A machine-learning approach to modeling picophytoplankton abundances in the South China Sea

Picophytoplankton, the smallest phytoplankton (<3 micron), contribute significantly to primary production in the oligotrophic South China Sea. To improve our ability to predict picophytoplankton abundances in the South China Sea and infer the underlying mechanisms, we compared four machine learning algorithms to estimate the horizontal and vertical distributions of picophytoplankton abundances. The inputs of the algorithms include spatiotemporal (longitude, latitude, sampling depth and date) and environmental variables (sea surface temperature, chlorophyll, and light). The algorithms were fit to a dataset of 2442 samples collected from 2006 to 2012. We find that the Boosted Regression Trees (BRT) gives the best prediction performance with R2 ranging from 77% to 85% for Chl a concentration and abundances of three picophytoplankton groups. The model outputs confirm that temperature and light play important roles in affecting picophytoplankton distribution. Prochlorococcus, Synechococcus, and picoeukaryotes show decreasing preference to oligotrophy. These insights are reflected in the vertical patterns of Chl a and picoeukaryotes that form subsurface maximal layers in summer and spring, contrasting with those of Prochlorococcus and Synechococcus that are most abundant at surface. Our forecasts suggest that, under the “business-as-usual” scenario, total Chl a will decrease but Prochlorococcus abundances will increase significantly to the end of this century. Synechococcus abundances will also increase, but the trend is only significant in coastal waters. Our study has advanced the ability of predicting picophytoplankton abundances in the South China Sea and suggests that BRT is a useful machine learning technique for modelling plankton distribution

Responses of marine phytoplankton communities to environmental changes: New insights from a niche classification scheme.

Predicting changes of phytoplankton communities in response to global warming is one of the challenges of ecological forecasting. One of the constraints is the paucity of general principles applicable to community ecology. Based on a synecological analysis of a decadal-scale database, we created a niche habitat classification scheme relating nine phytoplankton groups to fifteen statistically refined realized niches comprised of three niche dimensions: temperature, irradiance, and nitrate concentrations. The niche scheme assigned the nine phytoplankton groups to three types of niches: a cold type, a warm type, and a type associated with high irradiance and high nitrate concentrations. The fact that phytoplankton groups in cold niches were governed by irradiance and those in warm niches by nitrate is consistent with general ecological theories, but the fact that diatoms were the only dominant group in high-irradiance, high-nitrate niches challenges the idea based on autecological studies that diatoms are generally better adapted to low-irradiance, high-nutrient conditions. When combined with an irradiance model, the niche scheme revealed that photoinhibition of Prochlorococcus, which is predicted from autecological studies, is a function of temperature. We used the niche scheme to predict the responses of phytoplankton communities to environmental changes due to seawater warming and eutrophication. The results of the study suggest that a synecological analysis of large databases from field studies facilitates identification of general principles of community ecology that can be used to forecast responses of biological communities to environmental changes

Responses of marine phytoplankton communities to environmental changes : new insights from a niche classification scheme

Predicting changes of phytoplankton communities in response to global warming is one of the challenges of ecological forecasting. One of the constraints is the paucity of general principles applicable to community ecology. Based on a synecological analysis of a decadal-scale database, we created a niche habitat classification scheme relating nine phytoplankton groups to fifteen statistically refined realized niches comprised of three niche dimensions: temperature, irradiance, and nitrate concentrations. The niche scheme assigned the nine phytoplankton groups to three types of niches: a cold type, a warm type, and a type associated with high irradiance and high nitrate concentrations. The fact that phytoplankton groups in cold niches were governed by irradiance and those in warm niches by nitrate is consistent with general ecological theories, but the fact that diatoms were the only dominant group in high-irradiance, high-nitrate niches challenges the idea based on autecological studies that diatoms are generally better adapted to low-irradiance, high-nutrient conditions. When combined with an irradiance model, the niche scheme revealed that photoinhibition of Prochlorococcus, which is predicted from autecological studies, is a function of temperature. We used the niche scheme to predict the responses of phytoplankton communities to environmental changes due to seawater warming and eutrophication. The results of the study suggest that a synecological analysis of large databases from field studies facilitates identification of general principles of community ecology that can be used to forecast responses of biological communities to environmental changes

Integrated Space-Time Dataset Reveals High Diversity and Distinct Community Structure of Ciliates in Mesopelagic Waters of the Northern South China Sea.

Little is known about diversity distribution and community structure of ciliates in mesopelagic waters, especially how they are related to spatial and temporal changes. Here, an integrative approach, combining high-throughput cDNA sequencing and quantitative protargol stain, was used to analyze ciliate communities collected temporally along a transect from coastal to oceanic regions at depths ranging from the surface to 1000 m. The mesopelagic zone exhibited comparable alpha diversity to surface water which was consistent over temporal variation, with high diversity occurring at the interface with the euphotic zone. Comparison with the northeastern and the western Pacific Ocean revealed consistency of this vertical distribution of ciliates across oceanic basins. Mesopelagic ciliates harbored distinct community structure without significant seasonal differences, with the vertical variations driven largely by members of the classes Spirotrichea and Oligohymenophorea. Operational taxonomic units (OTUs) affiliated with Scuticociliatia, Astomatida and Apostomatida, members of which are known to be bacterivorous and/or commensal/parasitic species, were more abundant in mesopelagic waters than above, implying they are an important component of food webs in the mesopelagic zone. A combination of depth, geographic distance and environment shaped the ciliate communities, with depth being the most influential factor. Phylogenetic null modeling analysis further indicated that 57.1 and 33.3% of mesopelagic community variation was governed by dispersal limitation and heterogeneous selection, respectively, probably due to the marked biochemical and physical gradients down the water column. This suggests that ciliate community structure in the mesopelagic zone is mainly controlled by stochastic processes. Collectively, this study reports mesopelagic ciliates exhibited high diversity and distinct community structure across spatiotemporal scales and informs the processes mediating ciliate assembly in the mesopelagic zone. These should be fully considered in future studies to build a more comprehensive understanding of mesopelagic microbial assemblages

The impact of giant jellyfish Nemopilema nomurai blooms on plankton communities in a temperate marginal sea

Abstract(#br)This study focused on the bloom-developing process of the giant jellyfish, Nemopilema nomurai , on phytoplankton and microzooplankton communities. Two repeated field observations on the jellyfish bloom were conducted in June 2012 and 2014 in the southern Yellow Sea where blooms of N . nomurai were frequently observed. We demonstrated that the bloom was made up of two stages, namely the developing stage and the mature stage. Total chlorophyll a increased and the concentrations of inorganic nutrients decreased during the developing stage, while both concentrations maintained stable and at low levels during the mature stage. Our analysis revealed that phosphate excreted by growing N . nomurai promoted the growth of phytoplankton at the developing stage. At the mature stage, size compositions of microzooplankton were altered and tended to be smaller via a top-down process, while phytoplankton compositions, affected mainly through a bottom-up process, shifted to be less diatoms and cryptophytes but more dinoflagellates

Comparison of photosynthetic pigments and phytoplankton assemblages in two types of coastal regions in Southeast Asia-Indonesian Throughflow and river estuary

Water samples were collected in order to study the spatial variation of photosynthetic pigments and phytoplankton community composition in the Lembeh Strait (Indonesia) and the Kelantan River Estuary (Malaysia) during July and August 2016, respectively. Phytoplankton photosynthetic pigments were detected using high performance liquid chromatography combining with the CHEMTAX software to confirm the Chl a biomass and community composition. The Chl a concentration was low at surface in the Lembeh Strait, which it was 0.580–0.682 μg/L, with the average (0.620±0.039) μg/L. Nevertheless, the Chl a concentration fluctuated violently at surface in the Kelantan River Estuary, in which the biomass was 0.299–3.988 μg/L, with the average (0.922± 0.992) μg/L. The biomass at bottom water was higher than at surface in the Kelantan River Estuary, in which the Chl a concentration was 0.704–2.352 μg/L, with the average (1.493±0.571) μg/L. Chl b, zeaxanthin and fucoxanthin were three most abundant pigments in the Lembeh Strait. As a consequence, phytoplankton community composition was different in the two study areas. In the Lembeh Strait, prasinophytes (26.48%±0.83%) and Synechococcus (25.73%±4.13%) occupied ~50% of the Chl a biomass, followed by diatoms (20.49%±2.34%) and haptophytes T8 (15.13%±2.42%). At surface water in the Kelantan River Estuary, diatoms (58.53%±18.44%) dominated more than half of the phytoplankton biomass, followed by Synechococcus (27.27%±14.84%) and prasinophytes (7.00%±4.39%). It showed the similar status at the bottom water in the Kelantan River Estuary, where diatoms, Synechococcus and prasinophytes contributed 64.89%±15.29%, 16.23%±9.98% and 8.91%±2.62%, respectively. The different phytoplankton community composition between the two regions implied that the bottom up control affected the phytoplankton biomass in the Lembeh Strait where the oligotrophic water derived from the West Pacific Ocean. The terrigenous nutrients supplied the diatoms growing, and pico-phytoplankton was grazed through top down control in the Kelantan River Estuary

Linkages between bacterial community and extracellular enzyme activities crossing a coastal front

Exploring the responses of microbial communities and their functions to marine frontal systems are the foci of marine ecologists. However, most of the existing studies have focused on only microbial communities or their functions. The relationships between microbial communities and their functions across coastal fronts therefore remain unclear. Here we studied a coastal front in the Taiwan Strait during late spring and examined the bacterial community structure, extracellular enzymatic activity (EEA), and their linkages. The results showed that the coastal front strongly delineated zones of bacterial community composition and diversity and functioned as a transitional zone rather than a hotspot between the coastal water and offshore water. Co-occurrence network analysis indicated that the interaction of bacterial communities was much weaker in the frontal zone than in the water masses on both sides. The suggestion was that the highly fluctuating environment in the frontal zone reduced the complexity and stability of the bacterial co-occurrence network. The activities of β-glucosidase (BGA) and leucine aminopeptidase (LAPA) were as high in the frontal zone as in the coastal water and much higher than those in offshore waters. We therefore suggest that, despite obvious shifts in the bacterial community structure in the frontal zone, the bacterial community was able to maintain its ability to hydrolyze organic substrates via functional redundancy. The composition of key microbial assemblies differed among the three water masses, and the relative abundance of module 2 in the frontal zone was positively correlated with BGA and LAPA. The indication was that changing the bacterial assemblage was the mechanism that made it possible for the bacterial community to maintain EEA in the frontal zone. Our results help to improve understanding on how bacterial community-function linkages vary in marine frontal systems