Data integration in microbial genomics ... - Jacobs University

6 1. Introduction
croorganisms thrive in all kinds of habitats. They are found almost
everywhere on Earth: in arctic ice, acid mine drainages, air, soil and
water up to extremely hot hydrothermal vents in the deep sea [Rappé
and Giovannoni, 2003]. Furthermore, microorganisms perform almost
all metabolic processes that are thermodynamically possible [Henry
et al., 2007], many of which are likely to be of interest to industry 6 .
Especially in the oceans that cover two thirds of Earth’s surface [Rahmstorf,
2002], microorganisms are involved in the carbon and nitrogen
cycle 7 that profoundly affect Earth’s climate [Arrigo, 2005, Zehr and
Kudela, 2011]. In times of global climate change, knowledge about the
complex interplay of marine microbes in the biosphere is needed to
understand, predict, and potentially address global changes [Glöckner
and Joint, 2010].
It is therefore interesting to know ”Who is out there?”, ”How many of
which kind?” and ”What are they doing?”. These are the central questions
of marine molecular ecology, which is a subdiscipline in the field
of marine microbiology [Amann, 2000]. Though these three questions
sound trivial, it is hard to answer them. Microorganisms are so small
in size and large in number that it is hard to count and differentiate
them based on optical features. Microorganisms are mostly unicellular.
They replicate by cell division. The smallest nano bacteria are around
0.2 micrometer, the largest bacterium, namely Thiomargerita namibiensis
is 750 micrometer in diameter [Schulz and Jorgensen, 2001]. It
is estimated that one milliliter water contains roughly 5 ∗ 10 5 cells and
a gram of soil contains roughly 2∗10 9 cells [Whitman et al., 1998]. Due
to their small size, microbes are transported and globally dispersed,
when water evaporates to the atmosphere, with water currents in the
ocean and attached to host organisms. This has first been observed
in 1927 and led to the hypothesis that “everything is everywhere, but
the environment selects 8 ” [Meehan and Baas-Becking, 1927]. This hypothesis
is still debated among the life science community.
6 Together with the fact that microbes also have and impact to the health of higher, multicellular,
organisms, this points out their relevance to the medical and biotechnological field.
7 The impact is mainly due to greenhouse gases like carbon dioxide, methane and nitrogen
dioxide.
8 This means that due to their small size microbes are easily dispersed to all kinds of environments.
Then, environmental influences e.g. sun irradiation and temperature decide, if a
microorganism thrives or deteriorates [de Wit and Bouvier, 2006].