Data_Sheet_1_Picophytoplankton in the West Pacific Ocean: A Snapshot.docx

Marine picophytoplankton have crucial ecological value and make an important contribution to marine primary productivity. While biomass of phytoplankton in general is projected to decline as a result of global warming, picophytoplankton will likely dominate in the future oceans due to their growth advantages in an oligotrophic environment. To better understand the biography of picophytoplankton, we undertook a comprehensive study of the distribution patterns of picophytoplankton, carbon biomass, and Chl a concentrations, etc. based on large-scale sampling in the tropical Western Pacific Ocean. In terms of cellular abundance, Prochlorococcus was the most abundant group (averaging [1.03 ± 0.40] × 104 cells/mL), followed by Synechococcus (averaging [1.31 ± 1.22] × 103 cells/mL) and then picoeucaryote (averaging [4.83 ± 2.84] × 102 cells/mL). The picophytoplankton size-fractionated chlorophyll a (Pico-Chl a) accounted for about 30% of the total Chl a, with Prochlorococcus and picoeukaryotes contributing 41 and 35%, respectively, of the Pico-Chl a-normalized carbon biomass, indicating the ecological importance of picophytoplankton as the primary producers. In terms of biogeographic distribution, the picophytoplankton communities exhibited contrasting patterns. The surface distribution of Prochlorococcus and Synechococcus was concentrated in the low latitude of the 142°E section, while picoeucaryote was more abundant near the 130°E and equator sections. Synechococcus was higher in the shallow layer at 25 m, and it was extremely tolerant of high-light irradiation, while Prochlorococcus and picoeucaryote were distributed in the deep Chlorophyll maximum layer (DCM) (about 100 m). From the carbon-to-Chlorophyll a ratios, which was derived from Prochlorococcus and picoeucaryote population groups, we found that the ratio varied widely, from 0.19 to 75.56, and was highest at the depth of 200 m. Of these, Prochlorococcus had an important contribution. The correlation analysis of environmental factors showed that Prochlorococcus, Synechococcus, and picoeucaryote were negatively correlated with nutrient concentration. We concluded that Prochlorococcus group was dominant in the WPO, both in abundance and biomass, and the various abiotic factors such as temperature, salinity, and nutrient concentrations were closely correlated with the spatial variation in the picophytoplankton community. These findings aid our understanding of how contrasting environmental conditions influence picophytoplankton community and the importance of picophytoplankton in contributing the carbon pool in the oligotrophic ocean.</p

Data_Sheet_1_Comparative Analysis of Total and Size-Fractionated Chlorophyll a in the Yellow Sea and Western Pacific.docx

Measurements of different size-fractionated chlorophyll a concentrations (Chl a) of phytoplankton assemblages in situ are vital for advancing our understanding of the phytoplankton size structure and thus the marine biogeochemical cycle. In the present study, we thus made a comparative analysis of total and size-fractionated Chl a in the Yellow Sea (YS) and Western Pacific (WP). Our results suggest that the total Chl a was highly variable in the YS (averaging ~1.02 μg L−1) and was generally 3–4-fold more than that in the WP (averaging ~0.30 μg L−1). The pico-sized Chl a had a significant contribution to total Chl a in the WP (range 75–88%), while the average contributions of the nano-sized and pico-sized Chl a to total Chl a in the YS were 47 and 38%, respectively, suggesting that a majority of the total Chl a in the YS was associated with nano- and picophytoplankton. Moreover, we applied the generalized additive models (GAMs) to explore the relationships between the total Chl a and that contained in each of the three size classes. These GAMs relationships suggested a continuum from picophytoplankton dominated waters to large phytoplankton (cells> 2 μm) domination with increasing Chl a. Finally, we made a comparison of the total Chl a obtained with GF/F filters and that measured from size-fractionated filtration and revealed that their corresponding concentrations are in good agreement, indicating the size-fractionated filtration had no effect on total Chl a determination.</p

Data_Sheet_1_Integrating Stochastic and Deterministic Process in the Biogeography of N2-Fixing Cyanobacterium Candidatus Atelocyanobacterium Thalassa.doc

UCYN-A is one of the most widespread and important marine diazotrophs. Its unusual distribution in both cold/warm and coastal/oceanic waters challenges current understanding about what drives the biogeography of diazotrophs. This study assessed the community assembly processes of the nitrogen-fixing cyanobacterium UCYN-A, developing a framework of assembly processes underpinning the microbial biogeography and diversity. High-throughput sequencing and a qPCR approach targeting the nifH gene were used to investigate three tropical seas: the Bay of Bengal, the Western Pacific Ocean, and the South China Sea. Based on the neutral community model and two types of null models calculating the β-nearest taxon index and the normalized stochasticity ratio, we found that stochastic assembly processes could explain 66–92% of the community assembly; thus, they exert overwhelming influence on UCYN-A biogeography and diversity. Among the deterministic processes, temperature and coastal/oceanic position appeared to be the principal environmental factors driving UCYN-A diversity. In addition, a close linkage between assembly processes and UCYN-A abundance/diversity/drivers can provide clues for the unusual global distribution of UCYN-A.</p

DataSheet_1_Exploring the key factors affecting the seasonal variation of phytoplankton in the coastal Yellow Sea.doc

Marine phytoplankton play crucial roles in the ocean’s biological pump and have great impacts on global biogeochemical cycles, yet the knowledge of environmental variables controlling their seasonal dynamics needs to be improved further, especially in the coastal ecosystems. In order to explore the determinants affecting the seasonal variation of phytoplankton, here we conducted three surveys during spring, summer and autumn along the coastal Yellow Sea. Among the phytoplankton community, 49 species of diatoms and 9 species of dinoflagellates were observed in spring, 63 species of diatoms and 10 species of dinoflagellates in summer, and 62 species of diatoms and 11 species of dinoflagellates in autumn. These results thus suggested that there were obvious differences in the number of species across the three seasons, of which diatoms were the most diverse group, followed by dinoflagellates. Additionally, diatoms were the most dominant species of the phytoplankton community and varied largely during different seasons. According to the redundancy analysis, the abundance of phytoplankton community was mainly related to water temperature and dissolved inorganic nitrogen (DIN) during the three seasons, indicating that water temperature and DIN could be the key factors controlling the seasonal variability of phytoplankton community along the coastal Yellow Sea. Also, significant correlations were observed between phytoplankton abundance and heavy metals Zn, As, and Hg during the three seasons, suggesting that these metals also had potential influences on the seasonal dynamics of phytoplankton community in the coastal Yellow Sea.</p

Data_Sheet_1_Highly Diverse Synechococcus Pigment Types in the Eastern Indian Ocean.pdf

Marine picocyanobacteria Synechococcus exhibit highly diverse pigment types (PTs) and hence possess great advantage to utilize different spectrum of light effectively and to occupy a wide range of light niches. In this study, we explored the diversity of Synechococcus PTs in the eastern Indian Ocean (EIO), surface water of Strait of Malacca (SSM), and coastal waters of Sri Lanka (SSL). All the detected PTs were phycourobilin (PUB) containing PT 3 and showed distinct distribution patterns. Low PUB PT 3a and partial chromatic acclimater PT 3eA dominated in coastal and shallow waters (SSM and SSL). In contrast, high PUB and chromatic acclimaters PT 3dA and PT 3c/3dB were mainly distributed in open ocean (EIO). PT 3dA and PT 3c/3dB occurred at similar depths of the lower euphotic layers but showed distinct distribution pattern that are partially exclusive, indicating that they compete with each other for the same light niche. Interestingly, the newly described PT 3f was detected with high relative abundances at all stations and particularly dominated in the upper euphotic layer in EIO, which was confirmed with PT-specific quantitative polymerase chain reaction (qPCR). The relative abundance of PT 3f was negatively correlated with nutrient level, implying that PT 3f is adapted to oligotrophic waters. Pronounced niche partition of different PTs was observed in the upper and lower layers of euphotic zone in EIO and SSM/SSL. Light, nutrients, and strong stratification may play important roles in the niche partition of different PTs. Further analysis about ecologically significant taxonomic units revealed high diversity within each PT at different locations, which provided insights for understanding specific PT with wide range of niches.</p

DataSheet_1_Phytoplankton community structure in the Western Subarctic Gyre of the Pacific Ocean during summer determined by a combined approach of HPLC-pigment CHEMTAX and metabarcoding sequencing.docx

The Western Subarctic Gyre (WSG) is a cyclonic upwelling gyre in the northwest subarctic Pacific, which is a region with a high concentration of nutrients but low chlorophyll. We investigated the community structure and spatial distribution of phytoplankton in this area by using HPLC-pigment CHEMTAX (a chemotaxonomy program) and metabarcoding sequencing during the summer of 2021. The phytoplankton community showed significant differences between the two methods. The CHEMTAX analyses identified eight major marine phytoplankton assemblages. Cryptophytes were the major contributors (24.96%) to the total Chl a, followed by pelagophytes, prymnesiophytes, diatoms, and chlorophytes. The eukaryotic phytoplankton OTUs obtained by metabarcoding were categorized into 149 species in 96 genera of 6 major groups (diatoms, prymnesiophytes, pelagophytes, chlorophytes, cryptophytes, and dinoflagellates). Dinoflagellates were the most abundant group, accounting for 44.74% of the total OTUs obtained, followed by cryptophytes and pelagophytes. Sixteen out of the 97 identified species were annotated as harmful algal species, and Heterocapsa rotundata, Karlodinium veneficum, and Aureococcus anophagefferens were assigned to the abundant group (i.e., at least 0.1% of the total reads). Nutrients were more important in shaping the phytoplankton community than temperature and salinity. The 24 stations were divided into southern and northern regions along 44°N according to the k-means method, with the former being dominated by high Chl a and low nutrients. Although different phytoplankton assemblages analyzed by the two methods showed various relationships with environmental factors, a common feature was that the dinoflagellate proportion showed a significantly negative correlation with low nutrients and a positive correlation with Chl a.</p

Data_Sheet_1_Assembly Processes and Co-occurrence Patterns of Abundant and Rare Bacterial Community in the Eastern Indian Ocean.doc

Microbial communities are composed of many rare species and a few abundant species. Considering the disproportionate importance of rare species for ecosystem functioning, it is important to understand the mechanisms structuring the rare and abundant components of a diverse community in response to environmental changes. Here, we used a 16S ribosomal RNA gene sequencing approach to investigate the bacterial community diversity in the Eastern Indian Ocean (EIO) during the monsoon and intermonsoon. We employed a phylogenetic null model and network analysis to evaluate the assembly processes and co-occurrence pattern of the microbial community. We found that higher bacterial diversity was detected in the intermonsoon with high temperature and low Chlorophyll a concentrations and N/P ratios. The balance between ecological deterministic processes and stochastic processes varied with seasons in the EIO. Meanwhile, conditionally rare taxa (CRT) were more likely modulated by variable selection processes than always rare taxa (ART) and abundant taxa (AT) (CRT > ART > AT). By linking assembly process and species co-occurrence, we demonstrated that the microbial co-occurrence associations tended to be higher when deterministic processes (mainly variable selection) were weaker. This negative trend was observed in rare species rather than abundant species. The linkage could enhance our understanding of the underlying mechanisms underpinning the generation and maintenance of microbial community diversity.</p