Improving the genome and proteome annotations of the marine model diatom using a proteogenomics strategy.

Unlabelled: Diatoms are unicellular eukaryotic phytoplankton that account for approximately 20% of global carbon fixation and 40% of marine primary productivity; thus, they are essential for global carbon biogeochemical cycling and climate. The availability of ten diatom genome sequences has facilitated evolutionary, biological and ecological research over the past decade; however, a complimentary map of the diatom proteome with direct measurements of proteins and peptides is still lacking. Here, we present a proteome map of the model marine diatom using high-resolution mass spectrometry combined with a proteogenomic strategy.

Composition and assembly of the bacterial community in the overlying waters of the coral reef of China's Xisha Islands.

Coral reef ecosystems are one of the most diverse and productive habitats on Earth. Microbes in the reef-overlying waters are key players in maintaining this ecosystem through regulating biogeochemical and ecological processes. However, the composition structure and assembly mechanism of microbial community in the reef-overlying waters remain largely unknown.

Diel Fluctuation Superimposed on Steady High CO Generates the Most Serious Cadmium Toxicity to Marine Copepods.

Coastal systems experience diel fluctuation of CO and cadmium (Cd) pollution; nevertheless, the effect of fluctuating CO on Cd biotoxicity is poorly known. In this study, we initially performed the isotopically enriched organism bioassay to label with Cd (5 μg/L) to determine the Cd accumulation rate constant () under ambient (400 μatm) and steadily (1000 μatm) and fluctuatingly elevated (1000 ± 600 μatm) CO conditions for 48 h. Next, was interactively subjected to the above CO exposures at Cd (control, 5, and 500 μg/L) treatments for 7 d.

Multi-Omics Profiling Reveals Resource Allocation and Acclimation Strategies to Temperature Changes in a Marine Dinoflagellate.

Temperature is a critical environmental factor that affects the cell growth of dinoflagellates and bloom formation. To date, the molecular mechanisms underlying the physiological responses to temperature variations are poorly understood. Here, we applied quantitative proteomic and untargeted metabolomic approaches to investigate protein and metabolite expression profiles of a bloom-forming dinoflagellate at different temperatures.

Metabolic Adaptation of a Globally Important Diatom following 700 Generations of Selection under a Warmer Temperature.

Diatoms, accounting for 40% of the marine primary production and 20% of global carbon dioxide fixation, are threatened by the ongoing ocean warming (OW). However, whether and how these ecologically important phytoplankton adapt to OW remains poorly unknown. Here, we experimentally examined the metabolic adaptation of a globally important diatom species () to OW at two elevated temperatures (24 and 28 °C compared with 20 °C) under short-term (∼300 generations) and long-term (∼700 generations) selection.

Metaexoproteomics Reveals Microbial Behavior in the Ocean's Interior.

The proteins present in the extracellular environment of cells, named the "exoproteome," are critical for microbial survival, growth, and interaction with their surroundings. However, little is known about microbial exoproteomes in natural marine environments. Here, we used a metaproteomic approach to characterize the exoprotein profiles (10 kDa-0.

Metabolic tuning of a stable microbial community in the surface oligotrophic Indian Ocean revealed by integrated meta-omics.

Unlabelled: Understanding the mechanisms, structuring microbial communities in oligotrophic ocean surface waters remains a major ecological endeavor. Functional redundancy and metabolic tuning are two mechanisms that have been proposed to shape microbial response to environmental forcing. However, little is known about their roles in the oligotrophic surface ocean due to less integrative characterization of community taxonomy and function.

Polysaccharide utilization by a marine heterotrophic bacterium from the SAR92 clade.

SAR92 is one of the few examples of a widely distributed, abundant oligotroph that can be cultivated to study pathways of carbon oxidation in ocean systems. Genomic evidence for SAR92 suggests that this gammaproteobacterium might be a primary consumer of polysaccharides in the epipelagic zone, its main habitat. Here, we investigated cell growth, polysaccharide utilization gene expression, and carbohydrate-active enzyme abundance of a culturable SAR92 strain, HTCC2207, grown with different polysaccharides.

Illuminating Key Microbial Players and Metabolic Processes Involved in the Remineralization of Particulate Organic Carbon in the Ocean's Twilight Zone by Metaproteomics.

The twilight zone (from the base of the euphotic zone to the depth of 1,000 m) is the major area of particulate organic carbon (POC) remineralization in the ocean, and heterotrophic microbes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity directly associated with POC remineralization in this chronically understudied realm. Here, we characterized the microbial community proteomes of POC samples collected from the twilight zone of three contrasting sites in the Northwest Pacific Ocean using a metaproteomic approach.

Metaproteomics Reveals Similar Vertical Distribution of Microbial Transport Proteins in Particulate Organic Matter Throughout the Water Column in the Northwest Pacific Ocean.

Solubilized particulate organic matter (POM) rather than dissolved organic matter (DOM) has been speculated to be the major carbon and energy sources for heterotrophic prokaryotes in the ocean. However, the direct evidence is still lack. Here we characterized microbial transport proteins of POM collected from both euphotic (75 m, deep chlorophyll maximum DCM, and 100 m) and upper-twilight (200 m and 500 m) zones in three contrasting environments in the northwest Pacific Ocean using a metaproteomic approach.

Metagenomic Analysis Reveals Microbial Community Structure and Metabolic Potential for Nitrogen Acquisition in the Oligotrophic Surface Water of the Indian Ocean.

Despite being the world's third largest ocean, the Indian Ocean is one of the least studied and understood with respect to microbial diversity as well as biogeochemical and ecological functions. In this study, we investigated the microbial community and its metabolic potential for nitrogen (N) acquisition in the oligotrophic surface waters of the Indian Ocean using a metagenomic approach. Proteobacteria and Cyanobacteria dominated the microbial community with an average 37.

Alcanivorax profundimaris sp. nov., a Novel Marine Hydrocarbonoclastic Bacterium Isolated from Seawater and Deep-Sea Sediment.

Two novel Alcanivorax-related strains, designated ST75FaO-1 and 521-1, were isolated from the seawater of the South China Sea and the deep-sea sediment of the West Pacific Ocean, respectively. Both strains are Gram-stain-negative, rod-shaped, and non-motile, and grow at 10-40 °C, pH 5.0-10.

sp. nov., isolated from phycosphere microbiota of the toxin-producing dinoflagellate .

A Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterium, named strain LZ-16-2, was isolated from the phycosphere microbiota of the paralytic shellfish poisoning toxin-producing marine dinoflagellate LZT09. Strain LZ-16-2 grew optimally at 28 °C at pH 6.5 and with 3 % (w/v) NaCl.

sp. nov., isolated from the toxigenic marine dinoflagellate LZT09.

A Gram-stain-negative, strictly aerobic, non-motile and non-pigmented spirillum, designated strain LZ-5, was isolated from cultures of the paralytic shellfish poisoning (PSP) toxin-producing marine dinoflagellate LZT09 collected from the Zhoushan sea area in the East China Sea during an algal bloom. The isolate grew at 4-40 °C (optimum, 25-33 °C) and pH 5.0-9.

The diversity and biogeography of microeukaryotes in the euphotic zone of the northwestern Pacific Ocean.

Microeukaryotes are the key ecosystem drivers mediating marine productivity, the food web and biogeochemical cycles. The northwestern Pacific Ocean (NWPO), as one of the world's largest oligotrophic regions, remains largely unexplored regarding diversity and biogeography of microeukaryotes. Here, we investigated the community composition and geographical distribution of microeukaryotes collected from the euphotic zone of three different regions in the NWPO using high-throughput sequencing of the 18S rRNA gene and quantified the contributions of environmental factors on the distributions of microeukaryotes.

Proteomic Response to Rising Temperature in the Marine Cyanobacterium Grown in Different Nitrogen Sources.

is one of the most important contributors to global primary productivity, and ocean warming is predicted to increase abundance and distribution of in the ocean. Here, we investigated molecular response of an oceanic strain WH8102 grown in two nitrogen sources (nitrate and urea) under present (25°C) and predicted future (28°C) temperature conditions using an isobaric tag (IBT)-based quantitative proteomic approach. Rising temperature decreased growth rate, contents of chlorophyll a, protein and sugar in the nitrate-grown cells, but only decreased protein content and significantly increased zeaxanthin content of the urea-grown cells.

Functional Differences in the Blooming Phytoplankton Heterosigma akashiwo and Prorocentrum donghaiense Revealed by Comparative Metaproteomics.

Phytoplankton blooms are natural phenomena in the ocean, which are the results of rapid cell growth of some phytoplankton species in a unique environment. However, little is known about the molecular events occurring during the bloom. Here, we compared metaproteomes of two phytoplankton and in the coastal East China Sea.

Quantitative proteomics reveals the key molecular events occurring at different cell cycle phases of the in situ blooming dinoflagellate cells.

Dinoflagellate blooms are the results of rapid cell proliferation governed by cell cycle, a highly-ordered series of events that culminates in cell division. However, little is known about cell cycle progression of the in situ bloom cells. Here, we compared proteomes of the in situ blooming cells of a dinoflagellate Prorocentrum donghaiense collected at different cell cycle phases.

Quantitative Proteomics Reveals Common and Specific Responses of a Marine Diatom to Different Macronutrient Deficiencies.

Macronutrients such as nitrogen (N), phosphorus (P), and silicon (Si) are essential for the productivity and distribution of diatoms in the ocean. Responses of diatoms to a particular macronutrient deficiency have been investigated, however, we know little about their common or specific responses to different macronutrients. Here, we investigated the physiology and quantitative proteomics of a diatom grown in nutrient-replete, N-, P-, and Si-deficient conditions.

Unraveling the molecular mechanism of the response to changing ambient phosphorus in the dinoflagellate Alexandrium catenella with quantitative proteomics.

Phosphorus (P) is a key macronutrient limiting cell growth and bloom formation of marine dinoflagellates. Physiological responses to changing ambient P have been investigated in dinoflagellates; however, the molecular mechanisms behind these responses remain limited. Here, we compared the protein expression profiles of a marine dinoflagellate Alexandrium catenella grown in inorganic P-replete, P-deficient, and inorganic- and organic-P resupplied conditions using an iTRAQ-based quantitative proteomic approach.

Bacterial Diversity and Nitrogen Utilization Strategies in the Upper Layer of the Northwestern Pacific Ocean.

Nitrogen (N) is a primary limiting nutrient for bacterial growth and productivity in the ocean. To better understand bacterial community and their N utilization strategy in different N regimes of the ocean, we examined bacterial diversity, diazotrophic diversity, and N utilization gene expressions in the northwestern Pacific Ocean (NWPO) using a combination of high-throughput sequencing and real-time qPCR methods. 521 and 204 different operational taxonomic units (OTUs) were identified in the 16s rRNA and nifH libraries from nine surface samples.

Metaproteomics reveals major microbial players and their metabolic activities during the blooming period of a marine dinoflagellate Prorocentrum donghaiense.

Interactions between bacteria and phytoplankton during bloom events are essential for both partners, which impacts their physiology, alters ambient chemistry and shapes ecosystem diversity. Here, we investigated the community structure and metabolic activities of free-living bacterioplankton in different blooming phases of a dinoflagellate Prorocentrum donghaiense using a metaproteomic approach. The Fibrobacteres-Chlorobi-Bacteroidetes group, Rhodobacteraceae, SAR11 and SAR86 clades contributed largely to the bacterial community in the middle-blooming phase while the Pseudoalteromonadaceae exclusively dominated in the late-blooming phase.

Metaproteomics of marine viral concentrates reveals key viral populations and abundant periplasmic proteins in the oligotrophic deep chlorophyll maximum of the South China Sea.

Viral concentrates (VCs), containing bioinformative DNA and proteins, have been used to study viral diversity, viral metagenomics and virus-host interactions in natural ecosystems. Besides viruses, VCs also contain many noncellular biological components including diverse functional proteins. Here, we used a shotgun proteomic approach to characterize the proteins of VCs collected from the oligotrophic deep chlorophyll maximum (DCM) of the South China Sea.