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Characterization of Microbial Population Shifts during Sample Storage.
Heath J Mills1, Brandi Kiel Reese, Cruz St Peter
1Department of Oceanography, Texas A&M University College Station, TX, USA.
Frontiers in Microbiology
|February 25, 2012
Summary
Standard sediment core storage at 4°C alters microbial communities, impacting geochemical studies. This research reveals significant shifts in microbial lineages, potentially affecting scientific conclusions about subsurface environments.
Area of Science:
- Marine microbiology
- Geochemistry
- Sedimentology
Background:
- Standard Integrated Ocean Drilling Program (IODP) protocols store sediment cores at 4°C for geochemical analysis, potentially allowing microbial activity.
- Microbial communities in subsurface sediments may remain active over geological timescales under storage conditions.
- Investigating microbial shifts during storage is crucial for accurate interpretation of geochemical and geophysical data.
Purpose of the Study:
- To determine shifts in microbial community structure and function due to standard IODP sediment core storage procedures.
- To assess the impact of 4°C storage on metabolically active microbial populations in Great Barrier Reef sediment cores.
- To evaluate potential alterations in biogeochemical cycling inferred from stored sediment samples.
Main Methods:
- Characterization of the metabolically active microbial fraction from IODP Expedition 325 sediment cores.
- Extraction of total RNA from sediment samples at varying depths (2, 20, 40 m below sea floor).
- Reverse transcription to complementary DNA (cDNA) followed by 454 FLX sequencing to analyze microbial lineages.
Main Results:
- Over 14,800 sequences were generated from six sediment samples.
- A significant majority (97.3%) of detected microbial lineages showed altered detection frequencies after 3-month storage.
- Changes were observed in key biogeochemically relevant lineages involved in nitrogen, iron, and sulfur cycling.
Conclusions:
- Standard 4°C sediment core storage can significantly alter microbial community structure and inferred function.
- These microbial shifts have the potential to change sediment characteristics, leading to misleading conclusions about in situ biogeochemical environments.
- New lineages detected after storage suggest a broader viable subsurface microbial community than typically characterized, necessitating revised storage and analysis protocols.
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