Terrestrial dissolved organic carbon outweighs warming in shaping bacteria and ciliates in freshwater mesocosms

Abstract Climate warming and rising terrestrial dissolved organic carbon (tDOC) inputs are major stressors altering lake ecosystems. While their individual impacts on planktonic communities are well studied, their combined effects on heterotrophic microbes, key mediators of tDOC transfer to higher trophic levels, remain less understood. We conducted an in situ mesocosm experiment (METU Mesocosm System I, Türkiye) to assess the independent and combined effects of warming (+ 4 °C) and tDOC on bacterial and ciliate biomass and on ciliate community structure (taxonomic, functional, and size composition). Bacteria were enumerated using DAPI-stained epifluorescence microscopy, and ciliates analyzed with FlowCam imaging supported by Utermöhl microscopy for identification and counting. Synergistic effects were weak, with tDOC emerging as the dominant driver of nonlinear, temporally dynamic microbial responses. Bacterial biomass increased transiently under tDOC and combined treatments, whereas ciliate biomass rose only under tDOC. tDOC shifted ciliate feeding groups toward bacterivores, indicating bottom-up control, and functional size groups toward larger species, suggesting weakened top-down regulation. Overall, functional analyses revealed that brownification reshapes microbial food webs more strongly than moderate warming. Stronger warming or longer exposure may amplify temperature effects, while including nanoflagellates and grazing assays could further clarify microbial trophic dynamics under climate change.