Comparative metatranscriptomic profiling and microRNA sequencing to reveal active metabolic pathways associated with a dinoflagellate bloom Liying Yu a,1 , Yaqun Zhang a,b,1 , Meizhen Li a , Cong Wang a , Xin Lin a , Ling Li a , Xinguo Shi a,c , Chentao Guo a , Senjie Lin a,d, ⁎ a State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China b Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China c College of Biological Science and Engineering, Fuzhou University, Fujian 350116, China d Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA HIGHLIGHTS • Nutrient-addition bioassays showed that none of phosphate, nitrate and trace metal nutrients was limited for the growth of phytoplankton. • P. donghaiense highly expressed genes related to nutrient uptake, phagotrophy, energy metabolism and carbohydrate metabolism during the bloom. • Many genes in P. donghaiense were up- regulated at night, including phagotrophy and environmental com- munication genes, and showed active expression in mitosis. • Eight microbial defense genes were up- regulated in the bloom. • Seventy-six P. donghaiense microRNA were identified, and their target genes strongly regulated amino acid metabo- lism in the bloom. GRAPHICAL ABSTRACT abstract article info Article history: Received 10 July 2019 Received in revised form 5 September 2019 Accepted 5 September 2019 Available online 06 September 2019 Editor: Frederic Coulon Harmful algal blooms (HABs) have increased as a result of global climate and environmental changes, exerting increasing impacts on the aquatic ecosystem, coastal economy, and human health. Despite great research efforts, our understanding on the drivers of HABs is still limited in part because HAB species' physiology is difficult to probe in situ. Here, we used molecular ecological analyses to characterize a dinoflagellate bloom at Xiamen Har- bor, China. Prorocentrum donghaiense was identified as the culprit, which nutrient bioassays showed were not nutrient-limited. Metatranscriptome profiling revealed that P. donghaiense highly expressed genes related to N- and P-nutrient uptake, phagotrophy, energy metabolism (photosynthesis, oxidative phophorylation, and rho- dopsin) and carbohydrate metabolism (glycolysis/gluconeogenesis, TCA cycle and pentose phosphate) during the bloom. Many genes in P. donghaiense were up-regulated at night, including phagotrophy and environmental communication genes, and showed active expression in mitosis. Eight microbial defense genes were up- regulated in the bloom compared with previously analyzed laboratory cultures. Furthermore, 76 P. donghaiense Keywords: Dinoflagellate bloom Prorocentrum donghaiense Metatranscriptome microRNA sequencing Science of the Total Environment 699 (2020) 134323 ⁎ Corresponding author at: Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA. E-mail address: senjie.lin@uconn.edu (S. Lin). 1 These authors contributed equally to this work. https://doi.org/10.1016/j.scitotenv.2019.134323 0048-9697/© 2018 Elsevier B.V. All rights reserved. Contents lists available at ScienceDirect Science of the Total Environment journal homepage: www.elsevier.com/locate/scitotenv