Part C | 17.3
468 Part C Marine Genomics
Later, the investigation of PKS genes in cultivable
and uncultivable bacteria proved that some of the PKS
genes originating from the sponge metagenome appear
to form a sponge specific bacteria and it is phylogenetically distinct from other PKSs. The large number
of bacterial PKS genes that has been found using
these metagenomic approaches provides compelling evidence in support of the symbiont hypothesis and also
demonstrates the complexity of the bacterio sponge.
Studies with other marine invertebrates have clearly
demonstrated that microbial symbionts are the likely
producers of the metabolites bryostatin (Fig. 17.4(10))
and patellamide (Fig. 17.4(11)) [17.73–75].
The discovery of bryostatin eventually led to the
detection of a huge number of polyketide synthases
of biotechnological interest. Metagenomics strategies
have led to the identification of the Sup-PKS group,
which is dominant in marine sponges and encodes synthases that are present exclusively in these animals.
These synthases produce methyl branched fatty acids
and they are assumed to be of bacterial origin [17.76].
Sponges exhibit a high level of fatty acid diversity,
and it is generally assumed that the methyl branched
fatty acids are of microbial origin [17.77]. This finding is supported by the observation that methylated
fatty acids in bacterio sponges are more abundant than
in bacteria free sponges. Similarly, methyl branched
alkanes that are thought to originate from microbial
methylated fatty acids are commonly present in fossil
sediments and fuels [17.78]. A challenging hypothesis
has been put forward that sponges as the most ancient
metazoan animals might be extant reservoirs for ancient
microbes and their corresponding methylated fatty acid
encoding PKS genes.
The biological function of methyl branched fatty
acids in sponges is unclear. Interestingly, structurally
similar fatty acids are major constituents of the protective lipid cell layer of Mycobacterium tuberculosis [17.79]. Deletion mutants lacking intact mycolic
acids are significantly attenuated in the mouse model
and in macrophages [17.80]. Therefore, it is tempting
to speculate the importance of methyl branched fatty
acids. Marine sponges are also known to contain large
amounts of halogenated organic compounds such as
fatty acids and alkaloids and are thus a potential useful
source of both the halogenases and the dehalogenases
group of biotechnologically important enzymes, which
can be used in the production of pharmaceuticals, herbicides, and pesticides [17.32]. A novel halo-tolerant
lipase was isolated by following a functional screen of
a marine sponge fosmid metagenomic library. The activity and stability profile of the recombinant enzyme
over a wide range of salinities, pH, and temperatures,
and in the presence of organic solvent and metal ions
suggests that there would be a utility for this enzyme in
a variety of industrial applications [17.81].
17.3.3 Functions of the Bacterial Community
in Sponges
To date, the function of sponge-associated microorganisms lags behind the understanding of taxonomic
affiliation. However, recent research on marine sponges
has focused on the symbiont function, in particular for
nitrogen metabolism. Initially, stable isotope experiments demonstrated denitrification in sponges Geodia
barretti [17.82], Dysidea avara, and Chondrosia reniformis [17.83]. Further metagenomic analysis recovered gene encoding cytochrome cd1-type nitrite reductases (nirS) from sponge-associated Betaproteobacteria
and Gammaproteobacteria, which are responsible for
denitrification in sponges [17.82]. Gene encoding enzymes such as nitrite reductase and nitric oxide reductase were also identified in the metagenome of Poribacteria from the sponge Aplysina aerophoba [17.84].
Anammox activity was also demonstrated in the sponge
G. barretti [17.83]. Mohamed et al. [17.85] provided
the first molecular evidence for the presence of potential anammox bacteria in sponges. Liu et al. [17.86]
detected the expression of the ammonia mono-oxygenase membrane bound subunits ˇ and (AmoB and
C) and an ammonia transporter (AmtB) in the microbial community of C. concentric. The genes encoding
AmoB and C were adjacent and orientated in opposite
transcriptional directions on a contig of the C. concentrica metagenome. The contig also contains a gene for
the ˛-subunit (amoA) and has overall striking synteny
with a genomic region of N. maritimus.
Sponges are suggested to be capable of differentiating food bacteria from symbionts. Wilkinson
et al. [17.12] suggest that the chemical composition of
the bacterial outer layer may play a role in sponge
symbiont recognition. Wehrl et al. [17.87] demonstrated
that the retention rates of different food bacteria were
similar, despite the difference in cell surface properties. However, the question of how sponges discriminate between food and symbionts remains unsolved.
Metagenomic analysis of C. concentrica has led to the
discovery of a number of important genomic factors,
including tetratricopeptide repeat domain encoding proteins (TPR) and ankyrin repeat proteins (ARP). The
presence of the TPR and ARP proteins in the C. con-
468 Part C Marine Genomics
Later, the investigation of PKS genes in cultivable
and uncultivable bacteria proved that some of the PKS
genes originating from the sponge metagenome appear
to form a sponge specific bacteria and it is phylogenetically distinct from other PKSs. The large number
of bacterial PKS genes that has been found using
these metagenomic approaches provides compelling evidence in support of the symbiont hypothesis and also
demonstrates the complexity of the bacterio sponge.
Studies with other marine invertebrates have clearly
demonstrated that microbial symbionts are the likely
producers of the metabolites bryostatin (Fig. 17.4(10))
and patellamide (Fig. 17.4(11)) [17.73–75].
The discovery of bryostatin eventually led to the
detection of a huge number of polyketide synthases
of biotechnological interest. Metagenomics strategies
have led to the identification of the Sup-PKS group,
which is dominant in marine sponges and encodes synthases that are present exclusively in these animals.
These synthases produce methyl branched fatty acids
and they are assumed to be of bacterial origin [17.76].
Sponges exhibit a high level of fatty acid diversity,
and it is generally assumed that the methyl branched
fatty acids are of microbial origin [17.77]. This finding is supported by the observation that methylated
fatty acids in bacterio sponges are more abundant than
in bacteria free sponges. Similarly, methyl branched
alkanes that are thought to originate from microbial
methylated fatty acids are commonly present in fossil
sediments and fuels [17.78]. A challenging hypothesis
has been put forward that sponges as the most ancient
metazoan animals might be extant reservoirs for ancient
microbes and their corresponding methylated fatty acid
encoding PKS genes.
The biological function of methyl branched fatty
acids in sponges is unclear. Interestingly, structurally
similar fatty acids are major constituents of the protective lipid cell layer of Mycobacterium tuberculosis [17.79]. Deletion mutants lacking intact mycolic
acids are significantly attenuated in the mouse model
and in macrophages [17.80]. Therefore, it is tempting
to speculate the importance of methyl branched fatty
acids. Marine sponges are also known to contain large
amounts of halogenated organic compounds such as
fatty acids and alkaloids and are thus a potential useful
source of both the halogenases and the dehalogenases
group of biotechnologically important enzymes, which
can be used in the production of pharmaceuticals, herbicides, and pesticides [17.32]. A novel halo-tolerant
lipase was isolated by following a functional screen of
a marine sponge fosmid metagenomic library. The activity and stability profile of the recombinant enzyme
over a wide range of salinities, pH, and temperatures,
and in the presence of organic solvent and metal ions
suggests that there would be a utility for this enzyme in
a variety of industrial applications [17.81].
17.3.3 Functions of the Bacterial Community
in Sponges
To date, the function of sponge-associated microorganisms lags behind the understanding of taxonomic
affiliation. However, recent research on marine sponges
has focused on the symbiont function, in particular for
nitrogen metabolism. Initially, stable isotope experiments demonstrated denitrification in sponges Geodia
barretti [17.82], Dysidea avara, and Chondrosia reniformis [17.83]. Further metagenomic analysis recovered gene encoding cytochrome cd1-type nitrite reductases (nirS) from sponge-associated Betaproteobacteria
and Gammaproteobacteria, which are responsible for
denitrification in sponges [17.82]. Gene encoding enzymes such as nitrite reductase and nitric oxide reductase were also identified in the metagenome of Poribacteria from the sponge Aplysina aerophoba [17.84].
Anammox activity was also demonstrated in the sponge
G. barretti [17.83]. Mohamed et al. [17.85] provided
the first molecular evidence for the presence of potential anammox bacteria in sponges. Liu et al. [17.86]
detected the expression of the ammonia mono-oxygenase membrane bound subunits ˇ and (AmoB and
C) and an ammonia transporter (AmtB) in the microbial community of C. concentric. The genes encoding
AmoB and C were adjacent and orientated in opposite
transcriptional directions on a contig of the C. concentrica metagenome. The contig also contains a gene for
the ˛-subunit (amoA) and has overall striking synteny
with a genomic region of N. maritimus.
Sponges are suggested to be capable of differentiating food bacteria from symbionts. Wilkinson
et al. [17.12] suggest that the chemical composition of
the bacterial outer layer may play a role in sponge
symbiont recognition. Wehrl et al. [17.87] demonstrated
that the retention rates of different food bacteria were
similar, despite the difference in cell surface properties. However, the question of how sponges discriminate between food and symbionts remains unsolved.
Metagenomic analysis of C. concentrica has led to the
discovery of a number of important genomic factors,
including tetratricopeptide repeat domain encoding proteins (TPR) and ankyrin repeat proteins (ARP). The
presence of the TPR and ARP proteins in the C. con-