Part A | 8.3
228 Part A Marine Flora and Fauna
be used to predict possible functions, empirical conclusions cannot be conclusively drawn from phylogenetic biomarker data analyses. In addition, such predictions can only be made for microbes which have
been cultured and from which physiological characterizations have been elucidated. Other methods which
can be employed to determine sponge symbiont functions include genome reconstruction [8.137], singlecell genomics [8.138, 139], metatranscriptomics [8.94,
140], shotgun cloning and sequencing of sponge
metagenomic DNA [8.141], shotgun pyrosequencing [8.121], and the targeted PCR amplification of
functional genes from sponge metagenomes [8.20, 105,
142–148].
A good example of the successful application of
single-cell genomics to predict sponge symbiont functionality from uncultured microbes is the recent work
on the genome of Cenarchaeum symbiosum derived
from the marine sponge Axinella mexicana [8.138]
and on Poribacteria from the sponge Aplysina aerophoba [8.139]. While a shotgun sequencing-based
approach has also been used in the reconstruction of an unidentified ı-proteobacterium from shotgun sequence data from the sponge Cymbastela
concentrica [8.137], pyrosequencing of cDNA has
also recently been used to elucidate the diversity
and abundance of actively transcribed genes from
the sponge Geodia barretti ([8.140]; while shotgun approaches (cloning – [8.141]; pyrosequencing –
[8.121] have identified functional genes in the sponges
Cymbastela concentrica and Arenosclera brasiliensis,
respectively.
Researchers have also targeted functional genes
of particular interest for PCR amplification and sequencing, with genes involved in ammonia-oxidation,
nitrification, and putative host defence in particular being targeted. Ammonia-oxidation (amoA) genes
have been identified in the metagenomes of Aplysina
aerophoba [8.145], Ircinia strobilina, Mycale laxissima [8.147], and Phakiella fusca [8.105]; and nitrification genes (nirS) have been amplified from the
sponge Astrosclera willeyana [8.148]. Genes involved
in the production of bioactive secondary metabolites which may contribute to sponge defence have
also been targeted, with PKS genes being identified from the sponges Pseudoceratina clavata [8.143],
Discodermia dissoluta [8.142], Theonella swinhoei,
Aplysina aerophoba [8.1–6], and Haliclona simulans [8.77].
8.3.2 Discrimination Between
Food Microbes and Symbiotic Microbes
A long-standing question in the sponge microbiology
area centers on how sponges discriminate between food
and symbionts when both occur in the sponge mesohyl. Some recent progress has been made in this regard,
with genomic, metagenomic, and metatranscriptomic
analyses being employed to identify factors which may
play crucial roles in the symbiosis between sponges
and microbes. These include factors associated with
cell recognition, adhesion, and signalling. Gene transcripts for cell recognition factors such as polycystic
kidney domain-like (PKD) factor have been identified in the Geodia barretti metatranscriptome [8.140],
while Ig-like domain protein encoding gene sequences
have been found in the genome of Candidatus Poribacteria [8.139]. Adhesion related genes (ankyrin repeat, tetratrico peptide repeat, fibronectin type III, and
laminin-G domain proteins) were also noted in the
genomes of sponge-derived Poribacteria [8.139] and
ı-proteobacteria [8.137], and adhesion related gene
transcripts (ankyrin repeat domain proteins, tetratrico
repeat domain proteins, TonB-dependent receptors,
and collagen binding surface proteins) were observed
from the metatranscriptome of Cymbastela concentrica [8.141] and Geodia barretti with cell signalling
related protein transcripts also being noted [8.140].
Transposable insertion elements have been identified in the metagenome of Cymbastela concentrica [8.141] with transposase gene transcripts being reported from the metatranscriptome of Geodia barretti [8.140]. These elements are thought to
play roles in microbial genomic rearrangements and
streamlining to help with adaptation to a symbiotic lifestyle [8.141]. Factors with possible roles in
the maintenance of a symbiotic relationship including tetracycline resistance genes and gene encoding for multidrug resistance proteins were found in
the genome of a sponge-associated unidentified ıproteobacterium [8.137], while clustered regularly interspaced short palindromic repeat (CRISPR) gene
sequences with possible roles in resistance to viral
infection have been found in the metagenome C. concentrica [8.141]. Genes and gene transcripts involved
in the biosynthesis of essential vitamins (B 2 or B 12 )
have been noted in the genomes of Cenarchaeum
symbiosum [8.138], candidatus Poribacteria [8.139],
and a sponge-associated ı-proteobacterium [8.137],
228 Part A Marine Flora and Fauna
be used to predict possible functions, empirical conclusions cannot be conclusively drawn from phylogenetic biomarker data analyses. In addition, such predictions can only be made for microbes which have
been cultured and from which physiological characterizations have been elucidated. Other methods which
can be employed to determine sponge symbiont functions include genome reconstruction [8.137], singlecell genomics [8.138, 139], metatranscriptomics [8.94,
140], shotgun cloning and sequencing of sponge
metagenomic DNA [8.141], shotgun pyrosequencing [8.121], and the targeted PCR amplification of
functional genes from sponge metagenomes [8.20, 105,
142–148].
A good example of the successful application of
single-cell genomics to predict sponge symbiont functionality from uncultured microbes is the recent work
on the genome of Cenarchaeum symbiosum derived
from the marine sponge Axinella mexicana [8.138]
and on Poribacteria from the sponge Aplysina aerophoba [8.139]. While a shotgun sequencing-based
approach has also been used in the reconstruction of an unidentified ı-proteobacterium from shotgun sequence data from the sponge Cymbastela
concentrica [8.137], pyrosequencing of cDNA has
also recently been used to elucidate the diversity
and abundance of actively transcribed genes from
the sponge Geodia barretti ([8.140]; while shotgun approaches (cloning – [8.141]; pyrosequencing –
[8.121] have identified functional genes in the sponges
Cymbastela concentrica and Arenosclera brasiliensis,
respectively.
Researchers have also targeted functional genes
of particular interest for PCR amplification and sequencing, with genes involved in ammonia-oxidation,
nitrification, and putative host defence in particular being targeted. Ammonia-oxidation (amoA) genes
have been identified in the metagenomes of Aplysina
aerophoba [8.145], Ircinia strobilina, Mycale laxissima [8.147], and Phakiella fusca [8.105]; and nitrification genes (nirS) have been amplified from the
sponge Astrosclera willeyana [8.148]. Genes involved
in the production of bioactive secondary metabolites which may contribute to sponge defence have
also been targeted, with PKS genes being identified from the sponges Pseudoceratina clavata [8.143],
Discodermia dissoluta [8.142], Theonella swinhoei,
Aplysina aerophoba [8.1–6], and Haliclona simulans [8.77].
8.3.2 Discrimination Between
Food Microbes and Symbiotic Microbes
A long-standing question in the sponge microbiology
area centers on how sponges discriminate between food
and symbionts when both occur in the sponge mesohyl. Some recent progress has been made in this regard,
with genomic, metagenomic, and metatranscriptomic
analyses being employed to identify factors which may
play crucial roles in the symbiosis between sponges
and microbes. These include factors associated with
cell recognition, adhesion, and signalling. Gene transcripts for cell recognition factors such as polycystic
kidney domain-like (PKD) factor have been identified in the Geodia barretti metatranscriptome [8.140],
while Ig-like domain protein encoding gene sequences
have been found in the genome of Candidatus Poribacteria [8.139]. Adhesion related genes (ankyrin repeat, tetratrico peptide repeat, fibronectin type III, and
laminin-G domain proteins) were also noted in the
genomes of sponge-derived Poribacteria [8.139] and
ı-proteobacteria [8.137], and adhesion related gene
transcripts (ankyrin repeat domain proteins, tetratrico
repeat domain proteins, TonB-dependent receptors,
and collagen binding surface proteins) were observed
from the metatranscriptome of Cymbastela concentrica [8.141] and Geodia barretti with cell signalling
related protein transcripts also being noted [8.140].
Transposable insertion elements have been identified in the metagenome of Cymbastela concentrica [8.141] with transposase gene transcripts being reported from the metatranscriptome of Geodia barretti [8.140]. These elements are thought to
play roles in microbial genomic rearrangements and
streamlining to help with adaptation to a symbiotic lifestyle [8.141]. Factors with possible roles in
the maintenance of a symbiotic relationship including tetracycline resistance genes and gene encoding for multidrug resistance proteins were found in
the genome of a sponge-associated unidentified ıproteobacterium [8.137], while clustered regularly interspaced short palindromic repeat (CRISPR) gene
sequences with possible roles in resistance to viral
infection have been found in the metagenome C. concentrica [8.141]. Genes and gene transcripts involved
in the biosynthesis of essential vitamins (B 2 or B 12 )
have been noted in the genomes of Cenarchaeum
symbiosum [8.138], candidatus Poribacteria [8.139],
and a sponge-associated ı-proteobacterium [8.137],