Marine Sponge Metagenomics 17.1 Background and Problems of Sponge Research 459
Part C | 17.1
Delta, and Gamma Proteobacteria), Spirochaetes, and
Verrucomicrobia. Furthermore, a new phylum, Poribacteria, has also been found in a number of microbially rich sponges. Sequences from the Chlorobi
(green sulfur bacteria) have not been obtained from
sponges, although positive FISH signals were obtained
from Rhopaloeides odorabile. Two archaea have also
been reported from marine sponges, which belong to
the members of the phyla Crenarchaeota and Euryarchaeota [17.4].
Sponges also host eukaryotic microbes such as dinoflagellates and diatoms, with the latter seemingly
most prevalent in polar regions. Zoochlorella, an endosymbiotic microalgae, often reported from freshwater sponges. Two previous reports of cryptomonads
in sponges were made by Wilkinson [17.16]. Marine
sponges’ associated fungi are receiving increasing attention due to their biotechnological potential. Fungal
strains isolated from marine sponges, representing three
phyla of Ascomycota, Zygomycota, and Basidiomycota
fungi. In total 22 orders (Boliniales, Botryosphaeriales,
Capnodiales, Chaetosphaeriales, Claromycetales, Diaporthales, Dothideales, Eurotiales, Helotiales, Hypocreales, Microascales, Mitosporic Agricomycotina,
Moniliales, Mucorales, Onygenales, Phyllachorales,
Pleosporales, Polyporales, Saccharomycetales, Sordariales, Trichosphaeriales, and Xylariales) within Ascomycota, 8 orders (Agaricales, Agaricostilbales, Corticiales, Malasseziales, Polyporales, Sporidiobolales,
Tremellales, and Wallemiales) within Basidiomycota
and 4 orders (Rhizopus, Mucor, Rhizomucor, and Syncephalastrum) within Zygomycota have been recorded
in sponges [17.17]. Compelling evidence for symbiosis of yeast with sponges of the genus Chondrilla was obtained by extensive microscopy studies
of both adult sponge tissue and reproductive structures [17.18]. It thus remains unclear in most cases
whether such fungi are consistently associated with the
source sponge, or even whether they are obligate marine
species.
Viruses and virus-like particles (VLP) are abundant
in coral reef environments and have been found in the
water columns adjacent to sponges in coral reef environments. Virus-like particles have been observed in
cell nuclei in Aplysina (Verongia) cavernicola [17.19].
It was suggested that VLP could be involved in sponge
cell pathology. In another study, infection of an Ircinia
strobilina derived alphaproteobacterium by a seawater bacteriophage was also demonstrated in laboratory conditions [17.20], but infection in nature is not
known.
It has been assumed that the bacteria associated
with the sponge synthesize several bioactive compounds [17.21]. However, cultivation of invertebrates
for these bioactive compounds is too expensive and impossible, and hence cultivation of symbiotic microbes
may provide an inexpensive supply of the natural
compound. Yet, many sponge-associated bacteria have
not been cultivable. Thus, metagenomic approaches
are intended to isolate the bioactive genes responsible
for bioactive compounds and express them in surrogate hosts. Usually, metagenomics begins with the
construction and screening of metagenomic libraries
for the targeted genes. This approach has resulted in
the detection of numerous short biosynthetic pathways
and novel bioactive compounds [17.21]. However, to
date multidomain modular nonribosomal peptide synthetases (NRPS), type-I polyketide synthases (PKS-I),
and type-II polyketide synthases (PKS-II) involved in
the biosynthesis of secondary metabolites have been
screened based on polymerase chain reaction (PCR)
in the sponge metagenome for the novel bioactive
compounds.
Marine sponges contain a wide range of microbial communities of significant ecological importance [17.4]. Although the perceptive of sponge microbial diversity is rapidly improving, the role of these microbes are mostly remains unknown [17.4]. Specific microbial mediated processes such as photosynthesis, sulphate reduction, nitrogen fixation, and nitrification have
been quantified and identified by isotope enrichments,
metagenomics and functional gene analyses [17.22].
These studies have extended our knowledge of the microbial symbiont function in sponges, yet they remain
focused on specific processes or particular functional
groups of organisms. Further, community wide assessment of microbial symbionts would be useful to elucidate their ecological role and contribution to the host.
Several methods have been developed and applied
to evaluate sponge microbial symbiosis and diversity.
Early studies in microbial ecology and the biosynthesis
of natural products relied heavily on culturing bacteria on laboratory growth media. Unfortunately, most
symbiotic microbes cannot be cultivated in laboratory
conditions. The presence of abundant unculturable microbes in sponges makes it difficult to understand the
functional traits. Therefore, in the last decades, microbial diversity studies have focused on molecular,
culture-independent techniques based on the 16S rRNA
gene. Cloning and sequencing of 16S rRNA genes are
useful to infer phylogenetic relationships of the bacteria in a specific habitat. Cloning and characterization
Part C | 17.1
Delta, and Gamma Proteobacteria), Spirochaetes, and
Verrucomicrobia. Furthermore, a new phylum, Poribacteria, has also been found in a number of microbially rich sponges. Sequences from the Chlorobi
(green sulfur bacteria) have not been obtained from
sponges, although positive FISH signals were obtained
from Rhopaloeides odorabile. Two archaea have also
been reported from marine sponges, which belong to
the members of the phyla Crenarchaeota and Euryarchaeota [17.4].
Sponges also host eukaryotic microbes such as dinoflagellates and diatoms, with the latter seemingly
most prevalent in polar regions. Zoochlorella, an endosymbiotic microalgae, often reported from freshwater sponges. Two previous reports of cryptomonads
in sponges were made by Wilkinson [17.16]. Marine
sponges’ associated fungi are receiving increasing attention due to their biotechnological potential. Fungal
strains isolated from marine sponges, representing three
phyla of Ascomycota, Zygomycota, and Basidiomycota
fungi. In total 22 orders (Boliniales, Botryosphaeriales,
Capnodiales, Chaetosphaeriales, Claromycetales, Diaporthales, Dothideales, Eurotiales, Helotiales, Hypocreales, Microascales, Mitosporic Agricomycotina,
Moniliales, Mucorales, Onygenales, Phyllachorales,
Pleosporales, Polyporales, Saccharomycetales, Sordariales, Trichosphaeriales, and Xylariales) within Ascomycota, 8 orders (Agaricales, Agaricostilbales, Corticiales, Malasseziales, Polyporales, Sporidiobolales,
Tremellales, and Wallemiales) within Basidiomycota
and 4 orders (Rhizopus, Mucor, Rhizomucor, and Syncephalastrum) within Zygomycota have been recorded
in sponges [17.17]. Compelling evidence for symbiosis of yeast with sponges of the genus Chondrilla was obtained by extensive microscopy studies
of both adult sponge tissue and reproductive structures [17.18]. It thus remains unclear in most cases
whether such fungi are consistently associated with the
source sponge, or even whether they are obligate marine
species.
Viruses and virus-like particles (VLP) are abundant
in coral reef environments and have been found in the
water columns adjacent to sponges in coral reef environments. Virus-like particles have been observed in
cell nuclei in Aplysina (Verongia) cavernicola [17.19].
It was suggested that VLP could be involved in sponge
cell pathology. In another study, infection of an Ircinia
strobilina derived alphaproteobacterium by a seawater bacteriophage was also demonstrated in laboratory conditions [17.20], but infection in nature is not
known.
It has been assumed that the bacteria associated
with the sponge synthesize several bioactive compounds [17.21]. However, cultivation of invertebrates
for these bioactive compounds is too expensive and impossible, and hence cultivation of symbiotic microbes
may provide an inexpensive supply of the natural
compound. Yet, many sponge-associated bacteria have
not been cultivable. Thus, metagenomic approaches
are intended to isolate the bioactive genes responsible
for bioactive compounds and express them in surrogate hosts. Usually, metagenomics begins with the
construction and screening of metagenomic libraries
for the targeted genes. This approach has resulted in
the detection of numerous short biosynthetic pathways
and novel bioactive compounds [17.21]. However, to
date multidomain modular nonribosomal peptide synthetases (NRPS), type-I polyketide synthases (PKS-I),
and type-II polyketide synthases (PKS-II) involved in
the biosynthesis of secondary metabolites have been
screened based on polymerase chain reaction (PCR)
in the sponge metagenome for the novel bioactive
compounds.
Marine sponges contain a wide range of microbial communities of significant ecological importance [17.4]. Although the perceptive of sponge microbial diversity is rapidly improving, the role of these microbes are mostly remains unknown [17.4]. Specific microbial mediated processes such as photosynthesis, sulphate reduction, nitrogen fixation, and nitrification have
been quantified and identified by isotope enrichments,
metagenomics and functional gene analyses [17.22].
These studies have extended our knowledge of the microbial symbiont function in sponges, yet they remain
focused on specific processes or particular functional
groups of organisms. Further, community wide assessment of microbial symbionts would be useful to elucidate their ecological role and contribution to the host.
Several methods have been developed and applied
to evaluate sponge microbial symbiosis and diversity.
Early studies in microbial ecology and the biosynthesis
of natural products relied heavily on culturing bacteria on laboratory growth media. Unfortunately, most
symbiotic microbes cannot be cultivated in laboratory
conditions. The presence of abundant unculturable microbes in sponges makes it difficult to understand the
functional traits. Therefore, in the last decades, microbial diversity studies have focused on molecular,
culture-independent techniques based on the 16S rRNA
gene. Cloning and sequencing of 16S rRNA genes are
useful to infer phylogenetic relationships of the bacteria in a specific habitat. Cloning and characterization