Phytoplankton are the primary producers at the basis of aquatic food webs, and bacteria play an important role in energy flow and biochemical cycling in aquatic ecosystems. In this study, both the bacterial and phytoplankton communities were examined in the oligotrophic Lake Basomtso and the eutrophic Lake South (China). The results of this study showed that the phytoplankton density and diversity in the eutrophic lake were higher than those in the oligotrophic lake. Furthermore, Chlorophyta (68%) and Cryptophyta (24%) were the dominant groups in the eutrophic lake, while Bacillariophyta (95%) dominated in the oligotrophic lake. The bacterial communities in the waters and sediments of the two lakes were mainly composed of Proteobacteria (mean of 32%), Actinobacteria (mean of 25%), Bacteroidetes (mean of 12%), and Chloroflexi (mean of 6%). Comparative analysis showed that the abundance of bacteria in the eutrophic lake was higher than that in the oligotrophic lake (p < 0.05), but the bacterial diversity in the oligotrophic lake was higher than that in the eutrophic lake (p < 0.05). Finally, the bacterial abundance and diversity in the sediments of the two lakes were higher than those in the water samples (p < 0.05), and the Latescibacteria and Nitrospinae groups were identified only in the sediments. These results suggest that both the phytoplankton and bacterial communities differed considerably between the oligotrophic lake and the eutrophic lake.

The microbial food web is an important part in aquatic ecosystem, but studies on the microbial food web in freshwater ecosystem, especially in freshwater eutrophic lakes, still need further investigation. In the present study, using eutrophic Lake Nanhu as model, the community changes of phytoplankton, zooplankton, and bacteria between the bloom and non-bloom period were analyzed, and microzooplankton grazing experiments were also conducted to measure the grazing pressure and selectivity of microzooplankton on phytoplankton community. Phytoplankton community in Lake Nanhu was mainly dominated by Cyanophyta (49.44%), especially Anabaena circinalis and Microcystis flos-aquae, during bloom period. Rotifers were the main components of zooplankton in Lake Nanhu (44.15%), Brachionus calyciflorus and Moina macrocopa were the most dominant zooplankton in the non-bloom and bloom period, respectively. Bacteroidetes showed significantly higher mean proportion in bloom period than that in non-bloom period (p < 0.001). The growth rates of phytoplankton ranged from −1.00 d⁻¹ to 1.29 d⁻¹, while grazing rates of microzooplankton ranged from −1.15 d⁻¹ to 1.05 d⁻¹. Results indicated that microzooplankton could respond quickly to the increase of phytoplankton during bloom period. Meanwhile, microzooplankton showed grazing preference on Cyanophyta and Cryptophyta during bloom period and non-bloom period, respectively. The microzooplankton grazing selectivity during bloom period might depend on phytoplankton community composition.

Mesozooplankton have been known to be important consumers of phytoplankton, and the community plays an important role in removing the primary production in the marine ecosystem. In the present study, mesozooplankton grazing on phytoplankton were studied in situ at two sampling stations (TM4 and TM8) in Tolo Harbour. HPLC analysis showed that diatoms were the dominant phytoplankton in the two stations throughout the year, and contributed on average to over 40% of total phytoplankton biomass. Dinoflagellates were the second most abundant group of phytoplankton in the two monitoring stations, while the contribution of haptophytes, green algae, cyanobacteria, and cryptophytes was negligible. Feeding experiments, combined with HPLC pigment analysis, were conducted to measure mesozooplankton selective feeding on phytoplankton. The results demonstrated that mesozooplankton displayed a clear feeding selectivity for phytoplankton in Tolo Harbour. Firstly, mesozooplankton showed strong preference for the phytoplankton with the size of 20–200 μm, which suggested that the grazing selectivity and grazing rates of mesozooplankton were affected by the size of the food particles. On the other hand, mesozooplankton assemblages in Tolo Harbour displayed significant feeding selectivity for diatoms, dinoflagellates, and cryptophytes over other types of phytoplankton. The three algae groups are all the major phototrophic components in marine planktonic communities, and they often cause red tides in the marine environment. These results, taken together, suggested that mesozooplankton should play an important role in the regulation of red tides.