The Gobi.ome Project 2018

概要 (English below)

 近年メタゲノム解析の進展により、環境中のDNA情報から微生物やマクロに生物の生態を読み解こうとする環境DNA分析が注目されており、海洋、人間の腸内、土壌など様々な環境の微生物の群集構造への理解が進んでいる。メタゲノム解析とは、環境中のDNAを直接抽出して解析する手法だ。しかし、メタゲノム解析ではDNAのみを対象としているために、死菌の遺伝子や機能していない微生物も含まれた生物種の分布のみの情報しか得ることができない。生物の働きを明らかにするためには、活性する遺伝子情報をもつRNAを対象としたメタトランスクリプトーム解析が必要であるが、RNAはDNAと異なり一時的に発現されることから、サンプル処理が比較的に困難であり、あまり解析されてこなかった。

中でも、土壌微生物は、植物生育の面で農作物の生産に非常に深く関わっており、土壌診断も広く行われていながらも、1グラムあたり数百万種以上の細菌が生息している土壌もある程に微生物の群集構造や機能解析が困難であり、技術の確立が必要とされている。

そこで本研究では、RNAを正確に解析すべく、現地でのRNA精製が必要不可欠だと判断し、現場での土壌RNA精製を可能にするワークフローを確立した。具体的には、電気がないモンゴルのゴビ砂漠でもRNA精製に成功した。また、そのRNA精製法の評価を行うために、山形県鶴岡市のだだちゃ豆農家・庄内砂丘・都市部の土として先端生命科学研究室付近の土壌を用いて異なる土壌での技術比較検討と精製したRNAの品質評価を行っている。

[Twitter @gobiome1]

This year, we decided to go on a big adventure as a group, to assess biodiversity in the Gobi Desert (Mongolia). We brought portable equipment for molecular biology toolkit and extracted RNA from the desert soil using a gasoline-fueled inverter to produce electricity. We also collected microbiome swabs for the MetaSUB international consortium.

Main Themes / Goals

A.Environmental RNA for Biodiversity Assessment [環境RNA技術を用いた生物多様性の調査]
Environmental RNA is useful for a complete assessment of biological ecosystems, gives information about both the species distribution and their roles. However, RNA expression profiles change rapidly and thus RNA needs to be extracted immediately on the site of collection using portable molecular biology equipment. We expect to identify novel extremophile species this cold desert climate known for its high content in heavy metals. The Oyu Tolgoi copper/gold mine, in particular, is expected to contain interesting bacterial and archaeal species. 

B. Microbiomes of Monuments & Public Transportation sites [歴史的記念物と交通機関の微生物]
To analyze the microbiome of historical and cultural monuments (collaboration with MetaSUB)

Timeline

8/10 - 8/31 Preparations in Tsuruoka, Japan
9/01 - 9/12 Fieldwork in Mongolia
9/13 - 9/30 Return to Japan & wrap-up
10/1 - 3/31 Follow-up study for publication (Mariko, Sota)

The Team

Dr. Josephine GALIPON (Keio University, IAB, Japan) Project leader
Focus: Tardigrades, Monument Microbiome
Nationality: France + Canada
After two trips to Mongolia in 2013 and 2017, Josephine decided to apply her molecular biology expertise to fieldwork biology. She supervised the project, including organization, funding, choice of portable equipment, RNA extraction methodology, air/soil sampling methods and general supervision of swabs for the MetaSUB consortium.

Ms. Mariko USUI (Keio University, Japan) 4th-year undergrad
Focus: Health & Environment, Bacteria
Nationality: Japan
Mariko went to school in Singapore as a teenager and is interested in the impact of people’s environment and lifestyle on their health. She was in charge of logistics (ATA Carnet application for exporting/importing professional equipment) and air-soil sampling in the Gobi. She is now wrapping up the on-site soil RNA extraction method for her graduation thesis.

Ms. Marta CANO GUERRERO (University of York, UK) 3rd-year undergrad
Focus: Wildlife Conservation, Bacteria
Nationality: Spain
Marta spent part of her high school years in the USA and joined Josephine’s lab in 2017 as an intern. In the end, she couldn’t go to the Gobi due to urgent surgery on her knee, but she helped us during the summer of 2018 to optimize the soil RNA extraction method.

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Mr. Tomoro WARASHINA (Keio University, Japan) 3rd-year undergrad
Focus: Insects
Nationality: Japanese
Tomoro spent his whole life hunting for butterflies, starting with his father from a young age. He now has accumulated near-encyclopedic knowledge about the insect kingdom. This time, he surveyed insects found at the sampling sites during the project as well as helping out with others’ tasks.

Mr. Sota ITO (Keio University, Japan) 2nd-year undergrad
Focus: Plant Biology
Nationality: Plant Kingdom
Since the age of 9, Sota has been studying a variety of Heloniopsis orientalis (Order: Liliales, Family: Melanthiaceae), an interesting plant on which an “adventitious bud” (basically, a new baby plant) tends to appear at the extremity of leaves after they are cut from the mother plant. During the fieldwork, he surveyed plant species in the Gobi area and is now gathering DNA sequence data for the conserved genomic regions of species for which genetic information is currently unavailable on NCBI.

Mr. Tomoki TAKEDA (Keio University, Japan) 2nd-year undergrad
Focus: Environmental DNA, Microbiome
Nationality: Japanese
Tomoki has had experience with bioinformatics and comparative genomics in his first project as an undergraduate and his involvement in the GoSWAB project to sample the microbiome of cities and homes in Tokyo. During our time in Mongolia, he was in charge of swabbing touristic monuments and public transportation spots such as Ulaanbaatar Railway Station and the Chinggis Khaan International Airport.

Collaborators in Mongolia

  • Dr. Boldgiv BAZARTSEREN, Ph. D. (National University of Mongolia) – [Google Scholar]
     …  …  … 

  • Ms. Anne-Camille SOURIS, M. Sc. (Association GOVIIN KHULAN) – [Website] [LinkedIn] [ResearchGate]
    Focus: Wildlife Conservation, Mongolian khulan/hemione
    She has been studying Mongolian wild Equids for about 10 years, and in 2008, she started a conservation program that aims to enhance protection of the not well known but threatened Mongolian khulan/hemione (or Mongolian wild ass) and its habitat, and in which the local community is directly involved. She will bring to the Gobi Biome project her expertise on the Mongolian khulan and other Gobi wildlife, and on fieldwork in the south Gobi. The Gobi biome project could make a great contribution to Gobi wildlife conservation and could lead to further research and conservation actions in partnership with Anne-Camille’s non-profit conservation organization and local partners.

Itinerary

Ulaanbaatar to Dalangadzad (10-11 hours)

Dalangadzad to Small Gobi A (5-6 hours)

Small Gobi A to Oyu Tolgoi mine (2-3 hours)

Oyu Tolgoi mine to Dalangadzad (5-6 hours)

Dalangadzad to Ulaanbaatar (10-11 hours)

Sampling

  • Monument microbiome of Chingghis Khan statue – Ulaanbaatar
  • Monument microbiome of Warrior statue – Dalangadzad
  • Microbiome (air/soil) at the Oyu Tolgoi mining site
  • Microbiome (air/soil) at several locations inside Small Gobi A
  • Microbiome of Wildlife Intestinal Flora
  • Plants, Insects (according to international regulations)

Photos

View from the top of a mountain in the Gobi Small A Restricted Area

Melting agarose for gel electrophoresis in the steppes near Oyu Tolgoi

Meeting with domestic camels on our way to Oyu Tolgoi