Coastal lagoons are highly productive ecosystems. However, coastal lagoons are experiencing the effects of human disturbances at an increasing rate. Bacteria are key ecological players within lagoons, yet little is known about the magnitude, patterns, and drivers of diversity in these transitional environments. In this report, a seasonal study in the Fengxian artificial lagoon (China) was conducted, along with the adjacent sea, to simultaneously explore diversity in different domains and their spatio-temporal variability.Bacterioplankton community structures of surface waters from four sites over the course of four seasons were characterized with Illumina platform sequencing technology. The results showed significant differences in bacterioplankton communities between the four sites. In addition, the results indicated a difference between the enclosed lagoon and offshore waters during the same seasons. Seasonality was shown to be more important than spatial variability in shaping assemblages. The community barplot showed that, with the exception of January which had the same dominant genus in both the enclosed lagoon and offshore water, all other seasons had different genus. Likewise, the heatmap showed that the largest dissimilarity of bacterial species diversity occurred in July between the enclosed lagoon and offshore water, while the highest similarity was in January. This result paralleled genetic studies which also showed that gene expression had not only similar seasonal but spatial changes. Canonical correspondence analysis (CCA) analysis of all water samples showed that environmental indicators of dissolved oxygen, temperature, PO 4 , NO 2 , and Chemical Oxygen Demand (COD) contributed to the variation. Bacterial communities in the lagoon are affected by temperature, dissolved oxygen and NO 2 , while the dominant bacterial communities offshore are affected by COD and PO 4 . This study provided evidence for a temporally dynamic structure of bacterial assemblages in lagoons.In this vulnerable ecosystem, there is interplay of seasonally-influenced environmental drivers that works together to shape bacterial assemblages. The goal is to identify beneficial microbial population that improved water quality in an enclosed lagoon in order to provide a new perspective for optimizing the breeding environment.PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.26935v1 | CC BY 4.0 Open Access |

Coastal lagoons are highly productive ecosystems. However, coastal lagoons are experiencing the effects of human disturbances at an increasing rate. Bacteria are key ecological players within lagoons, yet little is known about the magnitude, patterns, and drivers of diversity in these transitional environments. In this report, a seasonal study in the Fengxian artificial lagoon (China) was conducted, along with the adjacent sea, to simultaneously explore diversity in different domains and their spatio-temporal variability. Bacterioplankton community structures of surface waters from four sites over the course of four seasons were characterized with Illumina platform sequencing technology. The results showed significant differences in bacterioplankton communities between the four sites. In addition, the results indicated a difference between the enclosed lagoon and offshore waters during the same seasons. Seasonality was shown to be more important than spatial variability in shaping assemblages. The community barplot showed that, with the exception of January which had the same dominant genus in both the enclosed lagoon and offshore water, all other seasons had different genus. Likewise, the heatmap showed that the largest dissimilarity of bacterial species diversity occurred in July between the enclosed lagoon and offshore water, while the highest similarity was in January. This result paralleled genetic studies which also showed that gene expression had not only similar seasonal but spatial changes. Canonical correspondence analysis (CCA) analysis of all water samples showed that environmental indicators of dissolved oxygen, temperature, PO4, NO2, and Chemical Oxygen Demand (COD) contributed to the variation. Bacterial communities in the lagoon are affected by temperature, dissolved oxygen and NO2, while the dominant bacterial communities offshore are affected by COD and PO4. This study provided evidence for a temporally dynamic structure of bacterial assemblages in lagoons. In this vulnerable ecosystem, there is interplay of seasonally-influenced environmental drivers that works together to shape bacterial assemblages. The goal is to identify beneficial microbial population that improved water quality in an enclosed lagoon in order to provide a new perspective for optimizing the breeding environment.