Marine Sponge Metagenomics 17.4 Future Perspectives 469
Part C | 17.4
centrica metagenome indicate that it interacts with
surrounding cells and proteins [17.88]. Ankyrins are
especially likely to be of relevance, as they might be
involved in the recognition of and protection from host
phagocytosis. This theory is further strengthened by the
fact that proteins with ankyrin domains are found in
other obligate intracellular pathogenic and symbiotic
systems, where they interfere with host cell function.
Thus, these proteins could represent potential mechanisms that allow the host sponge to discriminate between food and symbiont bacteria [17.88]. Functional
analysis performed via shotgun sequencing using the
COG (Clusters of Orthologous Group) database suggested that the majority of the detected genes belong
to bacteria. The authors also found a large number of
sequences identified as transposable insertion elements.
The sponge metagenomes contained a greater number of sequences identified as COG0610 (restriction
enzymes, type I helicase) and COG1715 (restriction endonuclease) than the surrounding seawater. Both COG
groups include specific DNA modification and restriction systems in bacteria, and therefore, the authors
hypothesized that this would facilitate horizontal DNA
exchange between sponge microorganisms and protect
against DNA exchange with planktonic organisms in
the surrounding seawater [17.61].
The symbiotic function of the microbial community in the sponge A. aerophoba was revealed by
whole genome amplification (WGA). The functional
data revealed a sponge specific PKS and an NRPS
from the Poribacteria from the Chloroflexi clade, respectively [17.89]. The carbon monoxide dehydrogenase detected in the metagenome of C. concentrica [17.88] demonstrated that the Poribacteria are
mixotrophs that can undertake autotrophic carbon fixation [17.84]. A large number of insertion elements was
observed for the first time within the C. concentrica
metagenome. Large numbers of mobile elements were
previously seen within intracellular symbionts in other
hosts [17.90] and were proposed to have important roles
in the evolution of bacterial genomes for symbiotic relationship with their hosts.
Second, a high frequency of clustered regularly
interspaced short palindromic repeats CRISPR and
CRISPR-associated proteins (CAS) were observed in
the metagenome data set. The elevated abundance of
these CRISPRs and CAS were proposed to form a viral specific defense system [17.91]. The defense system
may provide proteins that are effective against bacteriolytic viral infection for the sponge symbionts, as
sponge bacteria are expected to be exposed to as many
as 1000 viral particles on a single day. Therefore, the
system would be essential for the survival of high
cell density, nonmobile sponge microbial communities
and to maintain a barrier against phage-mediated gene
transfer from the surrounding planktonic community,
where a high phage load could be expected. Third,
several shared metabolic interactions between bacteria and host, including vitamin production, nutrient
transport and utilization, and redox sensing and response were found. These new previously unrecognized
genomic signatures and functions of sponge bacteria
provide an insight into the potential metabolic interdependency between host and microorganisms, and into
the specific mechanisms used by symbionts to remain
in sponge tissue. Also, these novel markers could be
used for monitoring the status of the symbiotic relationships between sponge and bacteria by assessing the
abundance, diversity, and expression of these functional
genes [17.88].
Liu et al. [17.86] unravel some of the interactions
between microbial community and the sponge Cymbastela concentrica through a combined metagenomic
and metaproteomic approach. They provided new data
for the first time on specific transport functions for
typical sponge metabolites (for example, halogenated
aromatics and dipeptides). This study also indicated
that there is a requirement for the microbial community to respond to variable environmental conditions
and hence express an array of stress protection proteins.
Finally, molecular interactions between symbionts and
their host might also be mediated by a set of expressed eukaryotic-like proteins and cell-cell mediators, and some sponge-associated bacteria (for example, the Phyllobacteriaceae phylotype) may be undergoing evolutionary adaptation process to the sponge
environment, as evidenced by active mobile genetic
elements.
17.4 Future Perspectives
The application of metagenomics provides access to
sponge microbiota as a rich resource for novel enzymes and metabolites, and opens new avenues for
the sustainable production of biotechnologically rele-
Part C | 17.4
centrica metagenome indicate that it interacts with
surrounding cells and proteins [17.88]. Ankyrins are
especially likely to be of relevance, as they might be
involved in the recognition of and protection from host
phagocytosis. This theory is further strengthened by the
fact that proteins with ankyrin domains are found in
other obligate intracellular pathogenic and symbiotic
systems, where they interfere with host cell function.
Thus, these proteins could represent potential mechanisms that allow the host sponge to discriminate between food and symbiont bacteria [17.88]. Functional
analysis performed via shotgun sequencing using the
COG (Clusters of Orthologous Group) database suggested that the majority of the detected genes belong
to bacteria. The authors also found a large number of
sequences identified as transposable insertion elements.
The sponge metagenomes contained a greater number of sequences identified as COG0610 (restriction
enzymes, type I helicase) and COG1715 (restriction endonuclease) than the surrounding seawater. Both COG
groups include specific DNA modification and restriction systems in bacteria, and therefore, the authors
hypothesized that this would facilitate horizontal DNA
exchange between sponge microorganisms and protect
against DNA exchange with planktonic organisms in
the surrounding seawater [17.61].
The symbiotic function of the microbial community in the sponge A. aerophoba was revealed by
whole genome amplification (WGA). The functional
data revealed a sponge specific PKS and an NRPS
from the Poribacteria from the Chloroflexi clade, respectively [17.89]. The carbon monoxide dehydrogenase detected in the metagenome of C. concentrica [17.88] demonstrated that the Poribacteria are
mixotrophs that can undertake autotrophic carbon fixation [17.84]. A large number of insertion elements was
observed for the first time within the C. concentrica
metagenome. Large numbers of mobile elements were
previously seen within intracellular symbionts in other
hosts [17.90] and were proposed to have important roles
in the evolution of bacterial genomes for symbiotic relationship with their hosts.
Second, a high frequency of clustered regularly
interspaced short palindromic repeats CRISPR and
CRISPR-associated proteins (CAS) were observed in
the metagenome data set. The elevated abundance of
these CRISPRs and CAS were proposed to form a viral specific defense system [17.91]. The defense system
may provide proteins that are effective against bacteriolytic viral infection for the sponge symbionts, as
sponge bacteria are expected to be exposed to as many
as 1000 viral particles on a single day. Therefore, the
system would be essential for the survival of high
cell density, nonmobile sponge microbial communities
and to maintain a barrier against phage-mediated gene
transfer from the surrounding planktonic community,
where a high phage load could be expected. Third,
several shared metabolic interactions between bacteria and host, including vitamin production, nutrient
transport and utilization, and redox sensing and response were found. These new previously unrecognized
genomic signatures and functions of sponge bacteria
provide an insight into the potential metabolic interdependency between host and microorganisms, and into
the specific mechanisms used by symbionts to remain
in sponge tissue. Also, these novel markers could be
used for monitoring the status of the symbiotic relationships between sponge and bacteria by assessing the
abundance, diversity, and expression of these functional
genes [17.88].
Liu et al. [17.86] unravel some of the interactions
between microbial community and the sponge Cymbastela concentrica through a combined metagenomic
and metaproteomic approach. They provided new data
for the first time on specific transport functions for
typical sponge metabolites (for example, halogenated
aromatics and dipeptides). This study also indicated
that there is a requirement for the microbial community to respond to variable environmental conditions
and hence express an array of stress protection proteins.
Finally, molecular interactions between symbionts and
their host might also be mediated by a set of expressed eukaryotic-like proteins and cell-cell mediators, and some sponge-associated bacteria (for example, the Phyllobacteriaceae phylotype) may be undergoing evolutionary adaptation process to the sponge
environment, as evidenced by active mobile genetic
elements.
17.4 Future Perspectives
The application of metagenomics provides access to
sponge microbiota as a rich resource for novel enzymes and metabolites, and opens new avenues for
the sustainable production of biotechnologically rele-