Upwelling, a common oceanographic event, can make great contributions, directly or indirectly, to deep ocean carbon sequestration. However, the extent of its contribution indirectly depends on the composition of microbial communities and the interactions between bacterioplankton and other microorganisms. This study provides insights into the influence of upwelling on bacterioplankton at the whole community level and predicts their potential functional profiles. The α diversity of the bacterial community exhibited no significant differences between the upwelling area and non-upwelling area, while the community composition varied clearly in different habitats. Proteobacteria, Cyanobacteria, Bacteroidota, Firmicutes, and Actinobacteria were the five dominant phyla in all of the habitats. The proportions of members of Firmicutes were increased whereas Cyanobacteria were reduced in upwelling water. However, the percentage of Cyanobacteria was enhanced in the upwelling deep water. Functional genes that are involved in signal transductions, which belong to environmental information processing, were more active in upwelling surface water than in the other habitats. Closer and more complex relationships between bacterioplankton and microbial eukaryotes were found in the upwelling area, which altered with the variation of the external environmental conditions. Cyanobacteria showed a positive correlation with microbial eukaryotes in upwelling deep water. Combined with the high proportions of Cyanobacteria in upwelling deep water, this might be strong evidence that Cyanobacteria contribute to a deep ocean carbon sink. Overall, our study reveals the impacts of upwelling on the bacterial community composition, metabolic functions, and microbial interactions, which are significant to further understanding the carbon sink effects of upwelling.

Cyanobacteria contribute to roughly a quarter of global net carbon fixation. During diel light/dark growth, dark respiration substantially lowers the overall photosynthetic carbon yield in cyanobacteria and other phototrophs. How respiratory pathways participate in carbon resource allocation at night to optimize dark survival and support daytime photosynthesis remains unclear. Here, using the cyanobacterium Synechococcus elongatus PCC 7942, we show that phosphoketolase integrates into a respiratory network in the dark to best allocate carbon resources for amino acid biosynthesis and to prepare for photosynthesis reinitiation upon photoinduction. Moreover, we show that the respiratory Entner-Doudoroff (ED) pathway in S. elongatus is incomplete, with its key enzyme 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase exhibiting alternative oxaloacetate decarboxylation activity that modulates daytime photosynthesis. This activity allows for the bypassing of the tricarboxylic acid (TCA) cycle when ATP and NADPH consumption for biosynthesis is excessive and imbalanced relative to their production by the light reactions, thereby preventing relative NADPH accumulation and ensuring optimal photosynthetic carbon yield. Optimizing these metabolic processes offers opportunities to enhance photosynthetic carbon yield in cyanobacteria and other photosynthetic organisms under diel light/dark cycles.

Marine protists Aurantiochytrium are recognized as promising sources for commercial lipid production, particularly due to their ability to produce high-value natural compounds like docosahexaenoic acid (DHA). However, wild-type strains isolated from natural environments typically fail to meet commercial demands for DHA yields, partly because they are poorly adapted to the decreased pH conditions encountered during fermentation. In this study, we employed a staged acidic adaptive laboratory evolution (ALE) strategy to develop a high DHA-producing strain from Aurantiochytrium sp. PKU#Mn16. By optimizing oxygen and temperature levels under low pH conditions, ALE resulted in a 171.4% increase in DHA concentration in the ALE strain compared to the wild-type strain. Comparative transcriptomics revealed that ALE enhanced the expression of key enzymes in glycolysis and the polyketide synthase (PKS) pathway during both early (metabolic peak) and late (metabolic decline) fermentation stages, promoting growth and polyunsaturated fatty acid synthesis. Additionally, key enzymes in the tricarboxylic acid (TCA) cycle and pentose phosphate (PPP) pathway were upregulated at early and late stages, respectively, suggesting differential ATP/NADPH supply mechanisms that drive DHA accumulation. Notably, the upregulation of glycerol kinase (GK) indicates the potential for using glycerol as an alternative carbon source to further enhance DHA production in our ALE strain. In this study, Aurantiochytrium sp. PKU#Mn16 was successfully acclimated using a synergistic approach combining high dissolved oxygen, low temperature, and citric acid-induced acidity. This strategy yielded significant increases of 106.3% in biomass, 243.8% in total fatty acid yield, and 171.4% in DHA yield. Transcriptomic analysis revealed extensive rewiring of central carbon and lipid metabolism, including the upregulation of PKS pathway enzymes and enhanced supply of ATP, NADPH, and acetyl-CoA. Additionally, reduced competing secondary metabolic fluxes optimized substrate allocation. This innovative acclimation strategy not only sheds light on the molecular mechanisms driving efficient fatty acid and DHA production but also lays the groundwork for future comparative genomics and genetic editing efforts aimed at further boosting yields of fatty acids and other natural secondary metabolites in thraustochytrids. The online version contains supplementary material available at 10.1186/s12934-025-02792-z.

The consequences of climate change may directly or indirectly impact the marine biosphere. Although ocean stratification has been recognized as one of the crucial consequences of ocean warming, its impacts on several critical aspects of marine microbes remain largely unknown in the Indian Ocean. Here, we investigate the effects of water stratification, in both surface and subsurface layers, on hydrogeographic parameters and bacterioplankton diversity within the equatorial eastern Indian Ocean (EIO). Strong stratification in the upper 200 m of equatorial EIO was detected with evidential low primary productivity. The vertical bacterioplankton diversity of the whole water columns displayed noticeable variation, with lower diversity occurring in the surface layer than in the subsurface layers. Horizontal heterogeneity of bacterioplankton communities was also in the well-mixed layer among different stations. SAR11 and Prochlorococcus displayed uncharacteristic low abundance in the surface water. Some amplicon sequence variants (ASVs) were identified as potential biomarkers for their specific depths in strongly-stratified water columns. Thus, barriers resulting from stratification are proposed to function as an ‘ASV filter’ to regulate the vertical bacterioplankton community diversity along the water columns. Overall, our results suggest that the effects of stratification on the structure and diversity of bacterioplankton can extend up to the bathypelagic zone in the strongly-stratified waters of the equatorial EIO. This study provides the first insight into the effect of stratification on the subsurface microbial communities in the equatorial eastern Indian Ocean.

The study of heterotrophic protists in the ocean is still in its early stages, compared to other microorganisms such as bacteria, archaea, and photoautotrophic protists. Labyrinthulomycetes protists (LP) are a type of unicellular protists that are widely distributed in global waters and have the potential to produce high-value products. In this study, the abundance, diversity, and community structure of LP in the coastal zone of Hainan Island in the South China Sea were investigated through quantitative PCR and high-throughput sequencing. The results showed that LP abundance varied by location and depth, with the highest levels (37.3 × 10³ copies/L) found in the middle layer offshore and the lowest (0.386 × 10³ copies/L) in the bottom layer offshore. The middle layer (chlorophyll maximum layer) had higher LP abundance both inshore and offshore than the surface and bottom layers. Interestingly, the highest LP richness and diversity was found in the inshore bottom. There was a significant difference in LP abundance between the offshore surface and bottom layers. The LP community was dominated by the genus Aplanochytrium, and four different ecotypes were identified. Additionally, the genus Aurantiochytrium had different cooperative and competitive strategies with bacteria in different habitats. This study sheds light on the abundance and community structure of LP in the coastal zone of Hainan Island, explores the potential interactions between LP and bacterial populations, and raises questions about the potential differentiation of LP ecotypes.