Marine Metag
497
Part C | 19.1
19. Marine Metagenome and Supporting Technology
Tetsushi Mori, Haruko Takeyama
Bacteria are known to be highly diverse and unique
to the various environments they reside in. Covering more than 70% of the earth’s surface, marine
bacterial ecosystems in particular have long been
regarded as reservoirs for novel and unique genes
important to industry and pharmaceutics. In the
first part of the chapter, we reviewed the importance and potential of bacteria from marine
environments as an important genetic resource
and some of the recent efforts in the implementation of marine metagenomic research to screen for
genes applicable in bioprocesses, bioremediation
and bioethanol production. Nevertheless, metagenomic research has also provided new challenges
that will need to be addressed in order to use
these resources efficiently. Here, in the second
part of the chapter, we introduced several supporting technologies that show great potential in
assisting metagenomic research to overcome such
challenges including high-throughput screening
using microfluidics, single-cell analysis and in sil19.1 Bacteria and Marine Ecosystems ........... 497
19.1.1 Marine Metagenomic Research ... 498
19.2 Technologies Supporting Metagenomic
Research ............................................. 502
19.2.1 High-Throughput
Analysis/Screening
of Metagenome Samples ............ 502
19.2.2 Increasing Throughput
Using Microfluidics .................... 502
19.2.3 Single-Cell Analysis ................... 503
19.2.4 In silico Analysis of Metadata
from Metagenome Samples ........ 504
19.3 Summary ............................................ 505
References................................................... 505
ico data mining of metagenomic data. The introduction of such technologies, with metagenomic
research, does not only allowed us to exploit these
genetic resources to the fullest but may also provide new perspectives and insights towards living
organisms and natural ecosystems.
19.1 Bacteria and Marine Ecosystems
Nature, as we know it, comprises various unique environments that have provided shelter and homes to
diverse organisms. These unique environments have
long been regarded as treasure boxes that have yet
to be revealed and explored. It not only provides a
unique environment to large vertebrates, invertebrates,
plants, etc., but to microorganisms, including bacteria. Based on recent studies, it seems prominent that
the bacteria present in each environment is highly diverse and their existence is not coincidental but instead
they are comprised of microecosystems that are highly
specific to the environment [19.1, 2]. It is, therefore,
considered that bacteria living within these microecosystems harbor unique and novel characteristics that
allow them to thrive and survive in their natural environment. The presence of these specific bacterial
populations clearly indicates that they play a direct
and crucial role either for the benefit of the bacteria themselves or for the environment they reside
in [19.3]. In the exploration of the terrestrial environment, for example, mainly soil has led to the identification of numerous bacterial ecosystems comprised
of diverse bacterial species [19.4–6]. The marine environment on the other hand, which covers more that
70% of the earth’s surface, provides both mild and
extreme conditions that allow the presence of bacterial species that harbor unique characteristics, which
have evolved to thrive in such conditions. Although
large collections of bacterial species are constantly being studied and identified, we are merely at the tip of
497
Part C | 19.1
19. Marine Metagenome and Supporting Technology
Tetsushi Mori, Haruko Takeyama
Bacteria are known to be highly diverse and unique
to the various environments they reside in. Covering more than 70% of the earth’s surface, marine
bacterial ecosystems in particular have long been
regarded as reservoirs for novel and unique genes
important to industry and pharmaceutics. In the
first part of the chapter, we reviewed the importance and potential of bacteria from marine
environments as an important genetic resource
and some of the recent efforts in the implementation of marine metagenomic research to screen for
genes applicable in bioprocesses, bioremediation
and bioethanol production. Nevertheless, metagenomic research has also provided new challenges
that will need to be addressed in order to use
these resources efficiently. Here, in the second
part of the chapter, we introduced several supporting technologies that show great potential in
assisting metagenomic research to overcome such
challenges including high-throughput screening
using microfluidics, single-cell analysis and in sil19.1 Bacteria and Marine Ecosystems ........... 497
19.1.1 Marine Metagenomic Research ... 498
19.2 Technologies Supporting Metagenomic
Research ............................................. 502
19.2.1 High-Throughput
Analysis/Screening
of Metagenome Samples ............ 502
19.2.2 Increasing Throughput
Using Microfluidics .................... 502
19.2.3 Single-Cell Analysis ................... 503
19.2.4 In silico Analysis of Metadata
from Metagenome Samples ........ 504
19.3 Summary ............................................ 505
References................................................... 505
ico data mining of metagenomic data. The introduction of such technologies, with metagenomic
research, does not only allowed us to exploit these
genetic resources to the fullest but may also provide new perspectives and insights towards living
organisms and natural ecosystems.
19.1 Bacteria and Marine Ecosystems
Nature, as we know it, comprises various unique environments that have provided shelter and homes to
diverse organisms. These unique environments have
long been regarded as treasure boxes that have yet
to be revealed and explored. It not only provides a
unique environment to large vertebrates, invertebrates,
plants, etc., but to microorganisms, including bacteria. Based on recent studies, it seems prominent that
the bacteria present in each environment is highly diverse and their existence is not coincidental but instead
they are comprised of microecosystems that are highly
specific to the environment [19.1, 2]. It is, therefore,
considered that bacteria living within these microecosystems harbor unique and novel characteristics that
allow them to thrive and survive in their natural environment. The presence of these specific bacterial
populations clearly indicates that they play a direct
and crucial role either for the benefit of the bacteria themselves or for the environment they reside
in [19.3]. In the exploration of the terrestrial environment, for example, mainly soil has led to the identification of numerous bacterial ecosystems comprised
of diverse bacterial species [19.4–6]. The marine environment on the other hand, which covers more that
70% of the earth’s surface, provides both mild and
extreme conditions that allow the presence of bacterial species that harbor unique characteristics, which
have evolved to thrive in such conditions. Although
large collections of bacterial species are constantly being studied and identified, we are merely at the tip of