The sponge holobiont in a changing ocean: from microbes to ecosystems

18 Pages·2017·1.73 MB·English

by  L. Pita

Pitaetal.Microbiome (2018) 6:46
https://doi.org/10.1186/s40168-018-0428-1
REVIEW Open Access
The sponge holobiont in a changing ocean:
from microbes to ecosystems
L. Pita1*† , L. Rix1† , B. M. Slaby1 , A. Franke1 and U. Hentschel1,2
Abstract
The recognition that all macroorganisms live insymbiotic association with microbial communities has openedup a
new field inbiology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of
thehost, the microbiota, and theinteractions among them. Accordingly, ecological concepts can be applied to
understand the host-derived and microbial processes that govern the dynamics of theinteractive networks within
theholobiont.In marine systems, holobionts are further integrated into larger and more complex communities and
ecosystems, a conceptreferred to as “nested ecosystems.”In this review, we discuss theconceptof holobionts as
dynamic ecosystems that interact at multiple scales and respond to environmental change. We focus onthe
symbiosis of sponges with their microbial communities—a symbiosis that has resulted inone of the most diverse
and complex holobionts inthe marine environment. Inrecent years, thefield ofspongemicrobiology has
remarkably advancedin terms ofcurated databases, standardizedprotocols, and information on the functions of
themicrobiota. Like a Russian doll, these microbialprocesses are translated into sponge holobiont functions that
impact the surrounding ecosystem. For example, thesponge-associated microbial metabolisms,fueled by the high
filtering capacity of the sponge host, substantiallyaffect thebiogeochemical cycling of key nutrients likecarbon,
nitrogen, and phosphorous. Since sponge holobionts are increasingly threatened by anthropogenicstressors that
jeopardize the stability oftheholobiont ecosystem, we discussthe linkbetween environmental perturbations,
dysbiosis, and spongediseases.Experimental studies suggest that the microbial community composition is tightly
linked to holobiont health,but whether dysbiosis is a cause or a consequence of holobiont collapse remains
unresolved. Moreover,thepotential role ofthe microbiome inmediatingthecapacity for holobionts to acclimate
and adapt to environmental change is unknown.Future studies should aim to identify the mechanisms underlying
holobiont dynamics at multiple scales, from themicrobiome to the ecosystem, and develop management
strategies to preserve the key functions provided bythe sponge holobiont in our present and future oceans.
Keywords: Sponges, Holobiont, Health, Symbiosis, Microbiome,Nested ecosystems, Stress, Climate change,
Dysbiosis, Disease
Background macroorganisms: animals, plants, and algae alike [3, 4].
Marineanimals live and evolve ina seaof microbes.The The prevalence of these associations implies that multi-
ocean is the largest habitat on our planet and microbes cellular organisms can no longer be considered as au-
are its most abundant inhabitants. These microorgan- tonomous entities [5] but rather as holobionts (syn.
isms (i.e., viruses, bacteria, archaea, microeukaryotes) “metaorganisms” [6]), encompassing the host plus its as-
play a key role in global biogeochemical cycles [1]; yet, sociated microbiota [7, 8]. The microbial partners con-
scientists are only beginning to reveal their genomic and tribute to the nutrition [9], defense [10], immunity [11],
metabolic diversity [2]. Marine microbes exist not only and development [12] of the host; thereby collectively
in a planktonic state but also in symbiosis with influencingitshealthandfunctioning.
The first approaches to define the holobiont consisted
*Correspondence:[email protected] ofcharacterizing the setofmicrobialtaxacommontoall
†Equalcontributors
1RD3MarineMicrobiology,GEOMARHelmholtzCentreforOceanResearch, individuals of a certain species, the core microbiota.
Kiel,Germany Later definitions, enabled by massively increased
Fulllistofauthorinformationisavailableattheendofthearticle
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InternationalLicense(http://creativecommons.org/licenses/by/4.0/),whichpermitsunrestricteduse,distribution,and
reproductioninanymedium,providedyougiveappropriatecredittotheoriginalauthor(s)andthesource,providealinkto
theCreativeCommonslicense,andindicateifchangesweremade.TheCreativeCommonsPublicDomainDedicationwaiver
(http://creativecommons.org/publicdomain/zero/1.0/)appliestothedatamadeavailableinthisarticle,unlessotherwisestated.
Pitaetal.Microbiome (2018) 6:46 Page2of18
sequencing efforts, included the core set of functional
Box1Glossary
genes that ensured homeostasis of the holobiont [13,
Acclimatization:Thecapacityofaholobionttoadjusttoa 14]. However, holobiont functioning is not only deter-
mined by the processes carried out by the individual
perturbationthroughhostphenotypicplasticityorrestructuringof
members, but also by the interactions among them.
themicrobiomeinordertoreachanewstablestate
Consequently, holobionts can be regarded as complex
Adaptation:Atransgenerationalprocessthatenhancesthefitness
ecosystems to which the concepts and methodologies
oftheholobiontthroughtransgenerationalacclimatization,heritable
from ecology can be applied to understandthe drivers of
microbialcommunitychanges,orhost/symbiontevolution holobiont stability [15–17]. Under this perspective, the
Coremicrobiome:Thesetofmicrobialtaxawhichareconsistently holobiont represents a dynamic equilibrium character-
andstablyprevalentinhostindividualsofthesamespecies ized by two important properties: resistance (the ability
Dysbiosis:Thedivergenceofasymbioticmicrobialcommunity to withstand perturbation unchanged) and resilience
(the capacity to recover upon disturbance). This view
fromthecommunityfoundinhealthyindividuals
contributes to understanding the dynamics of the micro-
Disease:Theimpairmentofnormalfunctionfollowing
bial and host-related processes involved in maintaining a
perturbationordamage.Maybe,butisnotnecessarily,induced
healthy holobiont [15–17] and its response to environ-
byapathogenicmicroorganism mental change [18–20].
Functionalconvergence:Intheholobiontcontext,symbiotic Moreover, the holobiont performs functions that can-
microbialcommunitieswithdifferentevolutionaryhistoriesthat not be accomplished by the partners separately. The
have,viadifferentbutanalogouspathways,convergedupon microbiome provides essential functions to the host and
similarfunctionalsolutions together they mediate the interactions of the holobiont
with the surrounding organismal community [5].
Functionalredundancy:Thepresenceofseveralmicrobialtaxa
Through cascading effects, the microbiome can ultim-
withinanecosystemorholobiontthatperformthesamefunctions,
ately impact ecosystem health and functioning. One
suchthatthelossofoneparticulartaxonorashiftinthe
prominent example is the symbiosis between corals and
communitydiversitywouldnotcompromiseecosystemfunction
their photosynthetic dinoflagellates (Symbiodinium spp.).
Holobionthealth:Adynamicequilibriumthatallowsminor By virtue of autotrophic CO fixation, Symbiodinium
2
fluctuationsintermsofdiversityorfunctionstoensurethe provide the necessary primary metabolism that enables
maintenanceofsymbiotichomeostasis corals to engineer the three-dimensional calcium car-
Microbiota:Theassemblageofmicroorganismspresentina bonate structure that,ultimately, supports the entire reef
ecosystem [21]. Conversely, coral bleaching resulting
definedenvironmentorhost
from the loss of dinoflagellate symbionts not only has
Microbiome:Thegroupofmicrobes,theirgeneticinformation,
severe consequences for coral health, but also has devas-
andthesurroundingenvironmentalconditionsinadefined
tating effects on the entire coral reef ecosystem [22].
environmentorhost
Therefore, an integrative approach that considers these
Nestedecosystem:Asmallerdistinctecosystemwhichis different scales is needed to evaluate holobiont function
containedwithinandinteractswithalargerecosystemorseries within these nested ecosystems.
ofsuccessivelylargerecosystems In this review, we will discuss how host- and
Opportunistic:Anorganismthatiscapableofcausingdamage microbial-mediated activities translate into the emerging
functions of the sponge holobiont that impact the sur-
toahostunderspecificconditions,butmayalsoexistasa
rounding ecosystem, and how the holobiont is in turn
commensalwithinthesamehostundernormalconditions
affected by the anthropogenic pressures increasingly
Perturbation:Atemporaryorpersistentchangeinbioticorabiotic
impacting marine ecosystems. Marine sponges (phylum
conditionsthatleadstoaresponsebyanecosystemorholobiont
Porifera) perfectly illustrate the idea of holobionts as
Resilience:Thecapacityofasystemtorecoveritsinitial ecosystems, given the exceptionally diverse microbial
functionalandtaxonomicalcompositionandreturntoaninitial communities housed within them [23, 24].Spongesare a
stablestatefollowingaperturbation successful (>8000 species) and evolutionarily ancient
Resistance:Thepropertyofasystemtoremainunchangedand phylum, their members being globally distributed and
abundant within the benthic communities of a wide
maintainatastablestateuponperturbation
range of habitats [25, 26]. Their sessile filter-feeding life-
Symbiosis(sensuDeBary):Thecloseassociationoftwoor
style constantlyexposesthemtothemicrobesinthesea-
moreorganismsofadifferentspecies.Thisassociationmaybe
water that form their primary food source; yet, they
mutualistic,commensal,orparasitic
harbor distinct symbiotic microbial communities.
Sponges influence ecosystem functioning by modifying
Pitaetal.Microbiome (2018) 6:46 Page3of18
particularly in the context of health, disease, and re-
Box2TheHMA-LMAdichotomy
sponsetoanthropogenicpressures.
Spongescanbeclassifiedintotwogroupsaccordingtothe
The marine sponge holobiont
abundanceanddensityofmicrobesintheirtissues.High
Microbialcorediversity
microbialabundance(HMA)spongesharbordensitiesof
The Global Sponge Microbiome Project, under the um-
microbes2–4ordersofmagnitudehigherthanlowmicrobial
brella of the Earth Microbiome Project, is a recent col-
abundance(LMA)sponges[225,226].Arecentpublication
laborative initiative to assess the microbial diversity in
madeuseoftheGlobalSpongeMicrobiomeProjectdatato sponges from around the world, following standardized
furtherinvestigatethemicrobialdiversityfeaturesofHMAand protocols [23, 24]. Similar to the Human Microbiome
LMAspongesatlargescalebywayofamachinelearning[227]. Project [37], the main goal was to create a publicly avail-
HMAspongesharborricherandmorediversemicrobial able database that would enable comparative studies in
order to discover common patterns and principles of
communitiesthanLMAsponges[227](althoughtherearefew
sponge-associated microbial assemblies. The first com-
exceptionstothispattern,e.g.,[228]).Additionally,certaintaxa
prehensive study [23], including 81 sponge species, re-
(fromphylumto97%OTU-levelresolution)aresignificantly
vealed that the sponge microbiome spans at least 39
enrichedineitheroneortheothergroup[227].Forexample,
microbial phyla and candidate phyla (Fig. 1). The most
LMAspongesareenrichedinProteobacteriaandCyanobacteria dominant bacterial symbiont groups belong to the phyla
whereasHMAspongesareenrichedinChloroflexi,Acidobacteria, Proteobacteria (mainly Gamma- and Alphaproteobac-
orPoribacteria,amongothers.Despitethesedifferencesinmi- teria), Actinobacteria, Chloroflexi, Nitrospirae, Cyano-
crobialdiversityandabundance,thefunctionalconvergenceof bacteria, and candidatus phylum Poribacteria, while
Thaumarchaea represents the dominant archaeal group
microbiomecorefunctionsappearstospantheHMA-LMAdi-
[23, 24]. The microbial communities are species-specific,
chotomy[31,53].However,differencesingeneabundancesbe-
but composed of both generalist microbes that are de-
tweencentralmetabolicfunctionsofLMAandHMAmicrobial
tected in the majority of sponge species from diverse
communitieshavebeenreported[64].Interestingly,spongespe-
geographic regions, as well as specialists that are
ciesdivergeinpresentingoneofthesetwomicrobialconfigura- enriched in particular species but are rare or absent in
tions,regardlessofhostphylogeny[226,227].Ithasbeen most other species [23, 38]. A second sequencing effort
proposedthatspongemorphologymaybeadeterminantfac- has recently expanded this dataset to over 260 sponge
tor:HMAspongeshavedensertissueswithless-developedwater species,yet,theoverallpatterns remain consistent[24].
In terms of community structure, complex host-
channelscomparedwithLMAsponges[226,229,230].Still,the
associatedmicrobialcommunitiesaredividedinto acore
processesunderlyingthisdichotomyremainunknown.
microbiome (members that are highly prevalent in all
host individuals of the same species) and a variable
biotic and abiotic factors (reviewed in [27]). For ex- microbiome (members of the microbial community that
ample, they provide habitat for a wide range of fauna are recovered only from some individuals or that vary in
and play an important role in benthic-pelagic coupling their relative abundance) [39]. Surveys along different
due to their impressive filtering capacity [26, 28–30]. environmental gradients (e.g., geographical distance [40],
The field of sponge microbiology has consolidated in re- season [41, 42], depth [43], and habitat [44]) have con-
cent years as collaborative efforts have developed stan- sistently confirmed that sponges harbor species-specific
dardized protocols and curated databases on sponge- and stable microbiomes at different prokaryotic taxo-
associated microbial diversity (i.e., the Global Sponge nomic levels [45] and prevalence thresholds [46]. This
Microbiome Project) [23, 24]. Novel approaches, com- stability is remarkable when compared with the dynamic
bined with state-of-the-art techniques, have begun to re- turnover of bacterioplankton in the surrounding water,
veal the functions of the collective microbial community upon which sponges feed [41], and hints to the import-
and individual symbiont groups [31–35]. One major ance of host-related factors in shaping the core micro-
finding is that many of the functional roles provided by biome. However,there is also evidencethat suggests that
sponges are indeed mediated by their associated mi- environmental conditions impact sponge-associated mi-
crobes. The natural variability across sponge holobionts crobial diversity, particularly the variable fraction. For
and environments, together with the possibility for lab example, two sponge species that were able to colonize
experiments, opens up the opportunity to address the and proliferate in the acidified environment of a CO
2
dynamics of these complex symbiotic systems [36]. It is seep [47], harbored significantly higher relative numbers
therefore timely toscaleupthemarinespongeholobiont of symbiotic Synechococcus at the CO seep compared
2
concept from the microbial to the ecosystem level, with specimens at control sites less than 500 m away.
Pitaetal.Microbiome (2018) 6:46 Page4of18
Fig.1MicrobialOTUrichnessinsponge-associatedmicrobialcommunitiesatphylumlevel.TheGreengenesannotationoftherepresentativese-
quencesforsponge-associatedOTUsdetectedbytheGlobalSpongeMicrobiome[23]wasusedtocreatethischart.Adiversityof43,034OTUs
from39classifiedmicrobialphyla(bacteriaandarchaea)wasdetectedinthemicrobiomesofthe81spongespeciesinthisproject[23]
Temporal variation, depth, and habitat type can also unidirectional interactions (i.e., amensalism (−/0) and
impact the composition of sponge-associated micro- commensalism (+/0) prevailed over cooperation (+/+)
biota [43, 48, 49]. An additional driver of sponge- and competition (−/−)) [23]. These findings are consist-
associated microbiota structure is the HMA-LMA ent with mathematical models that predict that weak
dichotomy. and non-cooperative interactions help to stabilize highly
Microbe-microbe interactions within the holobiont diverse microbial communities, whereas cooperation
can further affect the dynamics and stability of the sym- yields instability in the long term by fueling positive
biosis [50, 51]. Network and modeling analyses aim to feedbacks[52].
disentangle the strength and nature (positive, negative,
or neutral) of the interactions and predict their dynam- Microbialcorefunctions
ics. Bacteria-bacteria network analysis of the core micro- Since sponge symbionts remain largely uncultivable,
biota in different sponge species has revealed a low culture-independent methodologies have been instru-
connective network withvery fewstrong andmanyweak mental to gain genomic and thereby putative functional
Pitaetal.Microbiome (2018) 6:46 Page5of18
information on sponge symbionts. Indeed, a variety of from the seawater filtered by the sponge, as well as pro-
metagenomic, metaproteomic, and metatranscriptomic ducedbythespongehostitself[77].Withrespecttocar-
sequencing approaches have been employed to elucidate bon metabolism, the degradation of complex
the functions of the sponge microbiome [31, 53–56]. carbohydrates appears to be a dominant feature in
Single-cell genomics and metagenomic binning have ob- sponge symbioses and highlights the role of hetero-
tained a number of individual symbiont genomes [33, trophy inthese communities[32,33].Forexample,there
57–59]. Furthermore, novel visualization techniques is mounting evidence that the symbionts also feed on
have been developed and applied to test hypotheses de- sponge cell biomass and components of the sponge
rived from genomic data as well as gain valuable spatial extracellular matrix [32, 33, 78]. The core functions of
information[34,35]. the microbiota also encompass metabolic features that
Comparisons between metagenomes of sponge- potentially benefit the host. Sponge symbionts are
associated and seawater microbial consortia have identi- enriched in genes related to the synthesis of vitamins,
fied gene features enriched in sponge symbionts that such as vitamin B and vitamin B [31, 53, 72, 79] sug-
1 12 ,
mightberelevanttothesymbiosis[31,53,60,61].These gesting the symbionts may satisfy the host’s demand for
features havebeen found in the microbiomes of multiple these essential vitamins. For example, a recent holobiont
spongespeciesfromvariousgeographicregions,butthey transcriptomestudyshowedthatthespongemicrobiome
are mediated by different microbial taxa and carried out was enriched in gene functions related to anabolic path-
by different, although analogous, pathways [53, 62]. This ways of several amino acids and vitamins for which the
functional convergence hints to features that are neces- host Xestospongia muta expressed only catabolic reac-
sary formicrobialpersistence inthehost aswellasholo- tions[72].Thediverseandabundantrangeofmembrane
biont success, and therefore can be considered core transporters (e.g., ABC-type transporters) encoded by
functions of the sponge microbiome [23, 31, 53, 62]. Be- the sponge microbiome provides mechanisms to facili-
yond the housekeeping genes required for microbial life, tate these putativemetabolic exchanges [53].In addition,
we define core functions as the range of metabolic and microbial symbionts have been identified as the source
defensive features that allow the sponge microbiota to of certain secondary metabolites that constitute the
colonize, interact with, and adapt to the host environ- chemicaldefenseofthespongeholobiont[79,80].
ment (Table 1). Metabolic features within the core func- In order to persist within sponges, microbes must
tions include (a) the autotrophic and heterotrophic avoid phagocytosis by the host cells. Eukaryotic-like pro-
pathways for symbionts to utilize the nutrients available tein domains (ELPs), such as ankyrin repeat proteins,
in the sponge host environment—either produced by the tetratricopeptide repeat proteins, and leucine-rich repeat
host itself or filtered in from the surrounding seawa- proteins, were found to be highly enriched in and also
ter—and (b) the pathways that directly contribute to the expressed by sponge symbionts [31, 54, 81–83]. ELPs
symbiotic relationship with the host. Defensive features mediate protein-protein interactions and are hypothe-
include those that enable symbiont persistence within sized to play a role in the evasion of phagocytosis [81].
the sponge host. In addition, most studied sponge sym- Another possible strategy has been found in the cyano-
biont genomes lack genes encoding for flagella, which bacterial symbiont “Candidatus Synechococcus spon-
points to a non-motile existence within the mesohyl giarum” that lacks a lipopolysaccharide (LPS) antigen
matrix[33,61](but see[53,63]). [83]. This modification of the LPS in the symbiont vs
Nitrogen is generally a limiting nutrient in the marine free-living Synechococcus could represent a mechanism
environment but is excreted in large quantities by the for the sponge host to discriminate between food and
sponge host, which produces ammonia as a metabolic symbioticbacteria [84].
waste product. Consequently, it is not surprising that Additional defensive core functions relate to protec-
sponge symbionts are enriched in nitrogen metabolism tion and stress response (e.g., stress proteins, restriction
genes [53, 64–66]. Ammonia oxidation is particularly modification, toxin-antitoxin systems, and clustered
prevalent and predominant [53, 62, 64, 67, 68], but most regularly interspaced short palindromic repeats
major nitrogen cycling pathways occur, including both CRISPRs). These defensive functions likely shield sponge
aerobic (e.g. nitrification, nitrogen fixation) and anaer- symbionts against incoming foreign DNA, pathogens,
obic (e.g., denitrification, anammox) processes [59, 64, and toxins to which they are exposed due to the pump-
69–73]. The presence of anaerobic metabolism is likely ing activity of the host [31, 33, 61]. Interestingly, ele-
facilitated by the fact that the sponge tissue can rapidly vated GC content and larger genome sizes were
become anoxic during temporary cessation of sponge observed in sponge metagenomes in comparison to sea-
pumping[74–76]. watermetagenomes[61].Thelargergenomesizesareat-
A large part of the sponge microbiota relies on hetero- tributed to higher levels of horizontal gene transfer
trophic metabolism and uses nutrient sources derived (HGT) within the sponge host than in the seawater
Pitaetal.Microbiome (2018) 6:46 Page6of18
Table1Corefunctionsofthespongemicrobiome
Corefunction Interpretation Reference
Metabolicfeatures Nitrogenmetabolismwith Utilizationofenvironmentaland Reviewedin[77]
emphasisonammoniaoxidation host-derivednutrients
Carbonmetabolismwith Utilizationofenvironmentaland [32,33]
emphasison host-derivednutrients
complexcarbohydrates
Nitrogenandcarbon Utilizationofenvironmentaland [35,53]
metabolism host-derivednutrients
utilizingcreatinine
Vitaminsynthesis Overproductionofvitaminsthat [31,53,72]
(especiallythiamineandvitaminB12) arethenutilizedbythespongehost
Secondarymetabolism Microbe-microbeinteraction,
defenseoftheholobiont
Carnitine(vitaminBT)utilization Utilizationofhost-derivedcomponent [33]
Defensefeatures CRISPR-Cassystems Defenseagainstviruses/phages [31,33,61]
Toxin-antitoxinsystems DefenseagainstforeignDNA [31,33,61]
Restrictionmodificationsystems DefenseagainstforeignDNA [31,33,61]
Eukaryotic-likeproteindomains phagocytosisevasion [31,54,81–83]
Modificationsofthe phagocytosisevasion [83,84]
lipopolysaccharide
Other Mobilegeneticelements Increasedlevelsofhorizontal [31,53,61,85]
andtransposases genetransfer
environment and adaptations to the more variable and [35]. The thaumarchaeon and a Nitrospirabacterium are
nutrient-rich sponge-associated environment [61]. The hypothesized to be coupled in their nitrification activity,
hypothesis of increased levels of HGT is supported by producing nitrate that is subsequently used by the Phyl-
the high number of mobile genetic elements found in lobacteriaceaebacteriumandthediatom [35].
the genomic repertoires of sponge symbionts, as well as Studieson single symbiont groups highlight the poten-
transposases necessary for genetic transfer, which likely tial for high levels of specialization and interdependency
played a role in the evolutionary adaptation of the within sponge holobionts. They also complement com-
spongemicrobiota tothesymbioticlifestyle[31,53,85]. munity level approaches by linking diversity with func-
To elucidate their role within the community, single tion. In these complex ecosystems, it is particularly
members of the sponge microbiome have been studied challenging to identify which taxa contribute to each
individually and revealed examples of specialization. For functional trait and the degrees of redundancy of par-
example, metagenomic binning revealed three symbiont ticular functions remains unknown. Future studies
guilds in Aplysina aerophoba displaying metabolic should validate the genomic information presented here
specialization to different substrates [33]. Each guild was with a focus on those functions directly involved in the
composed of a phylogenetically diverse group of sym- symbiotic interaction. In this direction, further efforts
biont members, suggesting independent evolution to dif- for cultivation would provide valuable insight into the
ferent micro-niches within the sponge extracellular chemicalcharacterizationandenvironment-regulatedac-
matrix. A remarkable example of a function carried out tivity oftarget symbionts.
by a specific member of the microbiota is that of “Can-
didatus Entotheonella factor,” which produces almost all Thespongehost
polyketides and peptide families that were previously at- Sponge hosts may be viewed as ecosystem engineers
tributed to synthesis by the host sponge,Theonella swin- [52], since they provide a certain habitat that selects for
hoei [79]. This example is exceptional in that a specific the presence and persistence of certain microbes, but
bacterial clade associates with a specific sponge host and not others. They also control their microbial residents
endows the holobiont with defensive capacities. More- by specifically recognizing and differentiating between
over, a recent study merging metagenomic binning, foreignandsymbioticmicrobes[84,86],likelyviathein-
metatranscriptomics and visualization techniques has re- nate immune system. The innate immune system, trad-
vealed tightly interlinked metabolic pathways between itionally investigated in the context of pathogenesis,
members of the holobiont of the Cymbastella concen- allows colonization and long-term maintenance of the
trica;twoproteobacteria,athaumarchaeon andadiatom symbiosis (reviewed in [87]). Pattern recognition
Pitaetal.Microbiome (2018) 6:46 Page7of18
receptors (PRRs) sense microbial ligands, but the acti- nutrition for their hosts who in turn support the lar-
vated response is context-dependent: symbiont-derived ger communities in these unique ecosystems [5, 22,
signals promote homeostasis, whereas pathogens induce 99]. The sponge microbiome provides a number of
aninflammatoryresponse. functions that are amplified by host activity and
Theunderlyingmolecularmechanismsofmicrobialrec- through cascading effects mediate the functioning of
ognition by sponges remain elusive due to experimental the sponge holobiont at the community and ecosys-
limitations [36]. However, high-throughput sequencing tem level. Here, we provide five key examples where
datarevealedthatspongesharboracomplexgenomicrep- such microbial-mediated functions scale up to influ-
ertoire encoding a broad spectrum of immune receptors ence community structure and contribute to ecosys-
(including Toll- and NOD-like receptors and scavenger tem primary productivity, biogeochemical nutrient
receptor cysteine-rich (SRCR) family members) [60, 88, cycling, and benthic food webs (Fig. 2).
89],forwhichtheroleinrespondingtomicrobesisbegin-
ning to be elucidated [90, 91]. For example, the sponge Photosynthesis
Petrosia ficiformis displayed an increased expression of a Sponges can host photoautotrophic symbionts that not
gene containing the conserved SRCR domain when living only contribute to host nutrition through the transloca-
insymbiosiswithacyanobacterium,incomparisontothe tion of photosynthetically fixed carbon and nitrogen
aposymbiotic status [90]. Also, components of the Toll- [100–102], but also contribute to ecosystem primary
like receptor pathway such as MyD88 were involved in productivity [103]. In species hosting photosymbionts,
the response to microbial signals in different species [91, these symbionts can potentially supply more than 50%
92]. In a recent experiment on juvenile Amphimedon of the holobiont’s energy requirements [102–104]. Sym-
queenslandica [91], bacterial encounter involved regula- biont contribution to host nutrition appears to be highly
tion of SRCR-containing genes, but the downstream re- variableasonlysomespongesreceive anutritional bene-
sponsediffereddependingontheoriginofthebacteria.In fit from their photosymbionts, and reduced photosyn-
particular, the transcription factors FoxO and NFκβ were thetic capacity does not always correspond with a
upregulated upon exposure to own symbionts, but not to reduction in host growth [102, 105–107]. Nevertheless,
a bacterial fraction from another sponge species. These photosynthetic symbionts enable sponge holobionts to
new findings suggest that sponges actively recognize and contribute to the gross primary productivity that sup-
discriminate microbes via immune signaling. Host recog- ports the entire ecosystem [108]. Similarly, evidence for
nitionofthemicrobiotaalsoactsonsymbiontacquisition: chemoautotrophy [109–111] suggests that chemoauto-
thehostpromotescertainmicrobialspeciesthroughverti- trophic sponge holobionts may contribute to ecosystem
caltransmissionfromadulttoprogenyorbydirectrecog- primary productivity, particularly in deep-sea environ-
nition and uptake of symbionts from the environmental ments, such as hydrothermal vents and cold seeps [68,
pool. In sponges, both modes of microbial transmission 111–113], where such symbioses are essential for sup-
likely occur [93–98], yet the underlying mechanisms of portinglifeinthese extreme environments[99].
host-microbe crosstalk remain to be identified. Host-
related processes would impose a means to maintain spe- Thespongeloop
cific microbiomes, but it is likely that host-independent The assimilation of dissolved organic matter (DOM) by
process (e.g., stochasticity) also play a role, particularly in spongeholobiontsfacilitatesDOMcyclinginbenthichabi-
theenvironmentallyacquiredmicrobialfraction[18]. tats with cascading effects on marine food webs [29]. Mi-
crobes contribute to the assimilation of DOM by the
From microbes to ecosystems sponge holobiont [29, 114, 115], which can account for up
Highly diverse holobionts can be considered as complex to ~90% of the holobiont’s total heterotrophic carbon up-
ecosystems [15, 20, 52] in which the actions and interac- take[116–122].Inadditiontoprovidinganimportantfood
tions of the various members shape the overall function- sourcefortheholobiont,DOMuptakebyspongeshasbeen
ing of the holobiont. These individual ecosystems in turn proposedtoplayakeyroleinDOMcyclingwithintropical
interact with and influence neighboring holobionts, such and deep-sea coral reefs via a pathway termed the “sponge
that they are further integrated into larger communities loop” [29, 114]. By rapidly taking up the DOM released by
and ecosystems that interact at successively larger scales primary producers and converting it into particulate or-
[5]. Consequently, the actions of a single member of the ganicmatter(POM)intheformofdetritus,spongestrans-
microbiotacanexertaneffectfarbeyondthatoftheholo- formDOMintoafoodsourcethatismorereadilyavailable
biont. Key examples of this concept of “nested ecosys- tootherbenthicreeffauna[29,115,123,124](Fig.2).Simi-
tems” are the chemoautotrophic symbionts associated lartothemicrobialloop[1,125],thespongelooptherefore
withhydrothermalventanimalsorthephototrophicsym- enables the energy and nutrients in DOM to be retained
bionts associated with reef-building corals that supply and recycled within reef food webs. Although exact
Pitaetal.Microbiome (2018) 6:46 Page8of18
Fig.2Thespongeholobiontasanexampleoftheconceptofnestedecosystems.Keyfunctionscarriedoutbythemicrobiome(coloredarrows)
influenceholobiontfunctioningand,throughcascadingeffects,subsequentlyinfluencecommunitystructureandecosystemfunctioning.
Environmentalfactorsactatmultiplescalestoaltermicrobiome,holobiont,community,andecosystemscaleprocesses.Thus,factorsthatalter
microbiomefunctioningcanleadtochangesattheholobiont,community,orevenecosystemlevelandviceversa,illustratingthenecessityof
consideringmultiplescaleswhenevaluatingfunctioninginnestedecosystems.DOM,dissolvedorganicmatter;POM,particulateorganicmatter;
DIN,dissolvedinorganicnitrogen
quantification of DOM cycling by the sponge loop is lack- benefit the host through removal of the large quantities
ing, DOMuptake bycrypticsponges inthe Caribbean and of host-excreted ammonia [129]. Whether a sponge
Indo-Pacificisestimatedtobeonthesameorderofmagni- hosts large numbers of highly active nitrifying microbes
tude as gross reef primary productivity and may even ex- dictates if it releases nitrogen primarily as ammonia or
ceed DOM cycling by the microbial loop [29, 126]. Thus, nitrate [62,119, 127].Moreover, since the sponge micro-
byactingthroughthespongeloop,thespongemicrobiome biome can simultaneously perform competing nitrogen
may play an important role in driving DOM cycling at the cycling pathways (e.g., nitrification and denitrification)
ecosystem level, as well as facilitating energy transfer [69, 72, 75], the relative activities of different members
throughreeffoodwebs(Fig.2). of the microbiome can further influence whether the
holobiont acts as a net source or sink of bioavailable ni-
Inorganicnutrientcycling:nitrogenandphosphorous trogen [101, 128]. In oligotrophic marine environments
Sponge holobionts play an important role in the biogeo- like coral reefs, nitrogen can be released by sponges at
chemical cycling of nitrogen—one of the main nutrients ecologically relevant quantities [127, 130] and can facili-
limiting primary productivity in the marine environment tate the growth of nearby primary producers such as
[30, 127]. This capacity for nitrogen cycling is intimately corals and algae [131, 132]. Sponge-associated microbes
linked to nitrogen transformations carried out by the are also involved in the cycling of other key limiting nu-
sponge microbiome [72, 128]. Nitrification via ammonia trients such as phosphorous. While sponges have been
and nitrite oxidization is particularly prevalent and may shown to release inorganic-phosphorous in the form of
Pitaetal.Microbiome (2018) 6:46 Page9of18
phosphate [62, 119, 133, 134], the discovery of abundant species [152, 153]. They not only provide cytotoxic sec-
intracellular polyphosphate granules in the microbial ondary metabolites [154] but also photosynthates that
symbionts of three phylogenetically distinct reef sponge enhance the physiological performance of the host
species suggests the sponge microbiome may also medi- [153, 155]. Impairing the photosynthetic capacity of
ate a pathway for phosphorous sequestration on coral the symbionts through shading stops the growth of
reefs [135]. These microbial-generated storage granules the sponge and prevents it overgrowing adjacent
can account for up to 40% of the total sponge phospor- corals [153], demonstrating the importance of the
ous content, and thus may substantially influence phos- symbionts in mediating these competitive interactions.
phorous availability in habitats with high sponge Outbreaks of Terpios hoshinota have been implicated
biomasses [135, 136]. The sponge microbiome therefore in causing widespread coral mortality [156, 157]. Con-
influences both the quantity and speciation of inorganic sequently, this provides an example of how symbionts
nutrients made available to neighboring primary pro- can dramatically influence holobiont competitiveness
ducers in coral reefs and other benthic ecosystems and thereby alter benthic community dynamics with
(Fig. 2). catastrophic results.
These five examples highlight how the sponge
Chemicaldefenseandpredation microbiome can influence functioning at the holo-
The sponge microbiome also conveys defensive capaci- biont, community, and ecosystem scale through the
ties to the host that strongly influence the interactions concept of nested ecosystems. Moreover, these
between sponges and other organisms within benthic microbiome-mediated functions are in turn shaped by
communities (Fig. 2). Sponge holobionts produce a di- environmental factors that also act on multiple scales
verse array of secondary metabolites with antiviral, anti- [158] and feedback on the functioning of the holo-
microbial, cytotoxic, allelopathic, and antipredatory biont by modifying sponge primary productivity, nu-
effects [10, 129, 137, 138], some of which have been at- trient fluxes, and chemical defenses [134, 159–161].
tributed to the microbiome [79, 80, 139]. The produc- Thus, future studies need to target the mechanisms
tion of biologically active feeding deterrent compounds behind host-symbiont interactions and link multiple
is a common defensive strategy employed by sponges to scales if we are to unravel how the sponge micro-
avoid predation [140–142]. One of the earliest studies to biome may alter holobiont functioning under future
link a sponge-derived secondary metabolite to the environmental changes.
microbiome found that compounds isolated from the
cyanobacterial symbionts of the sponge Lamellodysidea Holobiont responses: stress, dysbiosis, and
herbacea deterred fish feeding [143]. Subsequent studies acclimatization
have found increasing evidence that the microbiome Holobionthealth
is actively involved in the production of bioactive Thehealthy holobiont is considered an ecosystem that is
compounds with putative anti-predatory effects in a ina state ofdynamic equilibrium. Like in any ecosystem,
range of chemically defended sponge species [10, 79, thestrengthandoutcome(i.e., beneficial,neutral,ordet-
144, 145]. Predation is a major process governing rimental) of the interactions among the members of the
benthic community structure and can alter sponge holobiont may be affected by perturbations that chal-
community composition at sub-meter to habitat scales lenge the healthy equilibrium (Fig. 3). Upon disturbance,
[146–148]. In habitats with high abundances of alternative scenarios are possible. On the one hand,
spongepredators,spongeswithoutchemicaldefensesmay homeostasis can maintain healthy baseline conditions
be entirely excluded [148–150]. By influencing holobiont through mechanisms of resistance or resilience [162].
susceptibility to predation, the sponge microbiome On the other hand, perturbations may disrupt the bal-
therebyinfluencesbenthiccommunitystructure. ance, leading to dysbiosis and, potentially, disease [163,
164]. Moreover, perturbations may act as a selective
Competition force (at the microbial, host, and/or holobiont level) so
Spatial competition is another important biotic factor that the system reaches a new healthy state that allows it
structuring benthic communities, and the sponge micro- to better cope with environmental change (i.e.,
biome can mediate such interspecific interactions acclimatization). If the new features enhance holobiont
throughacombinationofmetabolicandchemicaldefen- fitness and can be transmitted to new generations, they
sive functions that enhance the competitive capacity of may yield holobiont adaptation sensu lato [165]. The
the holobiont (Fig. 2). For example, the abundant cyano- holobiont concept provides the framework to elucidate
bacterial symbionts of the coral-killing sponge Terpios sponge responses to environmental change, the role of
hoshinota [151] play a key role in enabling the Terpios dysbiosis in disease, and the contribution of the micro-
holobiont to aggressively overgrow a wide range of coral biota toholobiontpersistence.
Pitaetal.Microbiome (2018) 6:46 Page10of18
Fig.3Conceptualrepresentationofholobionthealthandthepotentialoutcomesuponenvironmentalstress.Healthisregardedasadynamic
equilibriumbalancedbythehost,themicrobiome,aswellastheinteractionbetweenthem.Understandingtheunderlyingprinciplesofhealth
andholobiontdynamicswouldhelppredicttheresponsesuponperturbationandwhetherthefinaloutcomewillallowstability,yielddisease,or
turnintoanopportunityforadaptation
Stressanddysbiosis Stress can induce dysbiosis: a disruption of the symbi-
Human activities are modifying the marine environment otic community diversity. In sponges, it is often charac-
atapaceneverbeforerecorded[166].Someofthemajor terized by an increased alpha diversity [173] and/or a
anthropogenic stressors threatening the oceans are cli- shift from sponge-enriched microbes (closely related to
mate change (ocean warming and acidification) and the other sponge symbionts) to opportunists (microbes
deterioration of water quality (e.g., eutrophication, closely related to free-living organisms) [167]. Even in
sedimentation, and pollution). But what are the con- the absence of significant changes in alpha-diversity,
sequences of these environmental stressors for stress-related increases of beta-diversity (dissimilarity
sponge-associated microbial communities (Table 2)? between samples) have been observed in manipulative
Some studies report non-significant changes in the experiments [170, 174], as well as under natural pertur-
microbial community structure upon perturbations bations [41]. This observation is consistent with the re-
such as warming, increased sedimentation, or enriched cently proposed “Anna Karenina principle,” which
nutrient concentrations, at least at sub-lethal stress levels suggests that intraspecific variability is higher in dysbio-
[167–170]. The strength of the perturbations is therefore tic than in healthy individuals [175]. In terms of func-
a major factor determining the ability of the holo- tion, dysbiosis has been correlated with an enrichment
biont to maintain a stable state. For example, the re- of cell motility, chemotaxis, or virulence genes in
silience of Xestospongia muta to bleaching (i.e., the stressedtissuescomparedtohealthycontrols [158,176].
ability to recover its cyanobacterial population) was Stress may also compromise host physiology and im-
only possible as long as stress was kept below a cer- munity [177–179], entailing loss of control over the
tain threshold [171]. Beyond these thresholds, signifi- microbiome; thus, dysbiosis could be responsive rather
cant shifts of the sponge-associated microbiota are than causal. To date, few studies have investigated the
commonly reported, mainly in already necrotic tissues molecular response of the sponge host upon perturb-
as well as in apparently healthy tissues in contact ation, and they have mainly focused on thermal stress in
with necrotic areas [158, 172]. the sponge host using real-time quantitative PCR [158,