Impact of Noctiluca scintillans bloom and decay phases on coastal water quality and zooplankton dynamics in Indian coastal waters

Introduction: Understanding of ecosystem changes induced by harmful algal blooms (HABs) and their impacts on coastal water quality, bacteria, and zooplankton communities remains limited. Non-toxic HABs, particularly Noctiluca scintillans, are increasingly reported in Indian coastal waters.

Methods: In the present study, a greenish bloom of N. scintillans was observed along the Gulf of Mannar and the Southeastern Arabian Sea during November 2022, with a consequent bloom crash (evidencing surface foam) observed along the southern Kerala coast. We collected samples from bloom, decay, and non-bloom zones to assess changes in hydrobiological conditions.

Results and discussion: Physicochemical data showed negligible variations in temperature (28.71–29.66 °C) and salinity (34.6–35.06), whereas dissolved oxygen levels varied from 6.06 to 8.47 mg/L. Nutrients exhibited strong fluctuations, particularly with the ammonium concentration (15.80 μmol/L) being higher during the bloom decay phase. Elevated chlorophyll-a and DOC confirmed high biomass and organic release, while bacterial pathogens proliferated under nutrient-rich conditions. Moreover, the concurrent rise in pathogenic bacteria, including Vibrio cholerae, suggests N. scintillans may serve as a potential vector for bacterial proliferation when it forms blooms. Zooplankton assemblages showed distinct responses during the bloom and decay phases of N. scintillans. Micro- and meso-zooplankton densities were elevated during the bloom. In contrast, the mesozooplankton was primarily dominated by calanoid copepods; later, these dominant taxa declined sharply during the decay phase and was substituted by cladocerans, appendicularians, and hydrozoans. These shifts in zooplankton communities reflect changes in hydrographic conditions associated with eutrophication and enhanced bacterial production during bloom collapse.

1 Introduction

Various environmental factors alter the productivity, distribution, and community assembly of marine plankton (Dedo et al., 2024). These factors are influenced by a variety of natural (e.g., upwelling, cyclones, algal blooms) and anthropogenic (e.g., oil spills, sewage discharge, dredging) events, which can trigger the abnormal growth of microorganisms and phytoplankton blooms in various marine environments (e.g., estuarine, coastal, and open ocean). Such anomalies can cause serious problems in water quality, biogeochemical cycling, bacterial communities, and planktonic food web dynamics (Sellner et al., 2003; Glibert et al., 2005; Teeling et al., 2012), ultimately influencing overall ecosystem functioning. These changes can significantly affect the diversity, composition, and functional traits of the marine zooplankton community (Lin et al., 2014). Marine zooplankton are essential indicators in marine environments; they will react instantly to such environmental changes and migrate quickly away from chemical or biological contaminants, including harmful algal blooms (HABs) (Marques et al., 2008). These environmental stresses can disrupt their normal life cycles, resulting in lower survival and feeding rates, limited growth and reproduction, changed behaviour, and abnormalities in larval development (Almeda et al., 2011; Lin et al., 2014; Morgan, 2020).

Globally, the algal blooms are known to be a common phenomenon typically formed by five major microalgal groups involved in biogeochemical cycling, which are capable of forming blooms in aquatic ecosystems, including green algae, diatoms, dinoflagellates, cyanobacteria, and coccolithophores (Carstensen et al., 2015; Sathishkumar et al., 2021). Of these, dinoflagellates are considered a critical taxon due to their harmful effects on both biotic and abiotic components. Some dinoflagellate species (e.g., Alexandrium spp., Noctiluca scintillans) can cause significant harm to marine ecosystems during blooms, which leads to fish kills, human health issues, and other environmental problems (Samson et al., 2008; Anderson et al., 2012; Rameshkumar et al., 2023; Mariasingarayan et al., 2025). In India, both historical and recent reports indicate that bloom-associated fish kills are mainly caused by dinoflagellates, particularly Noctiluca scintillans (Gopakumar et al., 2009; Raj et al., 2020; Rameshkumar et al., 2023; Samanta et al., 2023; Peter et al., 2023; Mariasingarayan et al., 2025).

In the dinoflagellate community, N. scintillans stands out as a unique member due to its large, bubble-like morphology, with an average cell size typically ranging from 200 to 600 µm, and its prevalence is quite common in tropical and subtropical coastal waters worldwide (Roy et al., 2024; Manigandan et al., 2024). N. scintillans is a frequent bloom-forming dinoflagellate that occurs in two distinct forms, i.e., red and green. The red form, which lacks a photosynthetic system, is considered a heterotrophic dinoflagellate (HTD) and is widely distributed across various coastal regions, but its optimal occurrence is in colder (10 °C) to moderately warmer (25 °C) waters (Liu et al., 2025). The green form, which harbours a photosynthetic symbiont called Pedinomonas noctilucae, exhibits a mixotrophic lifestyle and is habitually well-adaptive in tropical coastal waters with temperatures ranging from 25 °C to 30 °C. This form is largely reported from regions across the Indian Ocean and the tropical Pacific (Liu et al., 2025; Manigandan et al., 2024). Although N. scintillans is predominantly known as a heterotrophic dinoflagellate, the present study reports the green form of N. scintillans, which exhibits mixotrophic behaviour due to the presence of endosymbiotic algae within the cytoplasm of the Noctiluca cell, which contains chlorophylls a and b, enabling photosynthetic carbon fixation during daylight. This photosynthetic activity supports the host’s metabolic requirements and allows N. scintillans to persist even in nutrient-depleted or stratified waters where prey availability is limited. In contrast, under dark or nutrient-enriched conditions, N. scintillans shifts to a phagotrophic mode, actively engulfing food particles such as diatoms, dinoflagellates, detrital matter, and bacteria, thus functioning predominantly as a heterotroph. Nowadays, the green variety of N. scintillans is the most common bloom-forming species in Indian coastal waters, including records from both the Arabian Sea and the Bay of Bengal (Baliarsingh et al., 2017; Sarma et al., 2019; Parvathi et al., 2021; Rameshkumar et al., 2023; Bharathi et al., 2023; Samanta et al., 2023; Roy et al., 2024; Manigandan et al., 2024; Natarajan et al., 2025; Zedi et al., 2025). Despite several investigations on the dynamics of N. scintillans blooms in Indian coastal waters, their effects on water quality, bloom-associated bacterial composition, and zooplankton communities are still poorly understood.

The N. scintillans bloom does not produce toxins, but its dense aggregations can create hypoxic conditions and increase the ammonium concentrations in the water column, which can initiate significant mortality in fish and invertebrate communities (Zahir et al., 2023; Nayak et al., 2025). N. scintillans is considered a heterotrophic dinoflagellate that can engulf fish and copepod eggs, as well as other co-occurring phytoplankton, which potentially contributes to ecosystem imbalance (He et al., 2021; Bharathi et al., 2023; Manigandan et al., 2024). Moreover, N. scintillans cells produce substantial amounts of dissolved organic matter (DOM) intensively during their decay phase of the bloom, through secretions and the lysis of aged cells. This process enhances DOM and other organic debris in surface water, which attracts and promotes the growth of opportunistic groups such as bacteria and protozoans (Zhang et al., 2022). Concurrently, bacterial nutrient recycling intensifies on and around the mucoid web and bloom patches of N. scintillans, further supporting recurrent bloom formation (Schaumann et al., 1988). This cyclical process causes deterioration in water quality, allowing a favourable environment for the growth of harmful bacteria (like Vibrio cholerae), and poses significant environmental problems, including threats to marine organisms (Greenfield et al., 2017; Liu et al., 2025). Earlier studies specified that N. scintillans might act as a vector for bacterial pathogens (including V. cholerae) (Seibold et al., 2001; Akselman et al., 2010; Liu et al., 2025). The foregoing factors, such as poor water quality and high bacterial density, could inhibit the growth of lower trophic levels, including zooplankton during bloom decomposition (Lin et al., 2014). Changes in zooplankton community structure can have both direct and indirect impacts on fish production (Lin et al., 2014), ultimately resulting in economic losses for fisheries.

In the recent past, several studies have assessed the impact of N. scintillans blooms across the Indian coastal waters, with results indicating varying effects on water quality, bacterial density, and marine fauna (e.g., Naqvi et al., 1998; Baliarsingh et al., 2016; Sarma et al., 2019; Parvathi et al., 2021; Mishra et al., 2022; Bharathi et al., 2023; Rameshkumar et al., 2023; Roy et al., 2024; Zedi et al., 2025). Yet, no studies have comprehensively investigated the complex interactions between bacterial proliferation and its effects on water quality and zooplankton communities during the bloom and decay phases of N. scintillans. With this view in mind, the present study investigates the impact of N. scintillans blooms on coastal water quality, bacterial densities, and zooplankton community distribution across different areas that correspond to bloom, bloom decay, and non-bloom zones in the Gulf of Mannar (GoM) and southeastern Arabian Sea (SEAS), India. Since the impact of these blooms on the zooplankton community is often case- and species-specific, this study establishes a baseline understanding of such interactions, providing a foundation for further research and informed monitoring of algal blooms.

2 Materials and methods

2.1 Cruise track, bloom observations, and sampling framework

A research expedition was conducted along the Tamil Nadu and Kerala coasts onboard CRV Sagar Anveshika, during the post-southwest monsoon period in November 2022 (Figure 1). During this expedition, a conspicuous bloom of green Noctiluca scintillans was observed along the Gulf of Mannar coast, resulting in several patches of greenish discoloration on the water surface. Further, we observed that these patches were drifting northward into the Arabian Sea, driven by prevailing winds and surface currents (satellite data shown in Figure 1), which aligned along with the cruise track. When the survey progressed towards the southeastern Arabian Sea, signs of bloom decay were recorded, with evidence of several white foam patches seen on the surface off the Kovalam region in the southern Kerala coast (Figure 2). This biological froth, formed from decomposed cells of N. scintillans, extended across ~2 km. The observation indicates that the coastal waters off the Kovalam region in southern Kerala experienced the peak stage of bloom disintegration. According to Natarajan et al. (2025), this N. scintillans bloom initially appeared in the Gulf of Mannar during mid-September 2022 and was subsequently advected toward the Arabian Sea, driven by surface currents. By the time of our sampling, the bloom had persisted for over 45 days since its initial formation. In general, N. scintillans blooms along the Indian coastal waters are short-lived due to the seasonally dynamic and frequently changing oceanographic conditions. Hence, the relatively moderate N. scintillans densities recorded in this study likely correspond to the bloom’s succession phase rather than its peak intensity. Although continuous temporal monitoring was not carried out, our field observations indicated that the bloom in the GoM coastal waters was still active, as evidenced by visible surface discolouration. In contrast, several other bloom patches that had been advected into the SEAS coastal regions were already in an advanced stage of decay, as indicated by severe disintegration and foam formation.

Figure 1

Figure 1. Map of the southwestern coast of India, showing locations in the Arabian Sea and Gulf of Mannar with markers indicating zones: ABZ (green), BDZ (red), and NBZ (yellow). Inset map highlights India's location. Below are four plots from 4/11/2022 to 7/11/2022 showing ocean current speeds around the region, represented by shades from yellow to red, indicating increased speed.

Figure 2

Figure 2. (a, b) Field photographs showing greenish discolouration on the water surface during the bloom at GoM coastal waters. (c) Microscopic view of the blooming dinoflagellate Noctiluca scintillans. (d–g) Thick Sea foam patches on the water surface during the bloom crash in the off-Kovalam region, Kerala.

Based on the observations above, a total of six transects were selected for this study, each consisting of two stations (cumulatively twelve stations), in order to investigate the ecological impacts and zooplankton community response in association with the green Noctiluca bloom. These transects were grouped into three zones according to bloom conditions each zone has two transects or four stations. These zones were categorized as in the following way: (i) Active Bloom Zone (ABZ) – where the regions with high Noctiluca biomass, (ii) Bloom Decay Zone (BDZ) – areas showing signs of decomposition and foam formation, (iii) Non-Bloom Zone (NBZ) – areas unaffected by the bloom or the reference sites. These distinct zones enabled a comparative analysis of ecological changes under fluctuating hydrobiological properties influenced by the Noctiluca bloom dynamics.

The bloom sample was collected by filtering 5 L of surface seawater through a 20 µm plankton net to concentrate the bloom species, and the concentrated sample was then transferred into 500 mL of filtered seawater and preserved with 2% acid Lugol’s iodine. For cell enumeration, 1 mL (with duplicate) of the concentrated sample was placed in a Sedgewick Rafter chamber, and all 1000 grids were examined under 100× magnification using an inverted fluorescence microscope (Leica DMi8, Germany), and the bloom specimen was identified as N. scintillans by following standard taxonomic reference (Tomas, 1996).

2.2 Hydrobiological data collection

In the study area, hydrobiological samples and environmental data were collected using onboard research facilities. In-situ data on surface water temperature and salinity were measured using a portable CTD Profiler SBE 25 plus (Seabird Electronics, USA). Then, 5 L of surface water was collected by using a Niskin water sampler for physicochemical analysis. Following collection, the water samples were immediately sub-sampled for the analysis of dissolved oxygen (DO), pH, nutrients, and chlorophyll-a (Chl-a) with the standard protocols (Grasshoff et al., 1999; Strickland and Parsons, 1972). The DO was estimated using the modified Winkler’s titration (Strickland and Parsons, 1972). The pH samples were measured onboard by the spectrophotometric method, adopting Dickson et al. (2007). Water samples for nutrient analysis were filtered through Millipore membrane filters (0.45 µm pore size) and stored in acid-washed polyethylene bottles under refrigerated conditions until analysis. Nutrient concentrations, like ammonium (NH₄⁺), total nitrogen (TN), and total phosphorus (TP), were quantified by a continuous flow analysis method (Grasshoff et al., 1999) using a Nutrient autoanalyser (AA3, Seal Analytical, Germany).

2.3 Zooplankton sampling

Microzooplankton (MiZP) samples were collected by filtering 5 litres of surface water through a 20 µm mesh. The retained organisms were immediately preserved in 2% Lugol’s iodine solution. Simultaneously, mesozooplankton (MeZP) were collected using a standard plankton net with a 330 µm mesh, equipped with a pre-calibrated flow meter (Hydro-Bios, Germany). Horizontal surface hauls were conducted at each station for 5 minutes at a constant towing speed of 2 knots. The collected specimens were preserved in a 5% formalin solution for subsequent laboratory analysis. In the laboratory, the MeZP biomass was estimated using the volume displacement method, and the unit was expressed in millilitres per cubic meter (mL/m³). Both MiZP and MeZP samples were identified to the lowest possible taxonomic level using a Nikon compound microscope for MiZP and a Leica M205 C stereo microscope (Germany) for MeZP. Taxonomic identification was performed using standard monographs and literature (Kofoid and Campbell, 1939; Kasturirangan, 1963; Krishnamurty et al., 1995; Perumal et al., 1998; Sewell, 1999; Conway et al., 2003), and abundances were expressed in individuals per litre (Ind/L) for MiZP and individuals per cubic meter (ind/m³) for MeZP.

2.4 Culture and enumeration of bacterial pathogens

Surface water samples were collected and immediately processed onboard to assess the presence and abundance of bacterial pathogens. All microbiological procedures were conducted under sterile conditions in the shipboard microbiological facility. Specific bacterial taxa were selectively isolated using the following differential and selective media: thiosulfate-citrate-bile salts-sucrose (TCBS) agar for Vibrio spp., cetrimide agar for Pseudomonas spp., membrane faecal coliform (MFC) agar for Escherichia coli, and xylose lysine deoxycholate (XLD) agar for Salmonella and Shigella spp., respectively. The collected seawater samples were serially diluted using sterile, filtered seawater. From the appropriate dilution (typically 10⁻¹ for open coastal waters), 100 µL aliquots were aseptically spread in triplicate onto the respective selective media. The inoculated plates were then incubated aerobically at 34 °C for 18–24 hours. After incubation, colony-forming units (CFUs) were counted manually, and bacterial concentrations were calculated and expressed as CFU/100 mL for E. coli and CFU/mL for other pathogens of original sample (Wohlsen, 2011; Behera et al., 2023). Negative controls (uninoculated media) and reference strains were used to validate media selectivity and ensure procedural accuracy.

2.5 Data analysis and visualisation

The hydrobiological data collected were subjected to statistical analyses to examine zone-wise differences during the onset and decay phases of the Noctiluca bloom. Surface ocean current data from the GLOBCURRENT product (CMEMS) were used to analyse coastal circulation and drifting object transport. The dataset combines Ekman and geostrophic currents, providing daily averaged vectors and magnitudes (m/s) for 04–07 Nov 2022, visualised with colour gradients (0–1 m/s) and directional arrows. Moreover, Kruskal–Wallis ANOVA, box plots, and Pearson’s correlation coefficient analysis were performed on normalised environmental and biological data and visualised using the ggplot2 package in RStudio version 4.3.0. Additionally, a multivariate Redundancy Analysis (RDA) was conducted using CANOCO version 4.5 to identify the underlying structure and relationships within the dataset.

3 Results

3.1 The outbreak of the Noctiluca scintillans bloom

In this study, bloom conditions were defined based on the abundance of N. scintillans exceeding 500 cells/L, which followed the quantitative criterion used by Kordubel et al. (2024b) from North Sea observations. Although this numerical value is lower than thresholds used for other micro-phytoplankton species, considering the large cell size, buoyant accumulation, and visible surface discolouration caused by N. scintillans, this lower numerical criterion is justified as ecologically relevant to bloom manifestation. The sampling locations were classified based on the bloom conditions, i.e., Active Bloom Zone (ABZ), Bloom Decay Zone (BDZ), and Non-Bloom Zone (NBZ). In the ABZ, N. scintillans abundance was highest, averaging 853 ± 270 cells/L (ranging from 560–1164 cells/L). As the bloom began to decay, most algal cells disintegrated with a strong odour, and surface foam formation (particularly at stations S6 and S7) indicates severe bloom decay (Figure 2), where the N. scintillans cell density was moderately lower (avg. 45 ± 20 cells/L). The remaining stations (e.g., Station S9–S12) were defined as non-bloom zones, which showed no visible signs of bloom and recorded much lower N. scintillans abundance (avg. 28.5 ± 20 cells/L) compared to the other zones.

3.2 Spatial variation in physicochemical variables

Environmental parameters exhibited moderate spatial variation across different phases of the N. scintillans bloom along the study region (Table 1). Salinity remained relatively consistent across all zones (34.61–35.06), with slightly higher values in ABZ (avg. 34.91 ± 0.15), when compared to NBZ (avg. 34.76 ± 0.06) and BDZ (avg. 34.71 ± 0.10). Sea surface temperature showed no significant variation among regions (Supplementary Table S1), though the bloom decay zone had a slightly lower average (29.03 ± 0.38 °C) compared to ABZ (29.06 ± 0.04 °C) and NBZ (29.15 ± 0.18 °C). The pH values showed minor variation (7.96–8.07) across the study region; however, the average pH values remained stable across the zones, respectively, for ABZ (avg. 8.03 ± 0.03), NBZ (avg. 8.02 ± 0.03), and BDZ (avg. 8.04 ± 0.02). As in the same pattern, the dissolved oxygen level also showed a higher value in BDZ (avg. 7.67 ± 0.58 mg/L), when compared to that of ABZ and NBZ regions (avg. 6.85 ± 0.65 and 6.96 ± 0.50 mg/L, respectively). In contrast, SPM and DOC values showed notable spatial variation across the bloom zones, with both parameters recording higher averages in the non-bloom zone (SPM: avg. 16 ± 0.88 mg/L; DOC: avg. 258 ± 33 µmol/L), while the ABZ (SPM: avg. 15 ± 1.52 mg/L; DOC: avg. 219 ± 31 µmol/L) and BDZ (SPM: avg. 12 ± 1.24 mg/L; DOC: avg. 231 ± 30 µmol/L) exhibited slightly lower values compared to NBZ.

Table 1

Table 1. Variations in physicochemical parameters at different stations during various phases of the Noctiluca scintillans bloom along the coastal waters of the GoM and SEAS.

3.3 Concentrations of dissolved nutrients and chlorophyll-a

The nutrient values showed marginal fluctuations between zones (Table 1). Particularly, the ammonium (NH₄⁺) exhibited a marginal variation among zones (p = 0.0586), and the concentration was conspicuously higher in BDZ (avg. 6.81 ± 5.21 µmol/L), registering its peak concentration at S7 (15.80 µmol/L), indicating the area of active decomposition and cell breakdown processes during bloom collapse. Whereas the ABZ and NBZ regions recorded minimal concentrations of ammonium (avg. 0.68 ± 0.26 and 0.95 ± 0.39 µmol/L, respectively), indicating no impact with lower rates of nitrogen regeneration. Likewise, the concentration of TN (avg. 34.54 ± 31.48 µmol/L) and TP (avg. 1.84 ± 0.52 µmol/L) was also higher in BDZ. Subsequently, the concentration of Chl-a was highest in ABZ (avg. 3.71 ± 0.56 µg/L), indicating an active bloom phase with high N. scintillans biomass. In contrast, BDZ had comparatively lower Chl-a (avg. 2.17 ± 1.57 µg/L), indicating the bloom decline phase.

3.4 Pathogenic bacterial assemblages

In this study, the abundance of bacterial pathogens such as Pseudomonas aeruginosa, Vibrio cholerae, Salmonella sp., Shigella sp., and Escherichia coli was assessed in water samples from three zones, as illustrated in Figure 3. A total of 12 samples were analysed, and the results revealed marked spatial variation in bacterial abundance. Among the sampling locations, the BDZ region exhibited the highest bacterial abundance compared to ABZ and NBZ. The bloom decomposition in the BDZ region triggers the proliferation of pathogens, e.g., Salmonella sp. and Shigella sp., together exhibiting clear dominance with an average of 608 ± 214 CFU/mL, followed by E. coli (avg. 340 ± 152 CFU/100 mL), P. aeruginosa (avg. 290 ± 90 CFU/mL), and V. cholerae (avg. 270 ± 330 CFU/mL). On the other hand, ABZ and NBZ displayed relatively lower bacterial abundance within the major groups, except E. coli (Figure 3). Overall, the bacterial composition was knowingly higher in the BDZ region, indicating that this environment is vulnerable and potentially at risk to the health of environmental and aquatic animals. The statistical analysis of bacterial communities revealed dynamic relationships with environmental variables. A strong positive correlation was observed between V. cholerae and TN (r = 0.83), while Salmonella sp. and Shigella sp. showed a strong positive correlation with NH₄⁺ (r = 0.92) and a negative correlation with Chl-a (r = –0.62), see Figure 4.

Figure 3

Figure 3. Abundance of bacterial pathogens under different bloom phases: ABZ (Active Bloom Zone), BDZ (Bloom Decay Zone), and NBZ (Non-Bloom Zone) (EC, Escherichia coli; PA, Pseudomonas aeruginosa; SAL, Salmonella sp.; SHIG, Shigella sp.; VC, Vibrio cholerae).

Figure 4

Figure 4. (a) Pearson Correlation Heatmaps of Environmental and Biological Variables. (b) Significant “p” values of correlation analysis as indicated by an asterisk (* = p < 0.05, ** = p < 0.01, *** = p < 0.001).

3.5 Variations of microzooplankton communities

The total MiZP count in the collected water samples ranged from 1040 to 3168 ind/L. As green N. scintillans exhibits mixotrophic behavior (both photosynthetic and heterotrophic), it was included as part of the microzooplankton community along with the other MiZP groups. There were four major groups were identified among the MiZP community, which include: N. scintillans (considered mixotrophic), ciliates, heterotrophic dinoflagellates, and other microzooplankton. Their abundance distribution showed notable variations across the stations, with values ranging from 22–1164 ind/L, 600–1560 ind/L, 120–840 ind/L, and 40–574 ind/L, respectively (Figure 5). ANOVA results indicated significant (p <0.05) differences between zones for N. scintillans and other microzooplankton, while no significant differences were observed for ciliates and heterotrophic dinoflagellates (Supplementary Table S2). The zone-wise comparison of the relative mean abundance of the MiZP community showed the highest value in the ABZ (45.7%), followed by the BDZ (37.3%) and NBZ (16.9%). Among the MiZP community, ciliates were the dominant contributors (50.8%), followed by heterotrophic dinoflagellates (22.7%), N. scintillans (15.9%), and other microzooplankton (10.6%). The correlation analysis revealed positive correlation with DO (r = 0.54), DOC (r = 0.59), and Ammonium (r = 0.56), while the group of other MiZP showed a strong negative correlation (r = –0.84) with SPM (Figure 4).

Figure 5

Figure 5. Bubble plot showing the abundance of micro- and meso-zooplankton communities across the sampling locations in different zones: ABZ, Active Bloom Zone; BDZ, Bloom Decay Zone; NBZ, Non-Bloom Zone.

3.6 Mesozooplankton community characteristics

Our analysis revealed considerable variation in the overall mesozooplankton (MeZP) abundance across the sampled stations, with abundances ranging from 303 to 7154 ind/m³ (Figure 5). The highest abundance was recorded at ABZ (avg. 2372 ± 2777 ind/m³), while the BDZ had the lowest (avg. 566 ± 177 ind/m³), and the NBZ exhibited an intermediate distribution (avg. 1481 ± 565 ind/m³). Consistently, the mesozooplankton biomass values also showed a similar pattern as compared to that of abundance results (data not shown). The relative contribution of mesozooplankton groups exhibited distinct patterns when compared with different bloom phases (Figure 6). In total, 11 taxa (at the group level) were recorded from the MeZP samples. Among them, Calanoida dominated the community in all zones, contributing 56.5% in ABZ, 38.0% in BDZ, and reaching a peak of 64.6% in NBZ. Cyclopoida displayed a contrasting trend, with higher abundance in BDZ (18.2%) compared to ABZ (11.3%) and NBZ (5.0%). Decapods were also prominent, contributing substantially in ABZ (13.0%) and NBZ (12.4%), but declining sharply in BDZ (3.3%). Cladocerans showed a similar pattern, with the highest contribution in BDZ (13.9%), followed by NBZ (9.0%) and ABZ (3.2%). Chaetognaths were more abundant in ABZ (6.0%) but decreased to 1.2% in BDZ and 2.6% in NBZ. Appendicularians exhibited notable abundance at BDZ (9.6%), whereas their contribution was much lower in ABZ (1.3%) and NBZ (1.4%). Minor groups, including tunicates (0.4–1.6%), hydrozoans (0.9–6.5%), molluscs (0.3–1.0%), and others (2.2–7.0%), contributed relatively less but displayed negligible variations across the zones (Figure 6). Mesozooplankton community metrics varied across zones, with richness ranging from 3.28 to 3.94 in ABZ, 2.06 to 3.59 in BDZ, and peaking at 5.10 in NBZ. Evenness remained relatively stable across zones (0.81–0.93), while diversity was moderate, ranging from 2.73 to 3.07 in ABZ, 2.22 to 2.96 in BDZ, and reaching the highest value of 3.24 in NBZ. The biotic indices, particularly richness and diversity, exhibited higher average values at NBZ compared to ABZ and BDZ (Figure 7). The correlation analysis revealed a significant (p < 0.05) positive relationship with Chaetognatha (r = 0.71), Mollusca (r = 0.73), and other MeZP groups (r = 0.67). While Hydrozoans exhibited a negative relationship with temperature (r = –0.62).

Figure 6

Figure 6. Percentage contribution of mesozooplankton communities across bloom zones.

Figure 7

Figure 7. Grouped box plots of MeZP diversity, evenness, and richness in response to Noctiluca bloom dynamics.

3.7 Statistical interpretation between environmental and biological variables

Redundancy analysis (RDA) was used to explore the relationships between N. scintillans bloom phases, environmental variables, bacterial groups, and zooplankton assemblages in the GoM and the SEAS (Figure 8). The first two RDA axes explained a combined 46.3% of the total variation (RDA1: 28.4%; RDA2: 17.9%), indicating major environmental gradients structuring the dataset. The high species–environment correlations for the first two axes (RDA1: 0.986; RDA2: 0.990) suggest a strong correspondence between the measured variables and community composition. Chlorophyll-a, salinity, total nitrogen (TN), and suspended particulate matter (SPM) were associated with stations in the active bloom zone (ABZ; Stations 1–4) and aligned with Mollusca, Chaetognatha, and Cyclopoida, suggesting that these taxa were more frequently observed under bloom and high-productivity conditions. In contrast, temperature, dissolved oxygen (DO), and dissolved organic carbon (DOC) were associated mainly with bloom decay (BDZ; Stations 5–8) and non-bloom zones (NBZ; Stations 9–12), where they clustered with Cladocerans and Ciliates, indicating their prevalence during bloom senescence or stable non-bloom conditions.

Bacterial groups (P. aeruginosa, V. cholerae, E. coli, Salmonella sp., and Shigella sp.) were positioned close to Tunicata, Noctiluca, Hydrozoa, and heterotrophic dinoflagellates, particularly in the bloom decay zone, reflecting elevated microbial activity during biomass decomposition. The distribution of stations across the RDA quadrants reflects environmental heterogeneity among bloom phases, with decay-zone stations associated with higher nutrients and bacterial abundance, whereas non-bloom stations represented comparatively stable conditions. Overall, the RDA ordination reveals consistent gradients and associations linking bloom phases with environmental variables, bacterial abundance, and zooplankton assemblages. As RDA is an exploratory technique, these patterns represent ecological relationships rather than direct statistical significance; accordingly, univariate analyses identified statistically significant differences in only a few variables (Supplementary Tables S1, S2). Nevertheless, these results support the hypothesis that N. scintillans blooms exert a zone-specific influence on coastal water quality and community structure. Nutrient enrichment, bacterial proliferation, reduced water quality, and enhanced productivity collectively shape mesozooplankton assemblage patterns, particularly within the bloom and decay zones.

4 Discussion

4.1 Factors triggering N. scintillans bloom

Nowadays, N. scintillans blooms are quite common along the Indian coastal waters, with a higher frequency of occurrence and more reports from the GoM and the Arabian Sea (Gopakumar et al., 2009; Baliarsingh et al., 2018; Sarma et al., 2019; Bharathi et al., 2023; Rameshkumar et al., 2023; Peter et al., 2023; Manigandan et al., 2024; Roy et al., 2024; Natarajan et al., 2025 References thereon). Generally, variations in the distribution of HTDs are likely associated with local environmental factors, including temperature, salinity, topography, hydrology, and nutrient availability (Wang et al., 2023). Consistent with this, several studies have reported that calm sea conditions promote the rapid increase of N. scintillans cell density in specific regions (Sarma et al., 2019; Zhang et al., 2022; Wang et al., 2023; Roy et al., 2024), including the GoM (Bharathi et al., 2023; Barathan and Sarangi, 2024). The GoM coastal province comprises small islands and bays, which act as natural barriers against strong currents and winds, thereby frequently creating favourable conditions for N. scintillans blooms. Most blooms have been recorded during the post–southwest monsoon period (September–November), when coastal currents and winds are relatively weaker (Bharathi et al., 2023; Rameshkumar et al., 2023; Mariasingarayan et al., 2025). In addition to these physical drivers, optimal temperature and salinity are critical factors contributing to the frequent occurrence of N. scintillans blooms during this season along the coastal waters of the GoM and SEAS. Previous reports from the GoM and SEAS coastal regions indicate that blooms typically occur under warmer (29–32 °C) and high-salinity (≥34) conditions (Raj et al., 2020; Bharathi et al., 2023; Rameshkumar et al., 2023; Roy et al., 2024; Mariasingarayan et al., 2025), which is consistent with our present observation. In particular, we found a positive correlation (r = 0.56) between salinity and the abundance of N. scintillans, suggesting that bloom development is conducive under high salinity combined with warmer coastal water conditions.

4.2 Influence of N. scintillans bloom on coastal water quality

High-biomass N. scintillans blooms pose a serious concern for coastal ecosystem health, as they are often associated with poor water quality resulting from algal metabolic activities (Dharani et al., 2004). The decomposition and respiration of Noctiluca cells typically lead to oxygen depletion, along with the release of ammonia and other nitrogenous compounds (Bharathi et al., 2023), which have been associated with mass mortalities of marine organisms reported by Rameshkumar et al. (2023). However, in contrast to those earlier findings, our study did not record any significant depletion of dissolved oxygen across the bloom, nor in the decay zones. In agreement with Lotliker et al. (2018), our present observation also showed no evidence of hypoxia during Noctiluca bloom events. Similarly, some other studies have also aligned with the findings of stable oxygen concentrations on the surface layer during N. scintillans bloom (Gomes et al., 2018; Roy et al., 2024; Manigandan et al., 2024). The absence of oxygen depletion, despite visible surface foam and degraded N. scintillans cells, could be due to the bloom being in a late successional phase with moderate chlorophyll-a levels and lower cell densities. Moreover, the open coastal setting, influenced by active mixing and advection, likely enhanced oxygen replenishment and prevented localized hypoxia (Atkinson, 1973; Bortkovskii, 2002). In addition, the presence of the endosymbiotic algae Pedinomonas noctilucae likely contributes to maintaining dissolved oxygen concentrations through active photosynthesis, which may also have contributed to maintaining oxygen concentrations during daylight, thereby counteracting oxygen loss from organic matter degradation (Manigandan et al., 2024). While the bloom crashes, the algal cells will not disintegrate uniformly, as some cells may still be photosynthetically active, while others lyse. This process is further supported by our in-situ Chl-a data, which showed a positive correlation with N. scintillans abundance (r = 0.40). Notably, our data provide evidence of a photosynthetic process, indicated by a considerable amount of DOC levels at the water surface, which further underscores the role of this endosymbiont in sustaining elevated oxygen concentrations during both bloom and decay phases. Similar patterns of increased Chl-a and DOC concentrations during N. scintillans blooms have been reported in previous studies (Sarma et al., 2019; Bharathi et al., 2023; Kordubel et al., 2024a; Manigandan et al., 2024; Mariasingarayan et al., 2025; Wang et al., 2025).

In the present study, the results for nitrogen and phosphate concentrations (NH₄⁺, TN, TP) showed notable differences across the bloom zones. Ammonium concentrations were considerably higher in the bloom decay areas (3.31–15.80 µmol/L), reaching levels about 7 to 10 fold greater than the concentrations observed in the NBZ and ABZ, respectively. This trend corroborates previous reports that have also registered abnormal ammonium enrichment during Noctiluca bloom (Bharathi et al., 2023; Rameshkumar et al., 2023) and the decomposition phase (Baliarsingh et al., 2016). Ammonium concentrations in surface seawater at the BDZ were considerably higher than the typical background levels (<1 µM) as reported by Zhu et al. (2018) for open waters. These high NH₄⁺ levels could have been released from the decomposition of Noctiluca cells. During the degradation of N. scintillans cells, the endosymbionts are released into the surrounding water, where they remain photosynthetically active for a short period. Their continued uptake of CO₂ helps counterbalance the acidification that would normally result from the release of CO₂ during organic matter decomposition and ammonium regeneration. The relatively stable pH values in the face of elevated NH₄⁺ concentrations can be reconciled through the strong buffering capacity of seawater. As highlighted by Middelburg et al. (2020) in their review of ocean alkalinity and carbonate system behaviour, seawater carbonate/bicarbonate/CO₃²⁻ equilibria act to neutralise hydrogen-ion perturbations arising from biogeochemical turnover. Even though ammonification and organic matter remineralisation may release H⁺ (and CO₂) and thereby pose a downward pressure on pH, the buffering mechanism mitigates substantial acidification. Consequently, pH may remain within a relatively narrow range despite elevated NH₄⁺ concentrations.

4.3 Influence of bloom decay on the microbial food web

Our field observations indicate that the accumulation of DOC and surface foam reflects poor water quality and a high microbial load during the bloom decay phase. Correspondingly, bacterial pathogens were isolated across all three zones, with BDZ stations showing markedly higher abundances of P. aeruginosa, V. cholerae, E. coli, Salmonella sp., and Shigella sp. This finding, together with the greater MiZP abundance, supports the notion that BDZ stations have a higher abundance of these pathogens compared to ABZ and NBZ stations. The decomposition of Noctiluca biomass releases large quantities of DOC, NH₄⁺, and other nutrients into the water, creating a nutrient-rich environment that fuels rapid bacterial proliferation (Dai et al., 2022). These conditions provide a distinct competitive advantage to opportunistic and pathogenic groups, such as V. cholerae, E. coli, P. aeruginosa, Salmonella, and Shigella (Behera et al., 2023). Consistent with this pattern, our RDA analysis suggests that nutrient enrichment is associated with higher bacterial abundance, with V. cholerae, P. aeruginosa, Salmonella, and Shigella showing stronger associations with NH₄⁺, TN, and TP, whereas E. coli exhibits a relatively weaker response (Figure 8). Further, it is important to note that although the enrichment and high abundance of pathogenic bacteria in open coastal waters may pose a serious threat to marine organisms (fish and invertebrates), it did not result in a marked increase in biological oxygen demand (BOD) across the study region; the values remained moderate (ABZ 0.37–1.87; BDZ 0.61–1.83; NBZ 0.94–1.95 mg L⁻¹; Supplementary Table S1). This indicates that the rapid dilution and dispersion of decaying Noctiluca biomass in open waters minimized localized oxygen demand. The dominance of dissolved organic products such as ammonium and DOC likely promoted microbial activity without substantially elevating BOD. Additionally, sampling during a partially mixed phase and residual photosynthetic activity from associated chlorophyll-a may have helped stabilise oxygen levels, thereby preventing a pronounced rise in BOD during the decay phase. Notably, earlier studies have reported that the proliferation of Vibrio spp. can lead to vibriosis, a common bacterial disease affecting a wide range of marine fish and shellfish (Deng et al., 2020; Hegde et al., 2023). The elevated Vibrio counts observed in our study could be associated with the bloom event, as N. scintillans is known to act as a vector of Vibrio spp., as proposed by Liu et al. (2025). This vector relationship provides strong support for our present findings in explaining why these bacteria thrived in exceptionally high numbers during the bloom outburst of N. scintillans.

Figure 8

Figure 8. Redundancy Analysis (RDA) illustrating the relationships between hydrobiological variables and study locations across different zones: ABZ (Active Bloom Zone), BDZ (Bloom Decay Zone), and NBZ (Non-Bloom Zone). The numbers displayed within the ordination plot correspond to Stations 1–12. (Temp, temperature; DO, dissolved oxygen; NH₄⁺, ammonium; TN, total nitrogen; TP, total phosphorus; SPM, suspended particulate matter; DOC, dissolved organic carbon; Chl a, chlorophyll-a; EC, Escherichia coli; PA, Pseudomonas aeruginosa; SAL, Salmonella sp.; SHIG, Shigella sp.; VC, Vibrio cholerae; NS, N. scintillans; H.dinofl, heterotrophic dinoflagellates; Oth-MiZP, other microzooplankton; Calanoid, Calanoida; Cyclopoi, Cyclopoida; Harpacti, Harpacticoida; Cladocer, Cladocerans; Appendic, Appendicularia, Chaetogn, Chaetognatha; Hydrozoan, Hydrozoans; Oth-MeZP, other mesozooplankton).

The sudden proliferation of pathogenic bacteria poses a serious threat to ecosystem sustainability and the biodiversity of planktonic assemblages (Maugeri et al., 2004), as these communities respond rapidly to contamination, often exhibiting shifts in abundance (e.g., microzooplankton). Remarkably, ciliates, HTDs, and other microzooplankton exhibited clear dominance during the bloom and decay phases. This pattern may be closely associated with deteriorating water quality, where the elevated pathogenic load could have attracted them. As recognised bio-indicators of water quality and active consumers of bacterial communities, these organisms play a crucial role in the microbial loop and the coastal food web (Haraguchi et al., 2018). In our study, the increased prevalence of these MiZP groups reflects their active role in regulating microbial loads during bloom decay and, at the same time, underscores their reliability as bioindicators of eutrophic conditions. Similarly, previous research has also recognised microzooplankton as important indicators of water quality in Indian coastal waters (Rakshit et al., 2017).

4.4 Bloom-induced variations in mesozooplankton distribution

The results indicate that N. scintillans blooms were closely linked to shifts in both the abundance and composition of mesozooplankton (MeZP) community. While the abundance and diversity of major MeZP taxa varied across bloom conditions, the most pronounced differences were observed in the ABZ (increased abundance) and BDZ (decreased abundance). During the active bloom phase, copepods (particularly Calanoida) numerically dominated the MeZP community. However, during the decay phase, the mesozooplankton community shifted markedly from calanoid copepod dominance to a community composed primarily of cladocerans, appendicularians, and hydrozoans. This compositional change appears closely linked to the elevated ammonium concentrations recorded in the decay zone. Although nitrogen enrichment typically supports phytoplankton growth, excessive dissolved inorganic nitrogen, particularly ammonium (NH₄⁺), can deteriorate food quality for calanoid copepods by favouring phytoplankton species deficient in essential fatty acids (EFAs) and other biochemical components crucial for their growth and reproduction (Bi and Sommer, 2020). Under such conditions, calanoids may experience metabolic stress or ammonium toxicity, further compromising their survival and reproductive efficiency, leading to the sharp decline observed in their abundance. In contrast, cladocerans and appendicularians are more tolerant of nutrient- and bacteria-enriched environments and can efficiently exploit fine detrital and microbial food sources that proliferate during bloom degradation. The concurrent increase in hydrozoans also indicates enhanced predation pressure on smaller zooplankton. Collectively, the decline of the calanoid copepod community, which is predominantly composed of herbivorous feeders, reflects a broader trophic shift from a phytoplankton-based food web to a detritivore–bacterivore–dominated pathway sustained by organic matter decomposition. A few other studies have also observed a reduction in copepod and other mesozooplankton abundance during dinoflagellate blooms in the Western Pacific (Lin et al., 2014) and the southern Indian Ocean (Bizani et al., 2023). For instance, the bloom of Lingulodinium polyedra in Algoa Bay region caused a significant decline in calanoid abundance and induced a community shift toward small cyclopoids and gelatinous zooplankton (Bizani et al., 2023).

4.5 Ecological indicator significance

Copepods are highly sensitive to deteriorating water quality (Drira et al., 2017), and their presence, absence, and abundance fluctuations are widely recognised as indicators of environmental conditions (Hooff and Peterson, 2006). In our study, calanoid copepod abundance was lower at BDZ than at ABZ and NBZ, suggesting that the BDZ stations were under strong environmental stress, possibly linked to poor water quality and surface foam formation. The breakdown of Noctiluca cells creates these surface foam layers, which can act as a physical barrier, limiting the motility of the organisms and interfering with feeding and respiration (Jenkinson et al., 2018). This likely forces these sensitive organisms (zooplankton) to migrate away from the bloom decay zone. Elevated NH₄⁺ concentrations in the BDZ may have further contributed to this decline, as excessive ammonium is toxic and closely associated with eutrophication stress. Previous studies have reported that ammonia concentrations above 10 µM can exert acute toxicity on copepods (Sullivan and Ritacco, 1985; Buttino, 1994), as well as some other zooplankton taxa (Buskey et al., 2003). Consistent with this, our RDA plot revealed a strong negative association of major MeZP communities with nutrient enrichment.

Although copepods dominated during the ABZ phase, their decline during bloom decay (BDZ) opened ecological space for opportunistic organisms such as cladocerans, appendicularians, and hydrozoans, which gradually became dominant in BDZ. This shift may be associated with seafoam formation during bloom crashes, as foam patches trap organic detritus, bacteria, and lysed algal material, creating localized enrichment that initially attracts these zooplankton groups for feeding. These taxa were already being documented as ecological indicators: cladocerans serve as indicators of high primary productivity and phytoplankton bloom (Bedikoğlu et al., 2022; Sahu et al., 2015; Ezhilarasan et al., 2018); appendicularians reflect bacterial and picoplankton enrichment as well as microbial loop activity (Koshikawa et al., 1999; King et al., 1980); and hydrozoans indicate water quality deterioration, prey shifts, and environmental stress (Richardson et al., 2009; Baliarsingh et al., 2020). Consequently, our findings confirm that the enrichment of opportunistic organisms such as cladocerans, appendicularians, and hydrozoans in the decay zone aligns with their established role as indicators of environmental perturbations. At the same time, the marked decline of calanoid copepods highlights their reliability as sensitive bioindicators of environmental degradation during N. scintillans bloom decay events.

5 Conclusion

Overall, this investigation documented the ecological consequences of the bloom and decay phases of N. scintillans along the coastal waters of the Gulf of Mannar (GoM) and the southeastern Arabian Sea (SEAS). The bloom succession was accompanied by notable shifts in water quality, bacterial abundance, and zooplankton community structure. During the study period, the waters remained warm, well-oxygenated, and had stable salinity, while most physicochemical parameters exhibited only minor variations. However, dissolved nutrients, particularly NH₄⁺, peaked in the bloom decay zone, stimulating the growth of bacterial loads and contributing, together with DOC, to the formation of extensive seafoam patches. These foam layers and eutrophic conditions placed the environment under stress, altering bacterial composition and driving shifts in both micro- and meso-zooplankton communities.

Our results further revealed that copepods, particularly calanoids, dominated during the active bloom phase but declined considerably during the decay phase. This decline was accompanied by the proliferation of opportunistic organisms, such as cladocerans, appendicularians, and hydrozoans, reflecting enrichment in DOM, high productivity, and eutrophic conditions during bloom decay. Furthermore, N. scintillans could serve as a potential vector, facilitating the dominance not only of Vibrio but also of other opportunistic bacterial groups during the bloom and decay phases, thereby posing risks to marine ecosystems and fisheries.

Interactively, these findings highlight the cascading ecological impacts of N. scintillans blooms and demonstrate that zooplankton responses can serve as reliable indicators of environmental perturbation. This study highlights the need for future research on bloom–decay dynamics in coastal waters, with a focus on unravelling shifts in lower trophic interactions and food web linkages, which is crucial for mitigating the cascading impacts of harmful algal blooms.

Data availability statement

The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding author.

Ethics statement

The manuscript presents research on animals that do not require ethical approval for their study.

Author contributions

RS: Conceptualization, Formal analysis, Investigation, Writing – original draft, Data curation, Visualization, Methodology. AA: Formal analysis, Methodology, Writing – review & editing. SR: Formal analysis, Investigation, Methodology, Writing – review & editing. MC: Formal analysis, Methodology, Validation, Writing – review & editing. CS: Formal analysis, Investigation, Writing – review & editing. LN: Formal analysis, Software, Writing – review & editing. SS: Supervision, Validation, Writing – review & editing. KR: Project administration, Supervision, Writing – review & editing.

Funding

The author(s) declared that financial support was not received for this work and/or its publication.

Acknowledgments

The study was conducted as part of the Sea Water Quality Monitoring (SWQM) project, supported by the Ministry of Earth Sciences, Government of India. The authors wish to express their gratitude to the Vessel Management Cell at the National Institute of Ocean Technology, Chennai, for their assistance in arranging the research cruise onboard CRV Sagar Anveshika. The authors acknowledge the use of AI-assisted tools for language refinement. All scientific content and interpretations were carefully reviewed and verified by the authors. NCCR contribution number: NCCR/MS/446.

Conflict of interest

The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Generative AI statement

The author(s) declared that Generative AI was not used in the creation of this manuscript.

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Supplementary material

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmars.2026.1706039/full#supplementary-material

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