Functional genes and bacterial community assembly dynamics: Key drivers of CO emission in the (sub-)deep reservoir biological carbon pump (BCP).

The biological carbon pump (BCP) plays a crucial role in carbon sequestration and sustaining water ecosystems, yet the functional genes and bacterial community assembly in (sub-)deep reservoirs BCP remain largely unexplored. In this study, carbon isotope composition (δC), High Throughput Quantitative Polymerase Chain Reaction (HT-qPCR), and 16S rRNA gene sequencing were used to explore the relationship between microbial dynamics and CO emissions in (sub-)deep reservoir systems. Despite exhibiting high primary productivity (δCᴅɪᴄ: 3.97 ‰ in lotic vs. -3.29 ‰ in lentic regions), surface waters in the lentic zone showed an average pCO of 879.09 μatm and CO fluxes of 2002.3 mmol m·d, which were significantly higher than those in the lotic zone (pCO: 594.08 μatm; CO fluxes: 456.03 mmol m·d). Lentic regions were notably enriched in key functional genes related to carbon degradation (e.g., acsB, mcrA, mrtA) and carbon fixation (e.g., rbcL). By incorporating analyses of particulate versus suspended states, and distinguishing between active and inactive, as well as abundant and rare taxa, bacterial communities in lentic zones formed highly modular and competitively interconnected co-occurrence networks. These networks enhanced energy and substrate transfer, thereby promoting the conversion of organic carbon into CO. In addition, pH and dissolved oxygen (DO) were key drivers of gene patterns, with the phyla Hydrogenedentes, Dependentiae, and Planctomycetota playing central roles in community assembly.