Planktonic ciliates have been recognized as major consumers of nano-and picoplankton in pelagic ecosystems, playing pivotal roles in the transfer of matter and energy in the microbial loop. However, due to the difficulties in identification, the species composition of ciliate assemblages, especially for the small, fragile, and naked species that usually dominate the ciliate communities in the oceanic waters, remains largely unknown. In the present study, 22 stations along the transect from Shenzhen (China) to Pohnpei (Micronesia) were sampled for the enumeration of picoplankton and nanoflagellates. In addition, pigment analysis of major phytoplankton groups along with the measurements of environmental variables including temperature, salinity, and nutrients were also carried out. Ciliates were identified at species level using quantitative protargol stain to reveal the species composition and their distribution patterns from off-shore to open ocean. Ciliate abundance was positively correlated with phosphate, silicate, and pico-sized pigmented eukaryotes (PPEs), whereas the biomass was closely related with PPEs, heterotrophic nanoflagellates, and chlorophytes. The combination of silicate and pigmented nanoflagellates was identified as the major factor driving the ciliate community composition. The close relationship between silicate and ciliate abundance and community structure needs further validation based on more data collected from oceanic waters. Our study showed the necessity of using techniques that can reveal the community composition at higher taxonomic resolutions in future studies on ciliates.

Impact statement Microorganisms, called anaerobic methane‐oxidizing archaea (ANME), can reduce a large amount of greenhouse gas methane and therefore have the potential to cool the Earth. We collected nearly all ANMEs genomes in public databases and performed a comprehensive comparative genomic analysis and molecular dating. Our results show that ANMEs originated in the late Archaean to early Proterozoic eon. During this period of time, our planet Earth was experiencing the Great Oxygenation Event and Huronian Glaciation, a dramatic drop in the Earth's surface temperature. This suggests that the emergence of ANMEs may contribute to the reduction of methane at that time, which is an unappreciated potential cause that led to the Huronian Glaciation.

Ciliates are pivotal components of the marine microbial food web, exerting profound impacts on oceanic biogeochemical cycling. However, the temporal dynamics of ciliate assemblages on a short time scale in the highly fluctuating estuarine ecosystem remain largely unexplored. We studied changes in the ciliate community during a short time frame in the high salinity waters (>26) of a subtropical estuary. Ciliate abundance, biomass, size and oral diameter structure, and community composition fluctuated considerably and irregularly over a few days or even a few hours. Spearman correlations and the generalized linear model revealed that heterotrophic prokaryotes (HPs) and viral abundances drove the dynamics of ciliate abundance and biomass. The structural equation model further identified a major path from the high-fluorescence content virus (HFV) to HPs and then ciliates. Given the substantial correlation between salinity and HPs/HFV, we proposed that the response of HPs and HFV to salinity drives the dynamics of ciliate biomass. Additionally, the Mantel test showed that phytoplankton pigments such as Lutein and Neoxanthin, phosphate, and pigmented picoeukaryotes were key covariates of the ciliate community composition. This study demonstrated the highly changing patterns of ciliate assemblages and identified potential processes regulating ciliate biomass and community composition on short timescales in a subtropical, hydrographically complex estuary.