the MARINE MICROBIOME

768 Pages·2022·27.467 MB·English

The Microbiomes of Humans, Animals, Plants,
and the Environment 3
Lucas J. Stal
Mariana Silvia Cretoiu Editors
The Marine
Microbiome
Second Edition
The Microbiomes of Humans, Animals,
Plants, and the Environment
Volume 3
Thisseriescoversmicrobiometopicsfromallnaturalhabitats.Microbiomeresearch
is a vibrant field of science that offers a new perspective on Microbiology with a
more comprehensive view on different microorganisms (microbiota) living and
working together as a community (microbiome). Even though microbial
communitiesintheenvironmenthavelongbeenexamined,thisscientificmovement
also follows the increasing interest in microbiomes from humans, animals and
plants. First and foremost, microbiome research tries to unravel how individual
species within the community influence and communicate with each other. Addi-
tionally, scientists explore the delicate relationship between a microbiome and its
habitat, as small changes in either, can have a profound impact on the other. With
individual research volumes, this series reflects the vast diversity of Microbiomes
andhighlightstheimpactofthisfieldinMicrobiology.
Moreinformationaboutthisseriesathttps://link.springer.com/bookseries/16462
Lucas J. Stal (cid:129) Mariana Silvia Cretoiu
Editors
The Marine Microbiome
Second Edition
Editors
LucasJ.Stal MarianaSilviaCretoiu
DepartmentofFreshwaterandMarine UniversityofUtrecht
Ecology–IBED Utrecht,TheNetherlands
UniversityofAmsterdam
Amsterdam,TheNetherlands
ISSN2662-611X ISSN2662-6128 (electronic)
TheMicrobiomesofHumans,Animals,Plants,andtheEnvironment
ISBN978-3-030-90382-4 ISBN978-3-030-90383-1 (eBook)
https://doi.org/10.1007/978-3-030-90383-1
#TheEditor(s)(ifapplicable)andTheAuthor(s),underexclusivelicensetoSpringerNatureSwitzerland
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Dedicated to
Prof. dr. Wolfgang Elisabeth Krumbein
Geomicrobiologist
1937–2021
In loving memory
Foreword
Marinemicrobiologyhasbeenalatecomertothefieldofmicrobialecology.Butthe
last three decades have been enough to revert the situation. The ocean is now
arguablythebestknownmajormicrobialecosystemonEarth.Itwastobeexpected
that its physical structure at first sight is much more amenable to sampling and
interpretationthantherichlymicro-structuredhabitatslikesedimentsorsoil,notto
mention animal microbiomes. The ocean is a single gigantic lake that is
homogenized by the equally colossal global circulation. It has relatively constant
andlargelymoderateconditions(apartfromextremeoligotrophy,forexceptionssee
Chap. 14). On the other hand, it is also the largest, oldest and likely most critical
ecosystem for the environmental health of the planet. It has also been the least
impactedbythearrivalofmulticellularplantsandanimalsca.500millionyearsago.
It is possible to envisage vast marine areas in which the conditions have changed
little after the great oxygenation event ca. 2.2 billion years ago. Only in the last
hundredyearshasanthropicimpactstartedtobenoticedinthePacificandAtlantic
central gyres that remained nearly pristine until the arrival of intensive whaling by
themid-nineteenthcentury.
Microbiologyisnowatacrossroadsor,ifyouwish,anewbeginning.Itturnsout
that the fathers of microbiology were lucky to be able to discover the causative
agents of the major infectious diseases of their time. Human pathogens tend to be
copiotrophswellsuitedforgrowthinlaboratorypurecultures,butmostmicrobesare
not,andthisincludesmostbacteria,archaeaandprotiststhatliveintheocean.We
know that because now we can sequence their genomes directly from the environ-
ment.However,thenewmicrobiologythatarosefromnucleicacidsequencingisnot
withoutlimitations anddrawbacks. Firstandforemost,thecapability ofannotating
genesandgenomes(thatisinferringfunctionfromsequence)isveryunsatisfactory
and largely based on a few model organisms very distant from their wild
counterparts. Too little effort is invested in detecting new functions and too many
mystifying sequences added to the humongous databases. What is worse, we still
missanevolutionarymodelthatwouldconsiderthemajorimpactofthepangenome
of prokaryotic species. The key role played by the pangenome dynamics in the
evolutionofmicrobesandtheirecologyisyettobefullyincorporatedinmodelsof
evolutionarybiologyorecosystemfunctioning.
Thereisalsoanoveralllackoffinesseinmicrobiomestudiesthatoftengravitate
over scale (big data) ratherthan detailedanalysisof individual depth profiles, time
vviiii
viii Foreword
seriesorspecificmicrobes.Tocompounditall,theclassification(nomenclature)of
microbeshassufferedfromindiscriminateabusebymajorrearrangementsbasedon
relationships,atthesequencelevel,ofribosomalcomponentswithoutcontemplating
thatamicrobeismuchmorethanthepedigreeofitsribosomes(andthatisassuming
that ribosomal RNAs or proteins really provide a reliable relationship). It is often
unclearwhatthenamesmeanintermsofthegenomemake-upandthebiologyofthe
microbes.
At this point in time, Lucas Stal and Silvia Cretoiu have undertaken the task of
publishing a book (this) that updates the field and aggregates a large amount of
relevant information; for that they have managed to gather a remarkable set of
distinguished authors who have collectively done an amazing job of using the
‘tsunami’ofdatageneratedbyhigh-throughputsequencingtechnologiestodescribe
mostofrelevanttopicsinthefield,coveringfrompopulationgenomicstobiogeog-
raphy. They have introduced novel perspectives like the micro-seascape ‘vast
expanses of extremely dilute background seawater punctuated by rich hotspots of
dissolvedandparticulatenutrientresources’(fromChap.2).EveryoneknowsIam
not an enthusiast of review books, although I believe they are certainly useful for
newcomers such as PhD or master’s students. The speed at which science is
progressingthesedayscoupledwiththetimerequiredtocollectandreviewchapters
detracts from their usefulness. However, some books have the power to change a
field.Ihopethisbookwillhelptomovemarinemicrobiologyintothenextfrontierin
which a better understanding of microbes (largely, but not only, derived from
genomics) will allow a more profound understanding of the oldest and largest
microbiomeonEarth.
UniversitatMiguelHernández, FranciscoRodriguezValera
SantJoand’Alacant,Spain
Preface
In2015,Springerinvitedustoeditabookonmarinemicrobiology.Atthetime,we
were leading the project ‘MaCuMBA’ (‘Marine Microorganisms: Cultivation
Methods for Improving their Biotechnological Applications’) with a large consor-
tium of European marine microbiologists and with funding of the European Com-
mission. We decided to produce the book with contributions of MaCuMBA
consortium members and entitled it The Marine Microbiome (with the subtitle An
Untapped SourceofBiodiversityandBiotechnologicalPotential).Wethoughtthat
with this title we emphasize the importance of considering the total of
microorganisms in the ocean and its adjacent seas, bays and estuaries as an entity,
andthat thisentity plays acritical role inthefunctioningofthemarine ecosystem,
andthatitwouldstimulateitsresearch.Thebookappearedin2016(StalandCretoiu
2016) and was successful, and indeed, the research on the marine microbiome
enjoyed more attention since (see below). The success of The Marine Microbiome
wasthereasonforSpringertoinquirewithusalreadyin2019,whetherwewouldbe
willing to edit a second edition. Meanwhile, Springer launched a book series The
Microbiomes of Humans, Animals, Plants, and the Environment and the second
editionofTheMarineMicrobiomefitsperfectlyinthatseries.Whileinouropinion
thefirsteditionisstillrecentandquiteup-to-date,wedecidedthatthesecondedition
wouldneedsubstantialnewmaterial,andtherefore,onlyafewofthechaptersofthe
firsteditionremainedandwererewrittenandupdated.Therefore,thesecondedition
of The Marine Microbiome might as well be considered The Marine Microbiome
Part2beinganimportantadditiontothefirst.
Mostoftheauthorsofthisvolumeagreedtotheircontributionsinlate2019and
early 2020, not knowing the impact that the COVID-19 pandemic would have on
their work routine. Many authors with young children were faced with closed
schoolsand whilemainlyworking from home had to divide theirattention to their
work as well as to the assistance of home education of their children. Also, their
workandworkloadchangedandfromonedaytoanotherroutineteaching,research
and administration had to be completely reorganized in a way never done before.
Meanwhilewe,theeditors,werepressingfordeliveryofthebookchapters.Weare
thereforereallygratefultoallcontributorsforthegreatchaptersthattheywrotefor
thisbook,andweapologizetothoseauthorswhomettheoriginaldeadlineandhad
towaitmuchlongertoseetheirworkinprintthanoriginallyanticipated.
ix
x Preface
We would also like to take this preface as an opportunity to exchange our
thoughts about the title of this book (and of the previous edition) and about the
use of the concept ‘microbiome’. We used it in the first edition more or less to
replacetheterm‘marinemicrobiology’,anditseemedtobecomefashionabletouse
the term ‘microbiome’ in a variety of situations in which microbiologists want to
describe the whole of all microorganisms in a certain ‘biome’. Now, although we
kepttheterm‘microbiome’asitseemsthatithasbecomecommonplaceinmicrobi-
ology,wefeelthatitissemanticallyincorrectlyused.
Let us consider the term ‘microorganism’. ‘Organism’ is defined as ‘a living
being or entity adapted for living by means of organs separate in function but
dependent on one another; any living being or its material structure; any complete
whole which by the integration, interaction and mutual dependence of its parts is
comparabletoalivingbeing’.And‘life’isthestateofanorganismcharacterizedby
certain processes or abilities that include metabolism, growth, reproduction and
response. ‘Micro-‘ as a prefix means small or minute, or a millionth of (e.g. a
metre). Therefore, ‘microorganism’ is a small, minute organism. These definitions
wereobtainedfromtheWebster’sDictionaryoftheEnglishlanguage.
Now, ‘biome’ is defined as ‘a large community of organisms having a peculiar
form of vegetation and characteristic animals’ and usually covers large areas. This
term was coined by Frederic E. Clements in his lecture ‘The development and
structure of biotic communities’ at the Ecological Society of America in 1916 and
publishedin2017intheJournalofEcology(p.120–121).Hewrote:
Thebioticcommunityisregardedasanorganicunitcomprisingallthespeciesofplantsand
animalsathomeinaparticularhabitat.Whileplantsareregardedasexertingthedominant
influenceinthecommunity,itisrecognizedthatthisrôlemaysometimesbetakenbythe
animals.Thebioticcommunity,orbiome,isfundamentallycontrolledbythehabitat,and
exhibitsacorrespondingdevelopmentandstructure.Initsdevelopmentthebioticformation
reactsuponthehabitat,andthusproducesasuccessionofbiomes,comparableinpractically
all essentials to the succession of plant communities. Every such succession, or biosere,
terminatesregularlyinaclimax.Thebioseresofeachclimaxareeitherprimaryorsecond-
ary,andthesemaybefurtherdistinguishedashydroseres,xeroseres,etc.
A‘microbiome’wouldthereforemeanasmallorminuteformofabiomewhichis
infactacontradictioninterms.Thisisnotwhathasbecomethemeaningofit.Ithas
unfortunately introduced more and unnecessary ‘jargon’ in scientific language—
jargonthatisrarelypreciselydefinedandincreasesconfusionamongourselvesbut
evenmoretosocietyforwhichourscientificresearchshouldberelevant.Nowthat
we seem to be stuck with ‘microbiome’, it may be good to briefly review its
definition.
Bergetal.(2020)adoptedthedefinitionofWhippsandhiscolleagues(1988)as
‘a characteristic microbial community’ in a ‘reasonably well-defined habitat which
has distinct physicochemical properties’ as their ‘theatre of activity’ (this book
chapter of Whipps et al. (1988) is cited in Berg et al. (2020), and these authors
madesomeexplanatorycommentstoit).