Long-term changes in summer phytoplankton communities and their influencing factors in Daya Bay, China (1991-2017)

Metabarcoding and co-occurrence network reveal significant effects of mariculture on benthic eukaryotic microalgal community: A case study in Daya Bay of the South China Sea

Benthic eukaryotic microalgae were analyzed by metabarcoding the partial 18S rRNA gene in Daya Bay bi-monthly in 2021. Altogether 941 eukaryotic microalgal OTUs were detected, belonging to 27 classes of 8 phyla. Dinophyta and Chlorophyta were the dominant phyla. Microalgal community in the mariculture zone differed significantly from those in non-mariculture zone, reflected by low alpha diversity indexes and increasing abundance and richness of chlorophytes and correspondingly decreasing of dinoflagellates. The abundant occurrences of the pico- and nano-sized taxa such as the chlorophyte Picochlorum in the mariculture zone suggested that nutrient enrichment might result in the miniaturization of the benthic eukaryotic microalgae. The co-occurrence network suggested more negative interactions between taxa in the mariculture zone. A total of 41 algal bloom and/or harmful algal bloom (HAB) species were detected in this study, suggesting a high potential risk of HABs in Daya Bay, especially for the recurrent bloom species Scrippsiella acuminata.

Regime shift in a coastal pelagic ecosystem with increasing human-induced nutrient inputs over decades

Human-induced nutrient inputs to global coastal waters are leading to increasing nutrients and escalating eutrophication. However, how aquatic ecosystem functioning responds to these changes remains insufficiently studied. Here we report the long-term changes in the nutrient regime and planktonic ecosystem functioning in the Daya Bay, a typical subtropical semi-enclosed bay experiencing rapid economic and social development for several decades. Time-series (from 1991 to 2018) data with a mostly quarterly resolution were collected to depict long-term changes in dissolved inorganic nutrients and plankton abundances, based on which we constructed simplified abundance size spectra (SASS) and plankton abundance ratios to describe the functioning of the planktonic ecosystem. The results revealed a long-term increase in system productivity but a decrease in integrated energy transfer efficiency of the planktonic ecosystem, with rising concentrations of dissolved inorganic nitrogen (DIN). Shifts in the nutrient regime and planktonic ecosystem functioning were detected at a tipping point or threshold around 2006-2007. The shifts were characterized by abrupt changes in the trends of nutrient (phosphate, ammonia, nitrite) concentrations, nutrient ratios (DIN/phosphate, silicate/phosphate), plankton abundance, and total plankton biomass. Compared to the nutrient regime, the planktonic ecosystem functioning shifted several years later. Overall, this study indicates that the pelagic ecosystem regime can shift significantly in response to long-term increasing input of human-induced nutrients in coastal waters such as the Daya Bay. The regime shifts may have profound implications for fishery production, and ecosystem management in the bay.

Exploring the impact of ocean warming and nutrient overload on macroalgal blooms and carbon sequestration in deep-sea sediments of the subtropical western North Pacific

The role of macroalgae as blue carbon (BC) under changing climate was investigated in the subtropical western North Pacific. Sea surface temperatures (SSTs) and nutrient influx increased over the past two decades (2001-2021). The proliferation of climate-resilient macroalgae was facilitated. Using Pterocladiella capillacea and Turbinaria ornata, outdoor laboratory experiments and elemental assays underscored the influence of nutrient enrichment on their resilience under ocean warming and low salinity. Macroalgal incorporation into marine sediments, indicated by environmental DNA barcoding, total organic carbon (TOC), and stable isotope analysis. Over time, an increase in δ13C and δ15N values, particularly at greater depths, suggests a tendency of carbon signature towards macroalgaeand nitrogen pollution or high tropic levels. eDNA analysis revealed selective deposition of these species. The species-dependent nature of macroalgae in deep-sea sediments highlights the role of nutrients on climate-resilient macroalgal blooms as carbon sinks in the western North Pacific.

Cognatishimia coralii sp. nov., a marine bacterium isolated from seawater surrounding corals

Coral reefs are declining due to the rising seawater temperature. Bacteria within and surrounding corals play key roles in maintaining the homeostasis of the coral holobiont. Research on coral-related bacteria could provide benefits for coral reef restoration. During the isolation of coral-associated bacteria, a Gram-stain-negative, motile bacterium (D5M38T) was isolated from seawater surrounding corals in Daya Bay, Shenzhen, PR China. Phylogenetic analysis revealed that strain D5M38T represents a novel species in the genus Cognatishimia. The temperature range for strain D5M38T growth was 10-40 °C, and the optimum temperature was 37 °C. The salinity range for the growth of this isolate was from 0 to 4.0 %, with an optimal salinity level of 0.5 %. The pH range necessary for strain D5M38T growth was between pH 5.0 and 9.0, with an optimal pH being 7.5. The predominant fatty acid was summed feature 8 (65.0 %). The major respiratory quinone was Q-10. The DNA G+C content was 56.8 %. The genome size was 3.88 Mb. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strain D5M38T and its two closest neighbours, Cognatishimia activa LMG 29900T and Cognatishimia maritima KCTC 23347T, were 73.2/73.6%, 73.2/73.6% and 19.7/19.5%, respectively. Strain D5M38T was clearly distinct from its closest neighbours C. activa LMG 29900T and C. maritima KCTC 23347T, with 16S rRNA gene sequence similarity values of 97.5 and 97.3 %, respectively. The phylogenetic analysis, along with the ANI, AAI, and dDDH values, demonstrated that strain D5M38T is a member of the genus Cognatishimia, and is distinct from the other two recognized species within this genus. The physiological, biochemical and chemotaxonomic characteristics also supported the species novelty of strain D5M38T. Thus, strain D5M38T is considered to be classified as representing a novel species in the genus Cognatishimia, for which the name Cognatishimia coralii sp. nov. is proposed. The type strain is D5M38T (=MCCC 1K08692T=KCTC 8160T).

Unveiling the evolution of phytoplankton communities: Decades-long insights into the southern Yellow Sea, China (1959-2023)

We obtained historical and observational data on phytoplankton communities from 1959 to 2023 to explore the responses of the phytoplankton community structure to long-term environmental changes in the southern Yellow Sea (SYS), China. The results revealed a decrease in the proportions of diatom cell abundance within the phytoplankton community by 8 %, accompanied by a corresponding increase in that of dinoflagellates. Dominant phytoplankton species were mainly chain-forming diatoms before 2000, and large dinoflagellate species from the genera Tripos and Noctiluca increased their dominance after 2000. Warm-water phytoplankton species have increased in dominance over the study period. Correlation analysis revealed that the ocean warming and alterations in nutrient structure (N/P and Si/N ratios) were mostly responsible for the long-term evolution trend, and these changes may result in an increase in dinoflagellate harmful algal blooms, reduced efficiency of the biological carbon pump, and heightened hypoxia in the future, which should draw our attention.

Neorhizobium turbinariae sp. nov., a coral-beneficial bacterium isolated from Turbinaria peltata

Coral reef ecosystems are facing decline due to climate change, overfishing, habitat destruction and pollution. Bacteria play an essential role in maintaining the stability of coral reef ecosystems, influencing the well-being and fitness of coral hosts. The exploitation of coral probiotics has become an urgent issue. A short-rod shaped aerobic bacterium, designated NTR19T, was isolated in a healthy coral Turbinaria peltata from Daya Bay, Shenzhen, PR China. Its cells were Gram-negative, motile with a polar flagellum. The activities of catalase and oxidase were positive. Strain NTR19T grew at 10-41 °C (optimum, 28 °C), with NaCl concentrations of 0-4 % (w/v; optimum, 0.5 %) and at pH 5.0-9.5 (optimum, pH 7.0-7.5). The predominant fatty acids (>10 %) were summed feature 8 (57.6 %), C19 : 0 cyclo ω8c (12.6 %) and C16 : 0 (12.0 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid and phosphatidylcholine. The major respiratory quinone was Q-10. The draft genome was 4.68 Mbp with 61.2 mol% DNA G+C content. In total, 4477 coding sequences were annotated and there were 64 RNA genes. The average nucleotide identity (ANI) and average amino acid identity (AAI) values between strain NTR19T and the related Neorhizobium species were 78.23-79.70% and 80.26-80.50 %, respectively. This strain encoded many proteins for the activities of catalase and oxidase in the genome. Strain NTR19T was clearly distinct from its closest neighbours Rhizobium oryzicola ACCC 05753T and Neorhizobium petrolearium ACCC 11238T with the 16S rRNA gene sequence similarity values of 96.86 and 96.36 %, respectively. The results of phylogenetic analysis, as well as ANI and AAI values, revealed that strain NTR19T belongs to Neorhizobium and was distinct from other species of this genus. The physiological, biochemical and chemotaxonomic characteristics also supported the species novelty of strain NTR19T. Thus, strain NTR19T is considered to be classified as a novel species in the genus Neorhizobium, for which the name Neorhizobium turbinariae sp. nov. is proposed. The type strain is NTR19T (=JCM 35342T=MCCC 1K07226T).

Roseomonas acroporae sp. nov., isolated from coral Acropora digitifera

A non-motile, rod-shaped, pink-pigmented bacterium NAR14^T was isolated from coral Acropora digitifera from Daya Bay, Shenzhen, PR China. Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-negative. NAR14^T grew with 0-6 % (w/v) NaCl (optimum, 2-4 %), at 10-41 °C (optimum, 28 °C) and at pH 4.0-9.5 (optimum, 5.0). The major respiratory quinone was Q-10. The predominant fatty acids (more than 10%) were summed feature 8 (65.6 %) and C_16 : 0 (17.6%). The DNA G+C content of NAR14^T was 73.6 %. The polar lipids of NAR14^T comprised one diphosphatidylglycerol, one phosphatidylethanolamine, one phosphatidylglycerol, one phosphatidylcholine, one aminolipid and three unknown polar lipids. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that NAR14^T formed a lineage within the genus Roseomonas of the family Acetobacteraceae, and it was distinct from the most closely related species Roseomonas wooponensis JCM 19527^T and Roseomonas riguiloci JCM 17520^T with the 16S rRNA gene sequence similarities of 94.61 and 93.98 %, respectively. Phenotypic characteristics (physiological, biochemical and chemotaxonomic) also supported the taxonomic novelty of this isolate. Thus, NAR14^T is considered to represent a novel species within the genus Roseomonas, for which the name Roseomonas acroporae sp. nov. is proposed. The type strain is NAR14^T (=KCTC 92174^T = MCCC 1K07275^T).

Aquimarina acroporae sp. nov., isolated from seawater surrounding scleractinian coral Acropora digitifera

A Gram-stain-negative, aerobic, rod-shaped bacterium (D1M17T) was isolated from the seawater surrounding scleractinian coral Acropora digitifera in Daya Bay, Shenzhen, PR China. Strain D1M17T grew with 0–10 % (w/v) NaCl (optimum, 3–4 %), at 15–37 °C (optimum, 28 °C) and at pH 4.5–8.5 (optimum, pH 7.0–7.5). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain D1M17T formed a lineage within the genus Aquimarina , family Flavobacteriaceae , and it was distinct from the most closely related species Aquimarina salinaria LMG 25375T, Aquimarina gracilis JCM 17453T and Aquimarina spongiae KCTC 22663T with 16S rRNA gene sequence similarities of 97.2, 97.2 and 97.1 %, respectively. The major respiratory quinone was MK-6. The predominant fatty acids (more than 10 %) were iso-C15 : 0 (28.8 %), iso-C17 : 0 3-OH (21.5 %) and iso-C15 : 1 G (13.1 %). The DNA G+C content of D1M17T was 34.4 mol%. The polar lipids in D1M17T comprised one phospholipid and five unknown polar lipids. Phenotypic characteristics (physiological, biochemical and chemotaxonomic) also supported the taxonomic novelty of this isolate. Thus, strain D1M17T is considered to represent a novel species within the genus Aquimarina , for which the name Aquimarina acroporae sp. nov. is proposed. The type strain is D1M17T (=KCTC 92172T= MCCC 1K07224T).

Algiphilus acroporae sp. nov. and Coraliihabitans acroporae gen. nov. sp. nov., isolated from scleractinian coral Acropora digitifera

Two Gram-staining-negative, aerobic, rod-shaped bacteria NNCM1T and NNCM2T were isolated from the scleractinian coral Acropora digitifera. NNCM1T grew with 0.5–12 % (w/v) NaCl (optimum, 3–6 %), at 18–37 °C (optimum, 28 °C) and at pH 6.0–10.0 (optimum, 7.0–8.0). NNCM2T grew with 0.5–10 % (w/v) NaCl (optimum, 2 %), at 18–37 °C (optimum, 28 °C) and at pH 6.5–9.0 (optimum, 7.0). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that NNCM1T formed a lineage within the genus Algiphilus of the family Algiphilaceae, and it was distinct from the most closely related species Algiphilus aromaticivorans DG1253T, with a 16S rRNA gene sequences similarity of 97.05 %. NNCM2T formed a lineage within the family Rhodobacteraceae, and it was distinct from the closely related genera Limibaculum halophilum CAU 1123T, Paroceanicella profunda D4M1T and Pseudoruegeria aestuarii MME-001T with 93.41, 92.78 and 91.09% identities, respectively. The major respiratory quinone was Q-8 and Q-10 for NNCM1T and NNCM2T, respectively. The predominant fatty acids (more than 10 %) were summed feature 8 (39.4 %) and C16 : 0 (19.4 %) for NNCM1T and summed feature 8 (62.8 %) and C16 : 0 (12.4 %) for NNCM2T. The DNA G+C contents of NNCM1T and NNCM2T were 63.3 and 63.4 mol% respectively. The polar lipids of NNCM1T comprised one diphosphatidylglycerol, one phosphatidylethanolamine, one phosphatidylglycerol and one unknown polar lipid, while those of NNCM2T comprised one phosphatidylethanolamine, one phosphatidylglycerol, one aminolipid and four unknown polar lipids. Phenotypic characteristics (physiological, biochemical and chemotaxonomic) also supported the taxonomic novelty of the two isolates. Thus, NNCM1T is considered to represent a novel species within genus Algiphilus , for which the name Algiphilus acroporae sp. nov. is proposed. The type strain is NNCM1T (=KCTC 82966T=MCCC 1K06445T). NNCM2T represents a novel genus and species within the family Rhodobacteraceae, for which the name Coraliihabitans acroporae gen. nov. sp. nov. is proposed. The type strain is NNCM2T (=KCTC 82967T=MCCC 1K06408T).

Trophic states regulate assembly processes and network structures of small chromophytic phytoplankton communities in estuarine and coastal ecosystem

Small chromophytic phytoplankton (SCP) are anticipated to be more important for a significant proportion of primary production in estuarine-coastal ecosystems. However, responses of SCP community to coastal eutrophication are still unclear. In this study, we investigated diversity, co-occurrence and assembly features of SCP communities, as well as relationship with environmental factors in subtropical Beibu Gulf. The results exhibited that the alpha diversity and beta diversity of SCP communities were significantly different among eutrophic states. Co-occurrence network revealed a complex interaction that most amplicon sequence variants (ASVs) in modules of the network were specific to trophic states. Further, phylogenetic based β-nearest taxon distance analyses revealed that stochastic processes mainly provided 69.26% contribution to SCP community assembly, whereas deterministic processes dominated community assembly in heavy eutrophic state. Overall, our findings elucidate the mechanism of diversity and assembly in SCP community and promote the understanding of SCP ecology related to subtropical coastal eutrophication.

Effects of organic nitrogen components from terrestrial input on the phytoplankton community in Jiaozhou Bay

Dissolved organic nitrogen (DON) from terrestrial input exacerbates eutrophication and induces harmful algal blooms. We investigated the effects of hydrophilic (Hic) and low molecular weight (LMW) DON on the phytoplankton community in Jiaozhou Bay during autumn (October 2017) and spring (May 2018). Our results showed DON additions significantly increased algal growth while decreasing community biodiversity and provide a competitive advantage for Skeletonema costatum. These situations were further intensified by increasing temperature in autumn. Additionally, Hic DON had a higher bioavailability than LMW DON. Based on emission-excitation matrix spectra, we identified protein-like components as the main components of Hic DON whereas humus-like components were the principal components of LMW. Correlation analysis confirmed a positive correlation between DON bioavailability and protein-like components. Therefore, our results indicate DON from terrestrial input disrupts the structural stability of the phytoplankton community and increases the risk of harmful algal blooms, which in turn threaten coastal ecosystems.

Photosynthetic Characteristics of Smaller and Larger Cell Size-Fractioned Phytoplankton Assemblies in the Daya Bay, Northern South China Sea

Cell size of phytoplankton is known to influence their physiologies and, consequently, marine primary production. To characterize the cell size-dependent photophysiology of phytoplankton, we comparably explored the photosynthetic characteristics of piconano- (<20 µm) and micro-phytoplankton cell assemblies (>20 µm) in the Daya Bay, northern South China Sea, using a 36-h in situ high-temporal-resolution experiment. During the experimental periods, the phytoplankton biomass (Chl a) in the surface water ranged from 0.92 to 5.13 μg L^-1, which was lower than that in bottom layer (i.e., 1.83-6.84 μg L^-1). Piconano-Chl a accounted for 72% (mean value) of the total Chl a, with no significant difference between the surface and bottom layers. The maximum photochemical quantum yield (F_V/F_M) of Photosystem II (PS II) and functional absorption cross-section of PS II photochemistry (σ_{PS II}) of both piconano- and micro-cells assemblies varied inversely with solar radiation, but this occurred to a lesser extent in the former than in the latter ones. The σ_{PS II} of piconano- and micro-cell assemblies showed a similar change pattern to the F_V/F_M in daytime, but not in nighttime. Moreover, the fluorescence light curve (FLC)-derived light utilization efficiency (α) displayed the same daily change pattern as the F_V/F_M, and the saturation irradiance (E_K) and maximal rETR (rETR_max) mirrored the change in the solar radiation. The F_V/F_M and σ_{PS II} of the piconano-cells were higher than their micro-counterparts under high solar light; while the E_K and rETR_max were lower, no matter in what light regimes. In addition, our results indicate that the F_V/F_M of the micro-cell assembly varied quicker in regard to Chl a change than that of the piconano-cell assembly, indicating the larger phytoplankton cells are more suitable to grow than the smaller ones in the Daya Bay through timely modulating the PS II activity.

Interspecies competition between Scrippsiella acuminata and three marine diatoms: Growth inhibition and allelopathic effects

Interactions between Scrippsiella acuminata and three diatoms, Chaetoceros curvisetus, Phaeodactylum tricornutum, and Skeletonema dohrnii, were investigated using bi-algal co-cultures and cell-free and sonicated-cell filtrates in this study. Volatile aldehydes in sonicated filtrates of the three diatoms were analyzed by GC/MS. Furthermore, effects of 2E, 4E-decadienal (2,4-D) on the growth and the photosynthetic efficiency of the four microalgal species were studied. The growth of Sc. acuminata was significantly inhibited by the three diatoms in all co-cultures, and the inhibitory effects were higher under nutrient-rich conditions. Both cell-free and sonicated-cell filtrates of the three diatoms showed significant inhibitions on the growth of Sc. acuminata, which highlighted that diatoms produce allelopathic compounds not only to the surrounding environments but also inside the cells. Fifteen aldehydes were detected in the sonicated-cell filtrates of the three diatoms, and 5, 5, and 12 types of aldehydes were detected in C. curvisetus, P. tricornutum, and Sk. dohrnii, respectively. Polyunsaturated aldehydes (PUAs) composition differed among the three diatom species. Phenylglyoxal (C₈H₆O₂) dominated in C. curvisetus, 2,4-D (C₁₀H₁₆O) predominated in P. tricornutum, and high proportions of 2-hexenal (C₆H₁₀O), 2E, 4E-heptadienal (C₇H₁₀O), and 2,4-D were detected in Sk. dohrnii. 2,4-D showed significantly inhibitory effects on the growth of algal cells including diatoms themselves in a dose-dependent manner, and photosynthetic efficiency was significantly decreased as well. Sc. acuminata was the most sensitive species. The 96 h EC₅₀ values of 2,4-D on the growth of the four microalgae were 1.64 μmol/L for Sc. acuminata, 3.09 μmol/L for C. curvisetus, 4.93 μmol/L for P. tricornutum, and 8.54 μmol/L for Sk. dohrnii, respectively. The results suggest that PUAs produced by diatoms may help them to take the competitive advantages in phytoplankton community, and thus to sustain diatom-dominated community structure in nutrient rich coastal waters.

Distribution of C/N/P stoichiometry in suspended particulate matter and surface sediment in a bay under serious anthropogenic influence: Daya Bay, China

The C/N/P stoichiometry of organic matter can provide useful information for better understanding of the effects of human activities on aquatic ecosystems. The Daya Bay is a semi-closed bay under serious anthropogenic influences in the southeastern China. This study investigated the contents and ratios of C, N, and P in suspended particulate matter (SPM) and surface sediment in Daya Bay during the spring of 2017. Average C/N/P ratios were 139/17/1 in the surface SPM, 129/16/1 in the bottom SPM, and 61/8/1 in the surface sediment. The C/N ratio of SPM was significantly lower in the western inner bay, suggesting that eutrophication can reduce this ratio. The N/P ratio of SPM was slightly higher in the inner bay, while no clearly distribution pattern was found in the C/P ratio of SPM. Compared with SPM, surface sediment showed significantly lower N/P and C/P ratios. The C/N, N/P, and C/P ratios and contents of total organic C, N, and P were higher in the surface sediment in the inner bay. Our results suggested that the distribution of C/N/P stoichiometry was uncoupled between SPM and surface sediment. The C/N/P stoichiometry of surface sediment can effectively reflect the regional variation of terrigenous input and the influence of nuclear power plant thermal effluent.