Marine Metagenomics

1. Front Matter

   Pages i-ix

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2. Technological Aspects of Marine Metagenomics: Sample Collection and Preparation Methods

   1. Front Matter

      Pages 1-1

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   2. Metagenomic Methods: From Seawater to the Database

      • Md. Shaheed Reza, Atsushi Kobiyama, Jonaira Rashid, Yuichiro Yamada, Yuri Ikeda, Daisuke Ikeda et al.

      Pages 3-16

   3. Collection of Microbial DNA from Marine Sediments

      • Tomoko Sakami

      Pages 17-20

   4. Primer Design, Evaluation of Primer Universality, and Estimation of Identification Power of Amplicon Sequences In Silico

      • Akifumi S. Tanabe, Satoshi Nagai, Yuki Hongo, Motoshige Yasuike, Yoji Nakamura, Atushi Fujiwara et al.

      Pages 21-36

   5. High Coverage Expression Profiling (HiCEP) of Microbial Community Genomes in the Ocean

      • Reiko Fujimura, Harunobu Yunokawa, Koji Hamasaki

      Pages 37-50

3. Technological Aspects of Marine Metagenomics: Metagenome Data Analysis

   1. Front Matter

      Pages 51-51

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   2. The Application of DDCA to Metagenomic Analysis

      • Kazutoshi Yoshitake, Kyohei Matsuno, Atsumi Tsujimoto

      Pages 53-63

   3. Horizontal Gene Transfer in Marine Environment: A Technical Perspective on Metagenomics

      • Yoji Nakamura

      Pages 65-84

   4. MAPLE Enables Functional Assessment of Microbiota in Various Environments

      • Hideto Takami

      Pages 85-119

4. Applications in Ocean and Fisheries Sciences: Diversity and Function of Microbial Community

   1. Front Matter

      Pages 121-121

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   2. Comparison of Microscopic and PCR Amplicon and Shotgun Metagenomic Approaches Applied to Marine Diatom Communities

      • Tsuyoshi Watanabe, Tomoko Sakami

      Pages 123-136

   3. Seasonal Dynamics of Bacterial Community Composition in Coastal Seawater at Sendai Bay, Japan

      • Tomoko Sakami, Tsuyoshi Watanabe, Shigeho Kakehi

      Pages 137-147

   4. Shotgun Metagenome Analyses: Seasonality Monitoring in Sendai Bay and Search for Red Tide Marker Sequences

      • Kaoru Matsumoto, Norikazu Kitamura, Kazuho Ikeo

      Pages 149-159

   5. Distribution and Community Composition of Ammonia-Oxidizing Archaea and Bacteria in Coastal Sediments in Response to Sediment Material Gradients at Sendai Bay, Japan

      • Tomoko Sakami, Shigeho Kakehi

      Pages 161-181

   6. Marine Metagenomic Sequence Counts of Reads Assigned to Taxa Consistently Proportionate to Read Counts Obtained for per g of Seawater Sample

      • Toshiaki Kudo, Md. Shaheed Reza, Atsushi Kobiyama, Jonaira Rashid, Yuichiro Yamada, Yuri Ikeda et al.

      Pages 183-188

   7. New Aquaculture Technology Based on Host-Symbiotic Co-metabolism

      • Miyuki Mekuchi, Taiga Asakura, Jun Kikuchi

      Pages 189-228

5. Applications in Ocean and Fisheries Sciences: Analysis of the Red Tide

   1. Front Matter

      Pages 229-229

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   2. Influences of Diurnal Sampling Bias on Fixed-Point Monitoring of Plankton Biodiversity Determined Using a Massively Parallel Sequencing-Based Technique

      • Satoshi Nagai, Noriko Nishi, Shingo Urushizaki, Goh Onitsuka, Motoshige Yasuike, Yoji Nakamura et al.

      Pages 231-248

   3. Mining of Knowledge Related to Factors Involved in the Aberrant Growth of Plankton

      • Yasuhito Asano, Hiroshi Oikawa, Motoshige Yasuike, Yoji Nakamura, Atushi Fujiwara, Keigo Yamamoto et al.

      Pages 249-271

This book presents the state-of-art marine metagenome research and explains the method of marine metagenomic analysis in an easy-to-understand manner.


Changes in the marine environment due to global warming and pollution have become a major global problem. Maintaining a healthy marine ecosystem requires advanced environmental monitoring and assessment systems. As such, the book presents a novel metagenomic monitoring method, which has been developed for comprehensive analyses of the DNA of microorganisms living in seawater to further our understanding of the dynamics of the marine environment. The book can be used as a primer for new researchers and as a manual on experimental methods.

• Megagenome
• Metagenomic methods
• Microbial diversity
• Phytoplankton diversity
• Hydropraphic events
• rRNA
• shot-gun metagenome data
• Digital DNA chip
• Fisheries
• Red tide
• Microorganisms
• Ocean metagenomics
• marine and freshwater sciences

• Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia

  Takashi Gojobori, Katsuhiko Mineta

• Japan Fisheries Research and Education Agency (Retired), Yokohama, Japan

  Tokio Wada

• Kitasato University School of Marine Biosciences, Sagamihara, Japan

  Takanori Kobayashi

Takashi Gojobori
Ph.D., King Abdullah University of Science and Technology, Computational Bioscience Research Center

Tokio Wada
Ph.D., Japan Fisheries Research and Education Agency
Takanori Kobayashi
Ph.D., Japan Fisheries Research and Education Agency

Katsuhiko Mineta
Ph.D., King Abdullah University of Science and Technology, Computational Bioscience Research Center

Policies and ethics