Coastal lagoons are common marine ecosystems that account for 13% of coastlines worldwide and generally restrict connections to adjacent oceans through sedimentary barriers (Barnes, 1980; Kjerfve, 1994). These ecosystems are known for being the most productive coastal zones and are highly rich in biodiversity; thus, they are very important for providing a variety of ecological services, including the supply of food and habitat for organisms, climate regulation, hydrological balance, and flood protection (Newton et al., 2018 and references therein). In addition, these areas, as transition zones, are characterized by highly dynamic systems with many biogeochemical processes because of the interactive effects of both terrestrial and marine environmental conditions (Pérez-Ruzafa et al., 2011; Chacón Abarca et al., 2021). Such hydrological and biogeochemical dynamics due to the geomorphological features of coastal lagoons may result in a high degree of spatiotemporal variability in the composition and diversity of natural biological communities as well as local environmental parameters (Carvalho et al., 2005; Garrido et al., 2011). Much scientific attention has been paid to understanding ecological processes through the relationships between environmental factors and assemblages of organisms, providing essential insights for developing effective restoration strategies in coastal ecosystems (Bec et al., 2005; Pitacco et al., 2018; Pérez-Ruzafa et al., 2019).

Bacteria are ubiquitous components of marine environments and play important roles in the biogeochemical cycling of elements and in the production and decomposition of organic matter (Azam et al., 1983; Danovaro and Pusceddu, 2007; Kuchi et al., 2021). Bacterial communities are taxonomically diverse, inhabit a variety of marine habitats, and represent the basis for ecosystem functioning (Ghai et al., 2012; Cadena et al., 2019). In particular, bacterioplankton are highly dynamic in response to monsoon-driven short-term temporal changes in environmental conditions, such as temperature, salinity, pH, and nutrient concentration (Lozupone and Knight, 2007; Jasna et al., 2020; Han et al., 2022). In addition, anthropogenic activities such as ballast water discharge, aquaculture, and seaport-related activity significantly influence bacterial communities in a multifactorial manner (Nogales et al., 2011; Kuchi et al., 2021; da Silva et al., 2022). Considering that estuarine and coastal systems are complex transition zones along environmental gradients with various anthropogenic disturbances, it is essential to study the responses of the composition and functionality of bacterioplankton communities to changing environmental conditions when assessing the synergetic effects of natural and anthropogenic factors on pelagic environments.

Several studies have focused on the dynamics of microbial community composition inhabiting transitional mixed ecosystems of freshwater and seawater based on metabarcoding approaches with the development of molecular techniques (Simon et al., 2014; Gutiérrez-Barral et al., 2021; Zhang et al., 2021). These approaches allow us to describe the metagenomic information of microbial components in relation to altered environmental conditions and/or biogeochemical processes in complex coastal ecosystems on which there is relatively scarce metacommunity data. In this context, the microbial community composition in estuarine and coastal lagoon systems has been reported to spatially shift along a salinity gradient, influenced by interactions between freshwater and seawater (Ghai et al., 2012; Cadena et al., 2019; Zhang et al., 2021; Han et al., 2022). Moreover, these techniques have shown that hydrological changes caused by water flow, tidal fluctuations, freshwater discharge, and heavy precipitation may lead to spatial and temporal variations in microbial diversity and composition in coastal systems (Crump et al., 2004; Wang et al., 2020; Zhao et al., 2020). Although the ecological and biogeochemical effects of variability in physical parameters on microbial diversity and composition have been reported on for various coastal systems, the responses of lagoon communities to such changes in heterogeneous environments have not yet been fully elucidated.

Several lagoons are located along the eastern coastline of the Korean Peninsula, and have been reported to exhibit considerable variability in abiotic and biotic factors owing to their different geomorphic features (Park et al., 2020; Lee et al., 2022). The geomorphology of Korean coastal lagoons can influence the hydrological balance between saline and freshwater masses, resulting in spatiotemporal variations in plant and animal communities (Moon and Lee, 2002; Park et al., 2014; Lee et al., 2015).

In the present study, we aimed to assess the monsoon-driven short-term temporal changes in microbial diversity and composition in coastal lagoons related to the variability in environmental factors by hydrological dynamics between the pre- and post-monsoon seasons. The microbial communities of the water columns of two contrasting lagoons with permanent and intermittent open systems were surveyed using metabarcoding of the 16S rRNA gene. We hypothesize that short-term temporal changes in environmental conditions due to hydrological changes caused by geomorphic characteristics in the lagoons may significantly affect bacterioplankton communities in these lagoons. In the Korean Peninsula, summer monsoon rainfall represents a major hydrological disturbance that alters lagoon connectivity, freshwater inflow, and residence time. The selection of pre- and post-monsoon periods in this study was intended to isolate pulse-driven hydrological effects, including osmotic ecological filtering, nutrient stoichiometry shifts, and terrestrial microbial seeding, which operate on shorter timescales than full seasonal succession. To the best of our knowledge, this is the first study to use the metabarcoding method coupled with next-generation sequencing (NGS) to compare bacterioplankton community compositions and environmental factors at the spatiotemporal scale in Korean coastal lagoons.

This study assessed monsoon-driven short-term temporal changes in the characteristics of environmental conditions and bacterial communities in two contrasting coastal lagoons (permanently and intermittently open) in Korea. The major finding was the identification of differences in the seasonal variations in bacterial communities in relation to environmental changes observed in the two types of lagoons. These results highlight the ecological importance of different bacterial communities in response to hydrological changes related to freshwater input between the two systems after a monsoonal event. Several studies have reported that salinity change due to freshwater intrusion is one of the most important factors controlling spatiotemporal variations in bacterial communities in estuarine and coastal systems (Ghai et al., 2012; Li et al., 2017; Ozbayram et al., 2024). Overall, the seasonal hydrological differences caused by the geomorphological characteristics of the two lagoons may lead to considerable spatiotemporal variations in the bacterial communities, which are expected to contribute to the dynamics of the biogeochemical cycles of the lagoons.

The present study found spatiotemporal variations in the bacterial communities of coastal lagoon systems despite similar seasonal tendencies at the Gyeongpoho and Hyangho sites. In general, bacterial communities in aquatic ecosystems, including lagoons, are characterized by spatial and temporal dynamics due to the high variability in environmental factors (Jasna et al., 2020; Han et al., 2022). In particular, differences in environmental conditions caused by the different hydrodynamic regimes of Gyeongpoho and Hyangho lagoons may lead to differences in the biogeochemical processes of suspended particulate organic matter (Lee et al., 2022). Such spatiotemporal variability is influenced by the geomorphological characteristics of the two systems, which can bring about changes in the hydrological conditions through the input of freshwater and seawater to the lagoons (Kjerfve, 1994). The mixture of organic matter present in coastal lagoons is highly heterogeneous and is composed of living micro/macroalgae and detritus from terrestrial and marsh materials (García-Ayllón, 2017). These differences in organic matter between Gyeongpoho and Hyangho may reflect monsoon-driven short-term temporal changes in dominant heterotrophic bacteria. Thus, such a difference in bacterial community composition between the lagoons suggests a relationship between the difference in freshwater- and seawater-dominated waters by geomorphological connectivity with the adjacent coast between the permanently and intermittently open lagoons. Several studies have reported that the degree of connection of the lagoon to the ocean by geomorphological features can lead to significant changes in microbial composition and diversity owing to seasonal and spatial variations in the origin of organic or inorganic matter (Laque et al., 2010; Boadella et al., 2021; Trombetta et al., 2022).

The dominance of heterotrophic bacteria in Gyeongpoho and Hyangho highlights their crucial roles in nutrient cycling, particularly in the degradation of organic matter (Nagata, 2008). In contrast to the consistent dominance of heterotrophic bacteria, photosynthetic cyanobacteria displayed seasonal variation, with a predominance in summer compared with fall in both Gyeongpoho and Hyangho. This seasonal increase is likely driven by greater sunlight availability and elevated nutrient concentrations during summer, which create favorable conditions for cyanobacterial growth (Pruvost et al., 2015). In this study, Proteobacteria exhibited a relatively stable distribution across all samples, whereas Bacteroidetes showed greater variability. The stability of Proteobacteria can be attributed to their adaptability to a wide range of environmental conditions and ability to utilize diverse organic substrates (Nagata, 2008). This resilience ensures their consistent presence, regardless of seasonal or spatial changes. However, the variability in the distribution of Bacteroidetes may reflect their reliance on specific organic substrates or environmental conditions that fluctuate over time and space. This suggests that Bacteroidetes populations are more responsive to changes in organic matter availability and other dynamic environmental factors, potentially influencing their roles in carbon cycling and organic matter degradation in coastal lagoon ecosystems. Although direct measurements of DOC, POC, and C:N ratios were not available, the dominance of heterotrophic taxa likely reflects potential metabolic capacity rather than quantified organic matter degradation rates. A comparison of the microbial communities in Gyeongpoho and Hyangho revealed distinct spatial patterns in bacterial composition. The unique enrichment of Bdellovibrionota in Gyeongpoho and Acidobacteriota and Chloroflexi in Hyangho suggests that local environmental conditions play a significant role in shaping microbial community structures. Bdellovibrionota are well known as obligate predators of Gram-negative bacteria, and their increased relative abundance in Gyeongpoho during June likely reflects a high availability of heterotrophic bacterial prey. This pattern suggests an intensified microbial trophic interaction, potentially associated with elevated organic matter and post-bloom conditions during the pre-monsoon period, rather than a simple response to physicochemical environmental factors. Monsoon-driven freshwater inputs can restructure lagoon bacterioplankton through multiple interacting mechanisms, including osmotic stress imposed by salinity depression, altered nutrient stoichiometry, increased availability of terrestrially derived organic substrates, and watershed-associated microbial loading. The enrichment of Acidobacteriota and Chloroflexi in Hyangho during September is therefore interpreted as reflecting soil runoff influence rather than intrinsic lagoon biogeochemical differentiation.

The results of the SOM analysis revealed a distinct clustering pattern of bacterial communities according to both the sampling period (June vs. September) and lagoon type (Gyeongpoho vs. Hyangho). Although SOM were applied to a relatively small dataset (N = 12), the method was used as an exploratory visualization tool to identify non-linear associations between bacterial communities and environmental gradients. SOM topology was heuristically constrained, and resulting clusters were cross-validated against Ward’s hierarchical clustering, indicating that SOM results primarily reflect underlying distance-based structure rather than independent overfitting. This finding highlights the significance of seasonal hydrological changes and geomorphological characteristics in determining the spatiotemporal dynamics of microbial communities in coastal lagoons (Han et al., 2022). Gyeongpoho, with its wider salinity range due to continuous seawater exchange, exhibited greater variability in bacterial community composition across the sites. In contrast, Hyangho, which is predominantly freshwater-dominated, showed less temporal variability but a higher abundance of specific taxa, such as Acidobacteriota and Chloroflexi in September. CCA further elucidated the relationship between environmental parameters and bacterial community structure. In Gyeongpoho, temperature and PO₄ were inversely associated with NH₄, NO₂, NO₃, and SiO₄, indicating distinct environmental conditions during the study period. Salinity and Chl-a were weakly correlated with other environmental variables, suggesting a complex interplay between physical and biological factors, such as water temperature, nutrients, and the euryhaline characteristics of bacterial assemblages, in structuring bacterial assemblages (Ghai et al., 2012). In Hyangho, PO₄, SiO₄, and Chl-a were negatively correlated with salinity, indicating that changes in water quality driven by freshwater dominance rather than seawater intrusion may significantly affect phytoplankton biomass and bacterial community structure (Crump et al., 2004). The observed bacterial community shifts in Hyangho are more plausibly explained by freshwater-driven ecological filtering rather than marine intrusion, as salinity decreased from June to September. The positioning of the bacterial taxa in the CCA biplots demonstrated strong correlations with these environmental variations, supporting the hypothesis that hydrological variability drives microbial community shifts. Together, the SOM and CCA results provide complementary insights into the spatiotemporal structuring of bacterial communities. The clustering patterns and environmental correlations observed in both analyses underscore the importance of lagoon geomorphology and seasonal rainfall in modulating microbial dynamics. The permanently open system (Gyeongpoho) was more influenced by broader environmental gradients induced by marine-freshwater mixing, whereas the intermittently open system (Hyangho) was characterized by more stable freshwater conditions and a greater influence of seawater inflow. These findings suggest that the amount of freshwater and marine water inflow, along with the degree of hydrological connectivity, are crucial factors shaping the bacterial community composition and, consequently, biogeochemical processes in temperate coastal lagoons (Nogales et al., 2011; Zhao et al., 2020). This study represents a snapshot comparison between pre- and post-monsoon conditions and does not capture recovery dynamics, winter microbial regimes, or long-term seasonal succession. In addition, the limited number of sampling stations per lagoon may not fully resolve fine-scale spatial heterogeneity at freshwater–seawater mixing zones.

This study highlights the significant role of seasonal hydrological variations and geomorphological characteristics in shaping bacterial community structures in two contrasting coastal lagoons (the permanently open Gyeongpoho and intermittently open Hyangho open lagoons). The observed monsoon-driven short-term temporal changes in bacterial communities suggest the ecological importance of hydrological connectivity and freshwater-seawater interactions in coastal lagoon ecosystems. These findings demonstrate that salinity fluctuations driven by freshwater inflow after monsoon events are important factors that influence bacterial diversity and composition. More dynamic seawater exchange in Gyeongpoho resulted in a higher degree of bacterial variability, whereas the relatively stable conditions in Hyangho promoted specific microbial assemblages adapted to freshwater dominance. These differences contribute to distinct biogeochemical processes, particularly organic matter degradation and nutrient cycling, emphasizing the role of microbial communities in sustaining lagoon ecosystem functions. The predominance of heterotrophic bacteria in both lagoons highlights their essential roles in organic matter decomposition and carbon cycling, which can influence trophic interactions and water quality. Furthermore, the correlations between environmental parameters and bacterial community structures, as revealed by SOM and CCA, enhance the ecological perspective that microbial assemblages serve as sensitive indicators of environmental changes. Our findings demonstrate that bacterial community structure in coastal lagoons is shaped by the interaction between monsoon-driven short-term freshwater disturbance and geomorphology-dependent spatial species sorting. While this study provides insight into disturbance-driven ecological filtering, higher-frequency temporal sampling will be required to resolve recovery processes and long-term microbial succession.

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