatic compounds. In addition, he joined
projects on the anaerobic degradation of cholesterol, where he contributed
to the molecular and biochemical elucidation of previously uncharacter­
ized catabolic pathways. In 2008, Dr. Wael was appointed as a Research
Assistant Professor at the Center of Environmental Biotechnology at the
University of Massachusetts, Amherst (USA), where he worked with Prof.
Derek Lovley. During that time, he conducted molecular biology studies
on Geobacter sulfurreducens and Rhodoferax ferrireducens, key players in
microbial fuel cells (MFCs). Currently, his research focuses on biodegrada­
tion of crude oil and steroids, biosurfactants production and applications,
biodesulfurization (BDS) of diesel fuel, as well as biocatalytic upgrading of
heavy oil and refinery residues. A major part of his research deals with the
application of systems biology to advance the understanding of biochemistry
and physiology of bacteria adopted in petroleum biotechnological processes.
vi About the Editors

He works in close association with the oil and gas authorities and research
institutes in Bahrain and Kuwait. He was recently appointed as an associate
editor at Frontiers in Microbiology and was also the lead guest editor for
two special issues on Petroleum Biotechnology and Biodesulfurization in
the same journal.

Jonathan Van Hamme, PhD

Department of Biological Sciences,
Thompson Rivers University, Kamloops,
British Columbia, Canada

Jonathan Van Hamme, PhD, is a Professor of Micro­

biology and founding Director of the TRUGen
Applied Genomics Laboratory, the only high-
throughput sequencing facility in central British
Columbia. He is an applied environmental microbiologist with over 25
years of experience in petroleum microbiology, industrial waste treatment,
contaminant biotransformation, phytoremediation, analytical chemistry,
proteomics, and genomics, including bacterial genome sequencing, micro­
bial community characterization, and eDNA detection of insects, plants, and
animals. He received an Honors BSc in Biology with a Chemistry Minor from
the University of Waterloo in 1996, and a PhD in petroleum microbiology
from the University of Waterloo in 2000. After three years with the National
Resources Canada at their National Center for Upgrading Technology, where
he was leading the work on microbial biotechnologies for heavy oil upgrading,
he joined Thompson Rivers University and established his own research
program. Since that time, he has built a world-class molecular microbiology
laboratory that includes equipment for aerobic and anaerobic microbiology,
fermentations up to 40 liters, proteomics, high-throughput sequencing (Ion
S5, Oxford Nanopore, Sanger), and stable isotope probing (SIP). With a
major focus on environmental remediation of both organic and inorganic
pollutants, he has a long history of academic and industrial collaborations
in a wide range of fields (petroleum, agriculture, food, brewing, chemical).
He is currently focused on uncovering the biochemical basis of bacterial
per- and poly-fluoroalkyl substance (PFAS) metabolism, as well as tracking
SARS-CoV-2 in sewage. He served for 10 years as an editor for Biodegra­
dation and is currently an editor for the Canadian Journal of Microbiology.
He collaborated with Dr. Ismail and others as a guest associate editor for a
special issue on Petroleum Microbiology in Frontiers in Microbiology.
Contents

Contributors.............................................................................................................ix
Abbreviations .........................................................................................................xiii
Acknowledgments.................................................................................................. xvii
Preface ................................................................................................................... xix

1. Petroleum Chemistry......................................................................................1
Dawoud Bahzad and Mohan S. Rana

2. Biotechnology in the Refinery ......................................................................23

Nour Sh. El-Gendy and James G. Speight

3. Novel Insights into Bioremediation of Petroleum-Polluted

Environments and Bacterial Catabolic Pathways......................................65
Laura Rodríguez-Castro, Roberto E. Durán, Constanza C. Macaya,
Flavia Dorochesi, Lisette Hernández, Felipe Salazar-Tapia, Vanessa Ayala-Espinoza,
Patricio Santis-Cortés, Ximena Báez-Matus, and Michael Seeger

4. Microbial Degradation of Spilled Oil in Aqueous

Environments: Beyond C15 Hydrocarbons.............................................. 113
Fernanda Lopes Motta, Nayereh Saborimanesh, and Heather D. Dettman

5. Functional Diversity of Microbial Communities in

Hydrocarbon-Polluted Ecosystems ...........................................................157
R. M. M. Abed, H. Mahmoud, and N. Sivakumar

6. Bacterial Chemotaxis, Current Knowledge and Future Need for

Application in Hydrocarbon Remediation Technologies.........................189
Nisenbaum Melina, Georgina Corti-Monzón, and Silvia E. Murialdo

7. Biosurfactants-Mediated Remediation of Hydrocarbon Pollution ........ 211

Punniyakotti Parthipan, Pattanathu K. S. M. Rahman, Matthew L. Smith,
Kadarkarai Murugan, Yen-Peng Ting, Subramania Angaiah, and Aruliah Rajasekar

8. Microbial Enhanced Oil Recovery ............................................................235

Geetha S. J., Yahya Al-Wahaibi, Saif Al-Bahry, Abdulkadir Elshafie,
Ali Al-Bemani, and Sanket J. Joshi
viii Contents

9. Biocatalytic Upgrading of Opportunity Crudes.......................................257

M. M. Ramírez-Corredores

10. Hydrogen and Electricity Production from Oil and Gas Wastes ...........317
Scott J. Satinover and Abhijeet P. Borole

Annex: Resources for Environmental Pollution and

Hydrocarbon Biodegradation ......................................................................367

Index .....................................................................................................................369
Contributors

R. M. M. Abed
Sultan Qaboos University, College of Science, Biology Department, P.O. Box – 36, Al Khoud,
Postal Code 123, Muscat, Sultanate of Oman, Tel.: +968-24141450, E-mail: [email protected]
Saif Al-Bahry
Department of Biology, College of Science, Sultan Qaboos University, Oman;
Oil and Gas Research Center, Sultan Qaboos University, Oman
Ali Al-Bemani
Petroleum and Chemical Engineering Department, College of Engineering, Sultan Qaboos University,
Oman
Yahya Al-Wahaibi
Petroleum and Chemical Engineering Department, College of Engineering, Sultan Qaboos University,
Oman
Subramania Angaiah
Electro-Materials Research Lab, Center for Nanoscience and Technology, Pondicherry University,
Puducherry – 605014, Tamil Nadu, India
Vanessa Ayala-Espinoza
Molecular Microbiology and Environmental Biotechnology Laboratory,
Department of Chemistry and Center of Biotechnology Daniel Alkalay Lowitt,
Universidad Técnica Federico Santa María, Valparaiso, Chile
Ximena Báez-Matus
Molecular Microbiology and Environmental Biotechnology Laboratory,
Department of Chemistry and Center of Biotechnology Daniel Alkalay Lowitt,
Universidad Técnica Federico Santa María, Valparaiso, Chile
Dawoud Bahzad
Petroleum Research Center, Kuwait Institute for Scientific Research, P.O. Box – 24885,
Safat – 13109, Kuwait
Abhijeet P. Borole
Bredesen Center for Interdisciplinary Research and Education, The University of Tennessee,
Knoxville – 37996, Tennessee, US; Chemical and Biomolecular Engineering,
The University of Tennessee, Knoxville – 37996, Tennessee, US
Georgina Corti-Monzón
Institute of Science and Technology in Food & Environment , National University of Mar del Plata,
CONICET. J.B. Justo – 4302, Mar del Plata, Bs. As., Argentina
Heather D. Dettman
Natural Resources Canada, CanmetENERGY Devon, 1 Oil Patch Drive, Devon, AB T9G 1A8, Canada,
E-mail: [email protected]
x Contributors

Flavia Dorochesi
Molecular Microbiology and Environmental Biotechnology Laboratory,
Department of Chemistry and Center of Biotechnology Daniel Alkalay Lowitt,
Universidad Técnica Federico Santa María, Valparaiso, Chile
Roberto E. Durán
Molecular Microbiology and Environmental Biotechnology Laboratory,
Department of Chemistry and Center of Biotechnology Daniel Alkalay Lowitt,
Universidad Técnica Federico Santa María, Valparaiso, Chile
Nour Sh. El-Gendy
Department of Process Design and Development, Egyptian Petroleum Research Institute (EPRI),
Nasr City, Cairo PO – 11727, Egypt; Center of Excellence,
October University for Modern Sciences and Arts (MSA), 6th of October City, Giza, PO – 12566,
Egypt, E-mail: [email protected]
Abdulkadir Elshafie
Department of Biology, College of Science, Sultan Qaboos University, Oman
Lisette Hernández
Molecular Microbiology and Environmental Biotechnology Laboratory,
Department of Chemistry and Center of Biotechnology Daniel Alkalay Lowitt,
Universidad Técnica Federico Santa María, Valparaiso, Chile
Sanket J. Joshi
Oil and Gas Research Center, Sultan Qaboos University, Oman;
Central Analytical and Applied Research Unit, College of Science, Sultan Qaboos University,
Oman, Phone: +96824142456, Fax: +96824414120,
E-mails: [email protected]; [email protected]
Constanza C. Macaya
Molecular Microbiology and Environmental Biotechnology Laboratory,
Department of Chemistry and Center of Biotechnology Daniel Alkalay Lowitt,
Universidad Técnica Federico Santa María, Valparaiso, Chile
H. Mahmoud
Kuwait University, Department of Biological Sciences, P.O. Box – 5969, Safat – 13060, Kuwait
Nisenbaum Melina
Institute of Science and Technology in Food & Environment , National University of Mar del Plata,
CONICET. J.B. Justo – 4302, Mar del Plata, Bs. As., Argentina
Fernanda Lopes Motta
Natural Resources Canada, CanmetENERGY Devon, 1 Oil Patch Drive, Devon, AB T9G 1A8, Canada
Silvia E. Murialdo
Institute of Science and Technology in Food & Environment , National University of Mar del Plata,
CIC. J.B. Justo – 4302, Mar del Plata, Bs. As., Argentina
Kadarkarai Murugan
Division of Entomology, Department of Zoology, School of Life Sciences, Bharathiar University,
Coimbatore – 641046, Tamil Nadu, India
Contributors xi

Punniyakotti Parthipan
Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology,
Thiruvalluvar University, Serkkadu, Vellore – 632115, Tamil Nadu, India;
Electro-Materials Research Lab, Center for Nanoscience and Technology,
Pondicherry University, Puducherry – 605014, Tamil Nadu, India
Pattanathu K. S. M. Rahman
Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK;
TeeGene Biotech and Tara Biologics, Wilton Center, UK
Aruliah Rajasekar
Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology,
Thiruvalluvar University, Serkkadu, Vellore – 632115, Tamil Nadu, India,
E-mails: [email protected]; [email protected]; [email protected]
M. M. Ramírez-Corredores
Energy and Environment S&T Division, Idaho National Laboratory, Idaho Falls, ID – 83415, USA
Mohan S. Rana
Petroleum Research Center, Kuwait Institute for Scientific Research, P.O. Box – 24885, Safat – 13109,
Kuwait, E-mail: [email protected]
Laura Rodríguez-Castro
Molecular Microbiology and Environmental Biotechnology Laboratory,
Department of Chemistry and Center of Biotechnology Daniel Alkalay Lowitt,
Universidad Técnica Federico Santa María, Valparaiso, Chile
Geetha S. J.
Department of Biology, College of Science, Sultan Qaboos University, Oman
Nayereh Saborimanesh
Natural Resources Canada, CanmetENERGY Devon, 1 Oil Patch Drive, Devon, AB T9G 1A8, Canada
Felipe Salazar-Tapia
Molecular Microbiology and Environmental Biotechnology Laboratory,
Department of Chemistry and Center of Biotechnology Daniel Alkalay Lowitt,
Universidad Técnica Federico Santa María, Valparaiso, Chile
Patricio Santis-Cortés
Molecular Microbiology and Environmental Biotechnology Laboratory,
Department of Chemistry and Center of Biotechnology Daniel Alkalay Lowitt,
Universidad Técnica Federico Santa María, Valparaiso, Chile
Scott J. Satinover
Bredesen Center for Interdisciplinary Research and Education, The University of Tennessee,
Knoxville – 37996, Tennessee, US
Michael Seeger
Molecular Microbiology and Environmental Biotechnology Laboratory,
Department of Chemistry and Center of Biotechnology Daniel Alkalay Lowitt,
Universidad Técnica Federico Santa María, Valparaiso, Chile, E-mail: [email protected]
N. Sivakumar
Sultan Qaboos University, College of Science, Biology Department, P.O. Box – 36, Postal Code 123,
Al Khoud, Sultanate of Oman
xii Contributors

Matthew L. Smith
Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
James G. Speight
CD&W Inc., Laramie, Wyoming, USA
Yen-Peng Ting
Department of Chemical and Biomolecular Engineering, National University of Singapore,
4 Engineering Drive 4, Singapore – 117585
Abbreviations

2DE two-dimensional gel electrophoresis

2-HBP 2-hydroxybiphenyl
ADH1 alcohol dehydrogenases
ALDH aldehyde dehydrogenase
AMO alkene monooxygenase
API American Petroleum Institute
AR atmospheric residue
BAC bacterial artificial chromosomes
BDC bioconversion
BDN biodenitrogenation
BDO benzene 1,2-dioxygenase
BDS biodesulfurization
BDS-ODS-RADS biodesulfurization/oxidative desulfurization/reactive
adsorptive desulfurization
BES bioelectrochemical systems
BMMs bacterial multicomponent monooxygenases
BMO benzene monooxygenase
BotB bottom of the barrel
bpd barrels of oil per day
BTEX benzene, toluene, ethylbenzene, and xylene
C carbon
CAPP Canadian Association of Petroleum Producers
CC closed circuit
CCE cathodic conversion efficiency
CCR carbon Conradson residue
CD current density
CFU colony-forming unit
CH4 methane
CMC critical micelle concentration
COD chemical oxygen demand
DBT dibenzothiophene
DGGE denaturing gradient gel electrophoresis
DRO diesel range organics
DST Department of Science and Technology
xiv Abbreviations

EBC Enchira Biotechnology Corporation

EEOR enzyme-enhanced oil recovery
EIA Energy Information Administration
EOR enhanced oil recovery
FBP final boiling point
FCC fluid catalytic cracking
FMN flavin mononucleotide
FTIR Fourier Transform Infrared Spectroscopy
GMOs genetically modified microorganisms
GRO gasoline range organics
GWPC Ground Water Protection Council
H hydrogen
H2S hydrogen sulfide
HAC high acid crudes
HC hydrocarbon
HCK hydrocracking
HDC hydroconversion
HDP hydroprocessing
HDS hydrodesulfurization
HDT hydrotreatment
IBP initial boiling point
IOR improved oil recovery
LC liquid chromatography
MAHs monocyclic aromatic hydrocarbons
MALDI-ToF matrix-assisted laser desorption ionization time-of­
flight mass spectrometry
MCDC microbial capacitive deionization cell
MCR microcarbon residue
MDCs microbial desalination cells
MECs microbial electrolysis cells
MELs mannosylerythritol lipids
MEOR microbial enhanced oil recovery
MFC microbial fuel cell
MIC microbial induced corrosion
MMO monooxygenase-like enzymes
MOFC microbial osmotic fuel cell
MS mass spectrometry
MWS midway sunset
N nitrogen
Abbreviations xv

Ni nickel
NMR nuclear magnetic resonance
NOx nitrogen oxides
O oxygen
OC open circuit
OPEC Organization of Petroleum Exporting Countries
OSC offshore California
OUT operational taxonomic unit
P phosphorus
PAH polycyclic aromatic hydrocarbon
PCT patent cooperation treaty
PDMS polydimethylsiloxane
PEDEC Petroleum Engineering Development Company
PEP phosphoenolpyruvate
PFPS bis-(3-pentafluorophenylpropyl)-sulfide
pMMO particulate MMO
PTS phosphotransferase system
PVT pressure-volume-temperature
RACDC repetitive alternating carboxylation-decarboxylation
cycle
RHDs ring-hydroxylating dioxygenases
RT-qPCR real time-quantitative polymerase chain reaction
S sulfur
SARA saturates-aromatics-resins-asphaltenes
SCMFC sediment column MFC
SCO synthetic crude oil
SDS sodium dodecyl sulfate
SERB Science and Engineering Research Board
SIP stable isotope probing
sMMO soluble MMO
SO2 sulfur dioxide
SOx sulfur oxides
SRB sulfate-reducing bacteria
SWDs saltwater disposal wells
TAN total acid number
TB2MO toluene/benzene 2-monooxygenase
TCA tricarboxylic acid
TDO toluene 2,3-dioxygenase
TDS total dissolved solids