Marine Spong
457
Part C | 17.1
17. Marine Sponge Metagenomics
Valliappan Karuppiah, Zhiyong Li
The sponge is one of the oldest multicellular invertebrates in the world. Because of its special pore
canal structure and characteristics of filter feeding,
a large amount of microorganisms adhere to it. After hundreds of thousands of years’ evolution, they
form a kind of symbiosis relationship. A rather large
amount of research shows the great diversity of microbes related to sponges using 16S rRNA (ribosomal
ribonucleic acid) or 18S rRNA gene-based methods.
Just in recent decades, many bioactive compounds
have been separated from sponges. However, more
and more studies confirm that those bioactive
compounds do not derive from the sponges themselves but rather their symbionts. Considering that
most of the microbes in sponges are unculturable,
the culture-dependent approach is greatly limited.
Using metagenomics, it may be possible to produce
enzymes of special characteristics and secondary
metabolites with biotechnological application
from the sponge derived uncultured microbes.
What is more, metagenomics can also serve as
a way to understand the community structure, as
well as the metabolism and function of a complex microbial community. This chapter focuses
on techniques and advances in marine bacterial
metagenomics, using sponge metagenomics as
an example. Several aspects will be considered:
The background and problems of sponge research
(Sect. 17.1), the principle of metagenomics and related techniques (Sect. 17.2), the application and
17.1 Background and Problems
of Sponge Research.............................. 457
17.2 The Principle of Metagenomics
and Related Techniques ....................... 460
17.2.1 Isolation of Metagenomic DNA .... 460
17.2.2 Library Construction................... 460
17.2.3 Function-Based Screening
of the Metagenomic Library........ 462
17.2.4 Sequence-Based Screening
of the Metagenomic Library........ 462
17.2.5 Next Generation Sequencing
Technologies ............................. 463
17.2.6 Metagenomics and Informatics... 463
17.2.7 Single-Cell Genomics ................. 464
17.3 Application and Latest Progress
in Sponge Metagenomics ..................... 465
17.3.1 Diversity of Bacterial Symbionts
in Sponges................................ 465
17.3.2 Functional Genes Related
to Natural Products
of Bacterial Symbionts
in Sponges................................ 466
17.3.3 Functions
of the Bacterial Community
in Sponges................................ 468
17.4 Future Perspectives.............................. 469
References................................................... 470
latest progress in sponge metagenomics (Sect. 17.3),
and future perspectives (Sect. 17.4).
17.1 Background and Problems of Sponge Research
Sponges are the simplest form of multicellular animals of the phylum Porifera, which literally means
pore-bearing. Their morphology caused ancient scientists like Aristotle and Pliny to consider them as
plants [17.1]. In 1765 John Ellis proved that they are actually animals [17.2]. Marine sponges represent one of
the extant metazoans of 700800 million years. They
are classified into three classes according to skeletal
type, calcareous sponges – Calcarea, demosponges –
Demospongiae, and glass sponges – Hexactinellida. So
457
Part C | 17.1
17. Marine Sponge Metagenomics
Valliappan Karuppiah, Zhiyong Li
The sponge is one of the oldest multicellular invertebrates in the world. Because of its special pore
canal structure and characteristics of filter feeding,
a large amount of microorganisms adhere to it. After hundreds of thousands of years’ evolution, they
form a kind of symbiosis relationship. A rather large
amount of research shows the great diversity of microbes related to sponges using 16S rRNA (ribosomal
ribonucleic acid) or 18S rRNA gene-based methods.
Just in recent decades, many bioactive compounds
have been separated from sponges. However, more
and more studies confirm that those bioactive
compounds do not derive from the sponges themselves but rather their symbionts. Considering that
most of the microbes in sponges are unculturable,
the culture-dependent approach is greatly limited.
Using metagenomics, it may be possible to produce
enzymes of special characteristics and secondary
metabolites with biotechnological application
from the sponge derived uncultured microbes.
What is more, metagenomics can also serve as
a way to understand the community structure, as
well as the metabolism and function of a complex microbial community. This chapter focuses
on techniques and advances in marine bacterial
metagenomics, using sponge metagenomics as
an example. Several aspects will be considered:
The background and problems of sponge research
(Sect. 17.1), the principle of metagenomics and related techniques (Sect. 17.2), the application and
17.1 Background and Problems
of Sponge Research.............................. 457
17.2 The Principle of Metagenomics
and Related Techniques ....................... 460
17.2.1 Isolation of Metagenomic DNA .... 460
17.2.2 Library Construction................... 460
17.2.3 Function-Based Screening
of the Metagenomic Library........ 462
17.2.4 Sequence-Based Screening
of the Metagenomic Library........ 462
17.2.5 Next Generation Sequencing
Technologies ............................. 463
17.2.6 Metagenomics and Informatics... 463
17.2.7 Single-Cell Genomics ................. 464
17.3 Application and Latest Progress
in Sponge Metagenomics ..................... 465
17.3.1 Diversity of Bacterial Symbionts
in Sponges................................ 465
17.3.2 Functional Genes Related
to Natural Products
of Bacterial Symbionts
in Sponges................................ 466
17.3.3 Functions
of the Bacterial Community
in Sponges................................ 468
17.4 Future Perspectives.............................. 469
References................................................... 470
latest progress in sponge metagenomics (Sect. 17.3),
and future perspectives (Sect. 17.4).
17.1 Background and Problems of Sponge Research
Sponges are the simplest form of multicellular animals of the phylum Porifera, which literally means
pore-bearing. Their morphology caused ancient scientists like Aristotle and Pliny to consider them as
plants [17.1]. In 1765 John Ellis proved that they are actually animals [17.2]. Marine sponges represent one of
the extant metazoans of 700800 million years. They
are classified into three classes according to skeletal
type, calcareous sponges – Calcarea, demosponges –
Demospongiae, and glass sponges – Hexactinellida. So