Table Of ContentTHE MYCOTA 5
A Comprehensive Treatise on Fungi as Experimental Systems
for Basic and Applied Research
Series Editors: Dee Carter · Anuradha Chowdhary
Joseph Heitman · Ulrich Kück
Barry Scott
Carl Mesarich Editors
Plant
Relationships
Fungal-Plant Interactions
Third Edition
The Mycota
A Comprehensive Treatise on Fungi as
Experimental Systems for Basic and Applied
Research
Volume 5
SeriesEditors
DeeCarter,SchoolofLifeandEnvironmentalSciences,TheUniversityof
Sydney,Sydney,NSW,Australia
AnuradhaChowdhary,DepartmentofMedicalMycology,VPChestInstitute,
UniversityofDelhi,Delhi,India
JosephHeitman,DukeUniversityMedicalCenter,Durham,NC,USA
UlrichKück,GeneralandMolecularBotany,Ruhr-UniversityBochum,
Bochum,Germany
Thefungirepresentaheterogenousassemblageofeukaryoticmicroorganisms
andhavebecomefavoredorganismsforresearchatthecellularandmolecular
level. Such research involvement has been stimulated by interest in the
biotechnologicalapplicationoffungiinprocessesrelatedtoindustry,agricul-
ture and ecology. Considering both yeasts and mycelial fungi, THE
MYCOTA highlights developments in both basic and applied research and
presents an overview of fungal systematics and cell structure. Foremost
authoritiesinresearchonmycologyhavebeenassembledtoeditandcontrib-
utetothevolumes.
(cid:129)
Barry Scott Carl Mesarich
Editors
Plant Relationships
Fungal-Plant Interactions
Third Edition
Editors
BarryScott CarlMesarich
SchoolofNaturalSciences SchoolofAgricultureandEnvironment
MasseyUniversity MasseyUniversity
PalmerstonNorth,NewZealand PalmerstonNorth,NewZealand
ISSN2945-8048 ISSN2945-8056 (electronic)
TheMycota
ISBN978-3-031-16502-3 ISBN978-3-031-16503-0 (eBook)
https://doi.org/10.1007/978-3-031-16503-0
Thefirsteditionwaspublishedintwovolumes
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Series Preface
The Mycota Series—2022
The Mycota is an encyclopaedic book series published by Springer as a
comprehensive treatise spanning the Fungal Kingdom through a focus on
fungiasexperimentalsystemsforbasicandappliedresearch.Articlesinthis
seriespresentintroductoryinformationinacomprehensivemannertobroaden
ourgeneralknowledge,alongwiththestate-of-the-artinformationonselected
topics in fungal biology. Thus, these articles serve as a timeless reference
source for historically relevant discoveries in fungal biology to drive further
advancesinthefield.
The Mycota was founded in 1994 by Karl Esser and Paul Lemke. Since
then15Volumeshavebeenpublished,withseveralnowintheirthirdedition.
ThesteadilygrowinginterestinTheMycota,reflectedinparticularbythehigh
numberofe-book downloads,encouragedSpringertocontinue this publica-
tionwithanewinternationalSeriesEditorialboardbeginningin2022.
Historically,thestudyoffungioriginatedasasub-disciplineofbotanyand
was a largely descriptive discipline until the early 19th century. Subsequent
experimentalresearchhaspropelledthefieldofmycology,andachievements
in the genetics and molecular biology of fungi have benefited studies in the
relatedfieldsoffungalbiochemistryandbiophysics,plantpathology,medical
mycology, and systematics. Ground-breaking research has been carried out
using fungi as recognized by the receipt of nine Nobel Prizes, including the
revolutionary1945NobelPrizeinPhysiologyandMedicineforthediscovery
of penicillin and the foundational 2006 Nobel Prize in Chemistry for
establishing the molecular basis of eukaryotic transcription. All such studies
expand our knowledge of fungi and of fungal processes and improve our
abilitytounderstand,utilize,andcontrolfungiforthebenefitofhumankind.
Fungi have invaded every conceivable ecological niche. Saprobic forms
abound,especiallyinthedecayoforganicdebris.Pathogenicformsexistwith
bothplantandanimalhosts.Fungievengrowonotherfungi.Theyarefound
inaquaticaswellassoilenvironments,andtheirsporeshavebeenfoundinthe
v
vi SeriesPreface
airofextremeenvironments.Fungicanbevariouslyassociatedwithplantsas
symbiontsintheformoflichens,mycorrhizae,andendophytesandalsooccur
asovertpathogens.Associationwithanimalsystemsvaries;examplesinclude
the predaceous fungi that trap nematodes, the micro-fungi that grow in the
anaerobic environment of the rumen, and medically important pathogens
afflictinghumans.Currently,taxonomistshaveidentifiedabout150,000spe-
cies, but it is thought that over 90% of fungal species remain undescribed,
with conservative estimates ranging from 2 to 5 million fungal species on
earth.
From this perspective, there are new topics in fungal biology to explore,
which will expand the current volumes and take them in new directions.
Further, there will be new volumes in areas (e.g., Cryptomycota) that were
notcoveredbefore.
Ourunderstandingoftheevolutionoffungiisstillincompleteandmainly
basedonspeciesthatcanbegrowninculture.ButrecentenvironmentalDNA
analyseshaverevealedahighlydiverseformofeukaryoticlifethatbranches
withtheFungi,andthustheresulting andhighlydiversecladeswerenamed
the Cryptomycota. The discovery of novel intermediate forms will redefine
the fungal tree of life. Other topics will consider the adaptation of fungi to
climatechanges,theoccurrenceoffungalpathogensintheenvironment,and
thedispersaloffungiduringglobalpandemics.
Fungal constituents of the microbiome have received much less attention
thusfar,yetrecentfindingsfromclinicalandanimalstudiesclearlyestablish
fungiasasignificantcomponentoftheoral,gastrointestinal,pulmonary,and
skin microbiomes. Finally, the relevance of fungal biology to society is
reflectedbytheincreasingnumberoffungalrelatedhumandiseases.
Inthehistoryofpharmacology,fungihavealwaysbeensourcesofuseful
molecules for humans, but the diversity of molecules that can be obtained
fromfungiisstilllargelyunderexplored.However,effortsinfungalgenomics
provide resources for data-driven genome mining and large-scale
comparisons to explore the molecular repertoires produced by fungi. The
result will be new compounds with applications in the pharmaceutical and
agriculturalscienceindustries.
Fungicanalsohelptheentireplanetandmay,forexample,berelevantin
specificsectors,suchasthatlinkedtopollutionfromplastic.Fungiproducea
wide range of enzymes that have the potential to break down the chemical
bonds of plastic polymers, and in this context the potential role of marine
fungi in plastic degradation may be of major relevance. Finally, new
biomaterials from fungal species may openthedoortoalternativestofossil-
basedmaterials,andthusreduceenvironmentalpollution.
Forconsistencythroughout thisseriesofvolumes,thenames adoptedfor
major groups of fungi should be followed according to the following paper,
which gives an overview of all of the orders in the fungal kingdom: https://
pubmed.ncbi.nlm.nih.gov/32660385/
SeriesPreface vii
We are grateful to Springer for continuing The Mycota series and are
especially thankful to all of the Volume Editors in selecting topics and
assemblingexpertsfromdiversefieldsoffungalbiology.
Sydney,Australia DeeCarter
Delhi,India AnuradhaChowdhary
Durham,USA JosephHeitman
Bochum,Germany UlrichKück
July15,2022
Volume Preface to the Third Edition
Filamentousfungicanformarangeofdifferentassociationswithplantsthat
vary from antagonistic through to mutualistic. However, the outcome of an
interaction is very dependent on the stage of development of both plant and
fungus, the genetic background of both organisms, and the ecological and
environmental conditions under which they interact. Consequently, a given
species may have a relatively benign interaction under one set of conditions
but be severely pathogenic under a different set of conditions or stage of
development. Despite this variability, some fungi are more generally
recognizedasplantpathogensandothersasplantsymbionts.
Itisnowover10yearssincethesecondeditionofTheMycota,VolumeV
(Plant Relationships) was published. In the two earlier editions, the volume
editors commented on the large number of fungi and vascular plants in the
Tree of Life and the enormous number and complexity of the different
interactionsthatoccurinnature.Itisthereforechallenginginasinglevolume
to capture this range of diversity. However, we hope that through the
examples presented in this third edition the reader can gain a sense of the
very significant new discoveries that have been made, what key biological
questions are being addressed, and where the new frontiers in this field of
researchlie.Tohelpthereaderexplorethehugerangeofresearchtopicsand
diversityoffungistudied,wehavedividedthevolumeintosixsectionswhich
we think capture the most important research themes within this very active
andfast-movingareaofresearch.
The theme of Chaps. 1–3 is Pathogen Fungus–Plant Interactions. These
chaptersprovideagoodoverviewofsomeofthekeyadvancesthathavebeen
made in understanding the molecular dialogue between pathogen and host,
especially in the field of effector biology. Understanding the biological
function of the protein effectors has been particularly challenging as most
share little homology with functionally characterized proteins. Despite this
challenge,verysignificantadvanceshavebeenmadeinidentifyingthefunc-
tion of many effectors, including in some cases the host target proteins with
which they interact. One of the most exciting emerging fields has been the
demonstration that small RNAs play a crucial role in the dialogue between
fungusandplant.Thisis,andwillremain,averyactivefieldofdiscovery.
ix
x VolumePrefacetotheThirdEdition
Chapters4–6(MutualisticFungus–PlantInteractions)provideasnapshot
ofthesymbioticinteractionsthatoccurbetweenfungiandplantsbothbelow
ground (the arbuscular mycorrhiza) and above ground (leaf endophytes). A
hugechallengewiththeformeristheinabilitytoculturemostofthesefungi
separatefromtheirhosttherebylimitingthemethodologiesthatcanbeusedto
dissect these interesting associations. Recent advances in long-read DNA
sequencing have enabled the complete assembly of a number of the large
and complex arbuscular mycorrhizal fungal genomes thereby facilitating for
thefirsttimenewinsightsintocomparativeandevolutionarygeneticsofthis
importantgroup of fungi. The mutualistic interaction ofEpichloë fungi with
grasses is now the most well-understood above-ground fungal-plant mutual-
isticassociation.Comparativegenomestudiescombinedwithgeneticanalysis
and new advances in metabolite chemistry reveal a remarkable diversity of
alkaloids synthesized by these seed endophytes. Among the more complex
fungal-plant mutualistic symbioses are the lichens—associations between
nutritionally specialized fungi and green algae and/or cyanobacteria
photobionts.Theseassociationsareverydiversewithapproximately 17%of
extant fungi species lichenized. The obligate nature of these associations
makesitverychallengingtostudytheindividualcontributionsofthepartners
but advances in microscopy and genome analysis have provided significant
newinsightsintotheseassociations.Genomeanalysisofthemycobiontshas
provided important new insights into the lifestyle of these fungi, and in
particular their potential to synthesize a remarkable range of secondary
metabolites. The use of heterologous expression systems combined with
mass spectrometry analysis has led to the identification of a range of novel
lichenmetabolites.Afuturechallengewillbedeterminingtheirbiologicalrole
innature.
Howfungisensesignalsfromtheirhostandrespondthroughtransduction
of those signalsinternally isthetheme ofChaps.8–10(Sensing and Signal-
linginFungus–PlantInteractions).Amongthemostwell-characterizedsignal
transduction systems are the Mitogen-Activated Protein kinase (MAPK)
pathways.Geneticanalysescombinedwithprotein–proteininteractionshave
revealed how fungi respond to external stimuli and regulate infection and
developmentalprocesses.Thesestudiesdemonstratethatthereareconserved,
aswellasspecies-specific,functionsassociatedwiththeMAPKpathways.In
addition, there is considerable crosstalk among the pathways, a result that
highlights the complexity of signalling associated with plant host coloniza-
tion.AmbientpHisoneofthekeyenvironmentalsignalsthatfungiencounter
in their environment. Fungi have an exquisitely tuned system to regulate
cytosolic pH in response to changes in external pH. Signalling through
MAPK pathways control this system and lead to changes in fungal growth,
development, and pathogenicity. Plant volatiles are key signals that control
fungal invasion of their hosts. Using the Trichoderma system, key volatiles
havebeenidentifiedthatcontrolplantcolonizationaswellasplantimmunity
anddevelopment.
ThethemeofChaps.11–14isRegulationofFungalGeneExpressionand
Development.
