Microbial Ecology of Extreme Environments

254 Pages·2017·5.099 MB·English

by  Caroline Chénard, Federico M. Lauro (eds.)

Caroline Chénard · Federico M. Lauro
Editors
Microbial
Ecology of
Extreme
Environments
Microbial Ecology of Extreme Environments
é
Caroline Ch nard Federico M. Lauro
(cid:129)
Editors
Microbial Ecology
of Extreme Environments
123
Editors
Caroline Chénard Federico M.Lauro
AsianSchool ofthe Environment AsianSchool ofthe Environment and
NanyangTechnological University SingaporeCentrefor Environmental Life
Singapore SciencesEngineering
Singapore NanyangTechnological University
Singapore
Singapore
ISBN978-3-319-51684-4 ISBN978-3-319-51686-8 (eBook)
DOI 10.1007/978-3-319-51686-8
LibraryofCongressControlNumber:2016961306
©SpringerInternationalPublishingAG2017
Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpart
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
orinformationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilar
methodologynowknownorhereafterdeveloped.
The use of general descriptive names, registered names, trademarks, service marks, etc. in this
publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfrom
therelevantprotectivelawsandregulationsandthereforefreeforgeneraluse.
The publisher, the authors and the editors are safe to assume that the advice and information in this
book are believed to be true and accurate at the date of publication. Neither the publisher nor the
authorsortheeditorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinor
for any errors or omissions that may have been made. The publisher remains neutral with regard to
jurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations.
Printedonacid-freepaper
ThisSpringerimprintispublishedbySpringerNature
TheregisteredcompanyisSpringerInternationalPublishingAG
Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland
For statistical purposes, this dedication has
been performed in triplicate. To our parents,
without whom we would not have been
possible and this book would have never
existed. To our partners, Rachelle and
Xavier, who still question why we study
microbes. To our own microbiomes, may they
keep us healthy and in good spirits.
Preface
Anyonewhohasrecentlyattendedaconferenceonmicrobialecologywouldagree
that it is hard not to appreciate how much the field has evolved in the past few
decades. We are gaining unprecedented insights in the lifestyles of microbes at
different spatial levels. With molecular tools, we can study microbial communities
atthelevelofsinglecellinteractionswhilewithremotesensingwecandetecttheir
presence and activity at a planetary scale. Nucleic acids and proteins can be
sequencedfromminuteamountsofstartingmaterialandinjustafewhours,giving
usdetaileddescriptionsofthediversityandactivityofmicrobialcommunities.And
using these techniques, everywhere we look, and as long liquid water is available,
we are discovering new branches of the microbial tree of life. In seemingly
inhospitable places, microbes are exploiting resources, cycling organic and inor-
ganiccompounds,fightingwitheachotherandpromiscuouslyexchangingmassive
amounts of genetic information. Extreme environments select for unique adapta-
tions at the level of enzymes, compounds, and processes which are the future
arsenal of biotechnology. The exploitation of these natural resources will require
notonlythedevelopmentofnewbioinformatictoolsfordatamining,butalsonew
culturing techniques and systems biology approaches for environmental
engineering.
This book is meant to provide a useful reference for those who want to start a
research program in extreme microbiology and, hopefully, inspire new research
directions. Assembling it has taken a long time. For one reason or another, there
wasalwaysanexcusesuchastoomuchteachingoradministrativedutiesorthelack
of enough material or just procrastinating because of another grant deadline
approaching. And it was just by chance that we ended up working at the same
institutionandfound thetime toconvinceenoughexperts inthefieldthatitwould
be fun to write this book.
So here it is. The chapters are organized so that they roughly follow a vertical
profile through the biosphere.
After a brief introductory chapter, we begin in the deepest depths of the Ocean
withChap.2comprehensivelyreviewingthephylogeneticdiversityofculturedand
uncultured piezophiles (pressure-adapted microbes) and discussing the need for a
vii
viii Preface
betterrepresentationofpiezophilicphylogeneticdiversityinculturecollections.We
also discover how the genomic features of pressure-adapted microorganisms differ
from those of close phylogenetic relatives from shallower waters.
The deep sea is further explored in Chap. 3, which goes into detailing the
adaptations of motility and cell envelopes of piezophiles and Chap. 4, which
explores the effects of hydrostatic pressure on extracellular electron transfer and
how this might be ecologically relevant to environments with low energy input.
Thefollowingtwochaptersdescribelifeinhotenvironments.Chapter5reviews
the diversity and activity of microbial populations in many high-temperature
habitats around the world. Thermophilic bacteria and archaea produce many
enzymes which have biotechnological applications but proteins from thermophilic
viruses might also have similar or even better potential. Chapter 6 describes the
ecology viruses and the concurrent coevolution of CRISPR/Cas systems in hot
springs.
Thenexttwochapterstakethereaderstotheoppositeextremeoftemperature.In
Chap.7,thediversityofbacteriainpolardesertsisdiscussedinthecontextoftheir
remarkableadaptations,whileChap.8looksattheecologicalfunctionofphagesin
high-latitude aquatic systems. A particular emphasis is devoted to phage–host
dynamics and their relevance to the control of biogeochemical fluxes though the
polar ecosystem.
Chapter 9 deals with solvent tolerance, which is important for many industrial
processes. The chapter discusses the evolution of efflux pumps as a way to cope
with solvent stress and how these can also provide resistance to antibiotics.
Therefore, understanding solvent tolerance has implications in the control of
infectious disease and human health.
And finally, Chap. 10 presents a comprehensive review of microbial life in
cloudsfromtheirdiversitytotheadaptationstoenvironmentalchallengesofliving
air.
This book only deals with a small subset of the extreme habitats of our bio-
sphere.NotableomissionsincludeextremesofpHorsalinityonwhichother,more
specificvolumeshavebeenwritten.Oneimportantpointmadebyallauthorsisthat
themolecularandphysiologicalbasisoflifeatanyextremeisstilllargelyunknown
andthatalotmoreworkisneededtofullyunderstandit.Itiseasytoseewhy,since
most of the habitats are difficult to access. Yet, if technology keeps progressing at
the same pace, it will not be long before we can answer many of the questions
raised in this book about evolution, biogeography, and biodiversity.
And even if the study of microbes in extreme environments will remain chal-
lenging, hence not for the faint-hearted, the potential rewards are worth the effort.
Singapore Caroline Chénard
Federico M. Lauro
Acknowledgements
First and foremost, a big thanks goes to Nanyang Technological University for
providingafertilegroundforourcollaborationandsomeamazingopportunitiesfor
doing science. We also thank Singapore’s Ministry of Education and Singapore’s
National Research Foundation for supporting us. We thank Hanna Hensler-Fritton
who initially suggested that we should write a book on the microbial ecology of
extremeenvironmentsandthestaffatSpringerwhohelpedusseethisbookthrough
to completion.
We are forever indebted to the authors of each chapter who have shared their
knowledge, expertise, and penmanship: Alice, Andrea, Andreas, Anne Marie,
Audrey, Beatrice, Belinda, David, Doug, Emiley, Gail († 27-12-2011), Jamie, Jan,
Joanna,Josie,Kamila,Laurent,Logan,Marco,Maria,Martine,Matt,Mi,Mickael,
Mike, Muriel, Nicole, Nolwenn, Pierre, Roberta, Rosa, and Theodora.
Itisabigdebttorepaynomatterhowlongyoumadeuswait.Andabigthanks
to all our readers: we hope you enjoy this book as much as we have.
ix
Contents
1 Introduction... .... .... ..... .... .... .... .... .... ..... .... 1
Caroline Chénard and Federico M. Lauro
2 Ecogenomics of Deep-Ocean Microbial Bathytypes .... ..... .... 7
Logan M. Peoples and Douglas H. Bartlett
3 Adaptations of Cold- and Pressure-Loving Bacteria
to the Deep-Sea Environment: Cell Envelope and Flagella ... .... 51
Kamila K. Myka, David J. Allcock, Emiley A. Eloe-Fadrosh,
Theodora Tryfona, Andreas F. Haag, Federico M. Lauro,
Douglas H. Bartlett and Gail P. Ferguson
4 Microbial Electron Transport in the Deep Subsurface.. ..... .... 81
Jamie Hinks, Mi Zhou and Jan Dolfing
5 Metagenomics of Hyperthermophilic Environments:
Biodiversity and Biotechnology .... .... .... .... .... ..... .... 103
Andrea Strazzulli, Roberta Iacono, Rosa Giglio,
Marco Moracci and Beatrice Cobucci-Ponzano
6 Crenarchaeal Viruses of Hot Springs: Diversity,
Ecology and Co-evolution..... .... .... .... .... .... ..... .... 137
Alice C. Ortmann
7 New Insights into the Microbial Diversity of Polar
Desert Soils: A Biotechnological Perspective.. .... .... ..... .... 169
Josie van Dorst, Nicole Benaud and Belinda Ferrari
8 Exploring the Viral Ecology of High Latitude
Aquatic Systems ... .... ..... .... .... .... .... .... ..... .... 185
Caroline Chénard and Federico M. Lauro
xi
xii Contents
9 The Nature and Relevance of Solvent Stress in Microbes
and Mechanisms of Tolerance . .... .... .... .... .... ..... .... 201
Mike Manefield, Matthew Lee and Joanna Koenig
10 Clouds: A Transient and Stressing Habitat
for Microorganisms. .... ..... .... .... .... .... .... ..... .... 215
Anne Marie Delort, Mickael Vaïtilingom, Muriel Joly,
Pierre Amato, Nolwenn Wirgot, Audrey Lallement,
Martine Sancelme, Maria Matulova and Laurent Deguillaume