Press Releases

July 2, 2007
The Japan Agency for Marine-Earth Science and Technology

The World's First Complete Genomic Analysis of
Dominant Chemolithoautotrophic Microorganisms
in Dee-sea Vent


Dr. Satoshi Nakagawa of Subground Animalcule Retrieval (SUGAR) program, Extremobiosphere Research Center (XBR: Dr Koki Horikoshi, Director-General), Japan Agency for Marine-Earth Science and Technology (JAMSTEC: Mr. Yasuhiro Kato, President) and his colleagues have analyzed complete genome*2 sequences of 2 chemolithoautotrophic microorganisms*1 strains from an active deep-sea hydrothermal field at north-west sea area of Okinawa's main island.

This research revealed many strategies (multiple systems for respiration, sensing and responding to environment, detoxifying heavy metals, and so on) for the microorganisms to be dominant in deep-sea hydrothermal vent environment on a genetic level for the first time in the world. This is significant achievement on understanding of microbial life that was supported by internal energy of earth. This result will be published online on "Proceedings of the National Academy of Science of the United States of America" week of June 2 issue.


Deep-sea hydrothermal vent environment is an extreme environment of dark and under high-pressure, having hydrothermal vents of more than 300 ℃ and keeps photosynthesis-independent unique ecosystem. Chemolithoautotrophic microorganisms feed high-density life community (Pic.1) typically seen in the environment, by using hydrogen and sulfur-compound oxidation in hydrothermal eruption.

The microorganisms were dominantly found in deep-sea hydrothermal vent environment around the world. They live independently or live symbiotically with inside or outside of cells of invertebrates at the fields. Among those microorganisms, ε(*throughout this article)-Proteobacteria were found with highest dominancy, and many scientists tried to isolate them, but it's so hard to culture in the laboratory that any properties of this group of bacteria have not been clarified yet. We succeeded to separate and culture ε-Proteobacteria live in deep-sea hydrothermal vent environment by reproducing similar environment with their habitats in a test tube. Currently, we possess the world's only exhaustive isolated strains of ε-Proteobacteria. Analysis of complete genomic sequences has been done of 2 strains of this group of bacteria to study their strategies to have dominance in the extreme environment of the deep-sea.

Study Method

The microorganisms analyzed this time are 2 strains of chemolithoautotrophic microorganisms (both are new species: Sulfurovum sp., Nitratiruptor sp.) isolated from a 30m tall sulfide mound (erupting 311℃ hot water) in the Iheya North filed (at a depth of 1,000m, 27N 47.5', 126E 53.8') (Fig.1), 200km north-northwest off of Okinawa's main island. Both strains obtain energy by oxidizing hydrogen and hydrogen sulfide, and use the energy to synthesize all cellular components from carbon dioxide. One of those is the mesophilic microorganism (Pic.2) which grows well around 30℃, the other is the thermophilic microorganism (Pic.3) which grows well around 55℃. After cultivate each strain to a great quantity and extract genomic DNA, genome sequences were completed by using the whole-genome shogun method*3.

Result and discussion

Complete genome sequences (Fig.2) show that they are 2,562,277 base pairs (bp) and 1,877,931 bp. They have relatively small genomes (less than 1/1000 of human's). High density coding sequences (2,466 and 1,857, respectively) were found on each genome. The genome features as follows became clear out of these analyses. (Fig.3)

Have CO2 fixation cycle (Reductive TCA cycle*4) to produce organics out of CO2.
Have multiple respiration systems to synthesize energy materials. Use some enzyme for versatile applications, oxidize sulfur compound and hydrogen by using oxygen and nitrate ion.
Since vent fluids contain heavy metals (such as iron, copper, and manganese) in high levels, they have systems to detoxify them.
Have many gene sets to sense and respond conditions outside cells such as nutrients concentration.

These are the world's first achievements revealing strategies of chemolithoautotrophic microorganisms to adapt to deep-sea hydrothermal vent environment on a gene level

Future prospect

Genomic analysis was performed for the ε-Proteobacteria this time which have ability to live independently from other organisms. But in the deep-sea hydrothermal vent environment, there are the same species which symbioses to inside or outside of cells of larger-size life forms and it is difficult for them to live independently. Now we precede comparative genomic analysis including these strict symbionts. Until now, genomic analysis of various bacterial symbionts had been performed. However, since such species have no close relatives that have free-living life style, it was difficult to study the origin of a symbiotic relationship on a gene level. ε-Proteobacteria is very relevant to study the origin and evolution of symbiotic system between microorganisms and large-sized life forms, for we can conduct comparative study with ε-Proteobacteria since the same species have different symbiotic abilities; one lives in a cell and the other lives outside of a cell of a large-sized life form.


*1 chemolithoautotrophic microorganism
Microorganisms that obtain energy by oxidize reductive inorganic compound such as hydrogen and sulfur-compound, synthesize all of intracellular organisms out of CO2.
*2 genome
All of genes or chromosomes of a life form that contain entire genetic information to determine the life form.
*3 whole-genome shot-gun method
Sequenced many fragments of DNA, combine and edit those sequences on computers, then one series of DNA sequence is completed eventually. Generally, 5 to 10 times as much as general genome size are required to be sequenced. In this study, 8 times as much as presumed genome size were sequenced.
*4 Reductive TCA cycle
It also called Reductive citric acid cycle. Most of life forms including human have TCA cycle (Reaction circuit to obtain energy by decomposing organic compound. Generate CO2). Synthesize organic out of CO2 by reversing the cycle. Energy materials need to be supplied for it.


(For this study)
Dr. Satoshi Nakagawa
Research Scientist, Subground Animalcule Retrieval (SUGAR) program
Extremobiosphere Research Center (XBR)
Mr. Noriyuki Murata, email;
Manager, Research Promotion Office, XBR
(For publication)
Mr. Shinji Oshima, email;
Manager, Planning Department, Press Office