Transcriptional difference of deep-sea microorganisms under different sampling methods

The metabolic potential and activity of deep-sea microbes have not been fully explored by metatranscriptomics using the samples obtained by different sampling methods. Here, we report active deep-sea microbes obtained by the methods of Multiple in situ Nucleic Acid Collection (MISNAC), in situ microbial filtration and fixation (ISMIFF), in situ microbial filtration without fixation (ISMIFU) and the Niskin bottle at 1,038-m depth in the South China Sea. Higher biodiversity and different dominant active microbial taxa in the metatranscriptomes were detected in the MISNAC and ISMIFF samples, compared with the other two approaches. The transcriptional profiles of 40 conserved genes were similar between the MISNAC and ISMIFF samples, while expression of a quarter of these genes was not detected in the ISMIFU sample. Genes related to the CO oxidation and nitrification processes were highly transcribed in the MISNAC and ISMIFF transcriptomes, whereas genes for chemotaxis and low-oxygen adaptation were highly transcribed in the Niskin samples. Overall, our result highlights the importance of in situ sampling and preservation for more precise quantification of the ecological function of active deep-sea microbiomes.