In situ sampling uncovers seasonal variability in community structure and metabolism of active deep-sea microbes

Learning about the metabolic activities and adaptations of deep-sea microbes is a challenging task, because the collection and retrieval of samples from the deep ocean induce RNA degradation and alteration of microbial communities. Here, we employed a in situ DNA/RNA co-extraction device to collect 18 time-course nucleotide acid samples for winter and summer seasons in the South China Sea to generate metatranscriptomes and metagenomes with the minimal possible sampling perturbation. Between the two seasons, the most active eukaryotic microbes were Ciliophora, whereas the most abundant but inactive eukaryotic microbes were Retaria. In the winter, autotrophic microorganisms contributed to organic matter production by CO₂ fixation associated with nitrification. In the summer, the primary source of energy originated from heterotrophic microorganisms that can utilize alkanes, aromatic compounds and carbohydrates, partially relying on anaerobic respiration in the particles. This may relate with nutrient source variations as reflected by the different levels of microbial network complexity between two seasons. Altogether, we uncovered the metabolic activities and adaptations of active microbial groups in two seasons with in situ metatranscriptomes, paving the way to identification of the real microbial contributors to element cycles in the deep ocean.