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Updated: Oct 12, 2025
10:30
Soil Lysimeter Excavation for Coupled Hydrological, Geochemical, and Microbiological Investigations
Published on: September 11, 2016
10.9K
Biologically-oriented mud volcano database: muddy_db.
Alexei Remizovschi1, Rahela Carpa1
1Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babes-Bolyai University, Cluj-Napoca, Cluj, Romania.
Peerj
|November 25, 2021
Summary
Mud volcanoes (MVs) are unique ecosystems. We developed muddy_mine and muddy_db to centralize data on microbial communities and hydrocarbon geology in MVs.
Area of Science:
- Geology
- Microbiology
- Environmental Science
Background:
- Mud volcanoes (MVs) are natural hydrocarbon seeps, crucial for methane release and global warming.
- They harbor specialized microbial communities capable of hydrocarbon oxidation.
- Existing MV data is fragmented, hindering comprehensive research in microbiology and hydrocarbon studies.
Purpose of the Study:
- To consolidate scattered data on mud volcanoes.
- To create a centralized, biologically focused database for mud volcano research.
- To provide accessible tools for data mining and exploration.
Main Methods:
- Developed a Natural Language Processing pipeline (muddy_mine) to extract data from open-access articles.
- Compiled extracted data into a comprehensive database (muddy_db).
- Created a user-friendly web application and R package for muddy_db.
Main Results:
- Successfully collected and integrated diverse MV data, including microbial taxonomy, hydrocarbon presence, and geological information.
- Launched the muddy_db web app and R package, offering a centralized resource.
- The muddy_mine and muddy_db tools are open-source (GPLv3).
Conclusions:
- muddy_db is the first biologically oriented database for mud volcanoes.
- The developed tools facilitate research on microbial ecosystems and hydrocarbon dynamics in MVs.
- Centralized data and user-friendly tools will advance the study of these unique geological features.
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