34
A. Meyerdierks and F.O. Glöckner
2.1 Introduction
Microorganisms are the most abundant form of life on Earth, and catalyse key
processes such as nitrogen fixation and the mineralization of organic matter.
Considering that about 70% of our Earth’s surface is covered by the oceans, a comprehensive understanding of microbial element cycling in marine environments is
crucial if we are to understand these processes on a global scale. In the light of
the current discussions about global warming, the formation, storage, emission, as
well as degradation of greenhouse gases in marine environments is receiving a lot
of attention. Although the importance of an investigation of biogeochemical cycles
in the ocean has generally been acknowledged, the study of microbial populations
in marine environments, their contribution to biogeochemical cycles, and the ecophysiology of individual species is still in its infancy. Metagenomics, defined as the
cultivation independent approach to assess the genetic potential of organisms, has
opened a new dimension in environmental research. This chapter is intended to provide an overview of the recent developments in metagenomics, ranging from lab
technology to bioinformatics.
Antoni van Leeuwenhoek provided the first microscopic evidence for the existence of microorganisms in the late seventeenth century (for review: Hall 1989). It
then took almost two centuries before microbiologists such as Louis Pasteur (for
review: Schwartz 2001), Robert Koch (for review: Kaufmann and Schaible 2005),
and Martinus Beijerinck (for review: Chung and Ferris 1996) started to describe
microorganisms based on culturing and enrichment techniques. Many of these early
studies in the nineteenth and early twentieth century targeted microorganisms of
medical relevance, but pioneers such as Ferdinand Cohn already studied algae
and photosynthetic bacteria. Cohn also described genera such as the large sulfur
bacterium Beggiatoa (for review: Drews 2000). It was Sergei Winogradsky, who
developed the concept of chemolithotrophy, revealing the essential role of microorganisms in biogeochemical processes. Moreover, he first isolated and described
nitrogen-fixing as well as nitrifying bacteria (for review: Schlegel 1996). These first
microbiological studies were all restricted to the isolation of microorganisms and
their characterization in the laboratory. This changed when molecular techniques
were introduced in the field of microbiology, and the 16S rRNA gene was discovered to be a phylogenetic marker that could be used to describe the diversity of
uncultured microorganisms (Olsen et al. 1994). Early cultivation-independent investigations reported an immense array of completely unexpected microbial diversity
in the environment (Torsvik et al. 1990). Moreover, the design and application of
specific rRNA-targeted oligonucleotide probes allowed insights into the composition of microbial communities in situ (Stahl and Amann 1991, Amann and Fuchs
2008).
It is estimated that only about 1% of the microbial diversity in the biosphere has
been revealed so far by means of standard cultivation techniques (Amann et al. 1995,
Curtis et al. 2002). New cultivation strategies have already been introduced to gain
access to this yet uncultured majority of microorganisms (Connon and Giovannoni
2002, Rappe et al. 2002, Zengler et al. 2002). However, currently cultivation is not
A. Meyerdierks and F.O. Glöckner
2.1 Introduction
Microorganisms are the most abundant form of life on Earth, and catalyse key
processes such as nitrogen fixation and the mineralization of organic matter.
Considering that about 70% of our Earth’s surface is covered by the oceans, a comprehensive understanding of microbial element cycling in marine environments is
crucial if we are to understand these processes on a global scale. In the light of
the current discussions about global warming, the formation, storage, emission, as
well as degradation of greenhouse gases in marine environments is receiving a lot
of attention. Although the importance of an investigation of biogeochemical cycles
in the ocean has generally been acknowledged, the study of microbial populations
in marine environments, their contribution to biogeochemical cycles, and the ecophysiology of individual species is still in its infancy. Metagenomics, defined as the
cultivation independent approach to assess the genetic potential of organisms, has
opened a new dimension in environmental research. This chapter is intended to provide an overview of the recent developments in metagenomics, ranging from lab
technology to bioinformatics.
Antoni van Leeuwenhoek provided the first microscopic evidence for the existence of microorganisms in the late seventeenth century (for review: Hall 1989). It
then took almost two centuries before microbiologists such as Louis Pasteur (for
review: Schwartz 2001), Robert Koch (for review: Kaufmann and Schaible 2005),
and Martinus Beijerinck (for review: Chung and Ferris 1996) started to describe
microorganisms based on culturing and enrichment techniques. Many of these early
studies in the nineteenth and early twentieth century targeted microorganisms of
medical relevance, but pioneers such as Ferdinand Cohn already studied algae
and photosynthetic bacteria. Cohn also described genera such as the large sulfur
bacterium Beggiatoa (for review: Drews 2000). It was Sergei Winogradsky, who
developed the concept of chemolithotrophy, revealing the essential role of microorganisms in biogeochemical processes. Moreover, he first isolated and described
nitrogen-fixing as well as nitrifying bacteria (for review: Schlegel 1996). These first
microbiological studies were all restricted to the isolation of microorganisms and
their characterization in the laboratory. This changed when molecular techniques
were introduced in the field of microbiology, and the 16S rRNA gene was discovered to be a phylogenetic marker that could be used to describe the diversity of
uncultured microorganisms (Olsen et al. 1994). Early cultivation-independent investigations reported an immense array of completely unexpected microbial diversity
in the environment (Torsvik et al. 1990). Moreover, the design and application of
specific rRNA-targeted oligonucleotide probes allowed insights into the composition of microbial communities in situ (Stahl and Amann 1991, Amann and Fuchs
2008).
It is estimated that only about 1% of the microbial diversity in the biosphere has
been revealed so far by means of standard cultivation techniques (Amann et al. 1995,
Curtis et al. 2002). New cultivation strategies have already been introduced to gain
access to this yet uncultured majority of microorganisms (Connon and Giovannoni
2002, Rappe et al. 2002, Zengler et al. 2002). However, currently cultivation is not