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Marine Metagenome and Supporting Technology

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Springer Handbook of Marine Biotechnology

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Abstract

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 silico 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.

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Abbreviations

BAC:

bacterial artificial chromosome

Cd:

cadmium

CoA:

coenzyme A

Cr:

chromium

DNA:

deoxyribonucleic acid

GDSLS:

amino acid residues considered as an important motif in the EstHE1 esterase

GDSL:

amino acid motif specific to the esterases

GEBA:

Genomic Encyclopedia of Bacteria and Archaea

GOLD:

Genomes OnLine Database

GOS:

Global Ocean Sampling

Gd:

gadolinium

MDA:

multiple displacement amplification

MEGAN:

meta genome analyzer

MG-RAST:

meta genomics rapid annotation using subsystem technology

Mon:

manganese

Ni-NTA:

nickel nitrilotriacetic acid

Ni:

nickel

ORF:

open reading frame

PCR:

polymerase chain reaction

PON1:

paraoxonase

RAST:

rapid annotation using subsystem technology

SGNH:

a motif representing amino acid residues

SMTH:

serine hydroxymethyltransferase

Se:

selenium

Sir:

strontium

WGA:

whole genome amplification

ppm:

parts per million

rDNA:

ribosomal DNA

rRNA:

ribosomal RNA

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Authors and Affiliations

  1. Department of Life Science and Medical Bio-Science, Waseda University, 2-2, Wakamatsu-cho, Shinjuku-ku, 162-8480, Tokyo, Japan

    Haruko Takeyama Prof.

  2. International Center for Science and Engineering Programs (ICSEP) , Faculty of Science and Engineering, Waseda University, Center for Advanced Biomedical Sciences (TWIns), 2-2, Wakamatsu-cho, Shinjuku-ku, 162-8480, Tokyo, Japan

    Tetsushi Mori

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Correspondence to Tetsushi Mori .

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  1. Department of Marine-Bio. Convergence Science Specialized Graduate School Science & Technology Convergence Marine Bioprocess Research Center, Pukyong National University, Yongdang Campus, 365, Sinseon-ro, Nam-gu, 608-739, Busan, Korea

    Se-Kwon Kim Prof.

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Mori, T., Takeyama, H. (2015). Marine Metagenome and Supporting Technology. In: Kim, SK. (eds) Springer Handbook of Marine Biotechnology. Springer Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-53971-8_19

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