Transcriptional Difference of Deep-Sea Microorganisms under Different Sampling Methods.

Area of Science:

• Marine Microbiology
• Metatranscriptomics
• Deep-Sea Ecology

Background:

• The metabolic activity of deep-sea microbes remains largely uncharacterized due to limitations in sampling techniques.
• Accurate assessment of microbial functions requires robust methods for collecting and preserving samples from extreme environments.

Purpose of the Study:

• To compare the effectiveness of different in situ sampling methods for capturing active deep-sea microbial communities.
• To evaluate the impact of sampling techniques on metatranscriptomic data and the inferred ecological functions of deep-sea microbes.

Main Methods:

• Collected deep-sea microbial samples at 1038 m in the South China Sea using multiple in situ nucleic acid collection (MISNAC), in situ microbial filtration and fixation (ISMIFF), in situ microbial filtration without fixation (ISMIFU), and Niskin bottle methods.
• Analyzed metatranscriptomes to assess microbial biodiversity, dominant taxa, and gene expression profiles.
• Compared transcriptional profiles of conserved genes across different sampling methods.

Main Results:

• MISNAC and ISMIFF methods revealed higher microbial biodiversity and distinct dominant active taxa compared to ISMIFU and Niskin bottle methods.
• Transcriptional profiles of conserved genes showed similarity between MISNAC and ISMIFF, with significant gene expression loss in ISMIFU samples.
• MISNAC and ISMIFF transcriptomes indicated high transcription of CO oxidation and nitrification genes, while Niskin samples showed high transcription of chemotaxis and low-oxygen adaptation genes.

Conclusions:

• In situ sampling and preservation methods, particularly MISNAC and ISMIFF, are crucial for accurate quantification of deep-sea microbial activity and ecological functions.
• Traditional sampling methods like the Niskin bottle may not adequately represent the active microbial community or their metabolic roles in the deep sea.