Yantao Liang

Complete genome sequence of the siphovirus Roseophage RDJLΦ 2 infecting Roseobacter denitrificans OCh114.

RDJLΦ2, a lytic phage that infects the marine bacterium Roseobacter denitrificans OCh114, one of the model organisms of the Roseobacter clade, was isolated. Here we report the overall genome architecture of RDJLΦ2. Morphological and genome analysis revealed that RDJLΦ2 is a siphovirus with a 63.5 kb genome that contains 76 putative gene products.

Horizontal and Vertical Distribution of Marine Virioplankton: A Basin Scale Investigation Based on a Global Cruise

Despite the fact that marine viruses have been increasingly studied in the last decade, there is little information on viral abundance and distribution on a global scale. In this study, we report on a global-scale survey covering the Pacific, Atlantic, and Indian Oceans on viral distribution using flow cytometry. Viruses were stained with the SYBR Green I, which targets only dsDNA viruses. The average viral abundance was 1.10±0.73×107 ml−1 in global surface oceans and decreased from the areas with high chlorophyll concentration (on average, 1.47±0.78×107 ml−1) to the oligotrophic subtropical gyres (on average, 6.34±2.18×106 ml−1). On a large-spatial-scale, viruses displayed significant relationships with both heterotrophic and autotrophic picoplankton abundance, suggesting that viral distribution is dependent on their host cell abundance. Our study provided a basin scale pattern of marine viral distributions and their relationship with major host cells, indicating that viruses play a significant role in the global marine ecosystem.

Estimating Primary Production of Picophytoplankton Using the Carbon-Based Ocean Productivity Model: A Preliminary Study

Picophytoplankton are acknowledged to contribute significantly to primary production (PP) in the ocean while now the method to measure PP of picophytoplankton (PPPico) at large scales is not yet well established. Although the traditional 14C method and new technologies based on the use of stable isotopes (e.g., 13C) can be employed to accurately measure in situ PPPico, the time-consuming and labor-intensive shortage of these methods constrain their application in a survey on large spatiotemporal scales. To overcome this shortage, a modified carbon-based ocean productivity model (CbPM) is proposed for estimating the PPPico whose principle is based on the group-specific abundance, cellular carbon conversion factor (CCF), and temperature-derived growth rate of picophytoplankton. Comparative analysis showed that the estimated PPPico using CbPM method is significantly and positively related (r2 = 0.53, P < 0.001, n = 171) to the measured 14C uptake. This significant relationship suggests that CbPM has the potential to estimate the PPPico over large spatial and temporal scales. Currently this model application may be limited by the use of invariant cellular CCF and the relatively small data sets to validate the model which may introduce some uncertainties and biases. Model performance will be improved by the use of variable conversion factors and the larger data sets representing diverse growth conditions. Finally, we apply the CbPM-based model on the collected data during four cruises in the Bohai Sea in 2005. Model-estimated PPPico ranged from 0.1 to 11.9, 29.9 to 432.8, 5.5 to 214.9, and 2.4 to 65.8 mg C m-2 d-1 during March, June, September, and December, respectively. This study shed light on the estimation of global PPPico using carbon-based production model.

Effects of temperature and photosynthetically active radiation on virioplankton decay in the western Pacific Ocean

In this study, we investigated virioplankton decay rates and their responses to changes in temperature and photosynthetically active radiation (PAR) in the western Pacific Ocean. The mean decay rates for total, high-fluorescence, and low-fluorescence viruses were 1.64 ± 0.21, 2.46 ± 0.43, and 1.57 ± 0.26% h−1, respectively. Higher temperatures and PAR increased viral decay rates, and the increases in the decay rates of low-fluorescence viruses were greater than those of high-fluorescence viruses. Our results revealed that low-fluorescence viruses are more sensitive to warming and increasing PAR than are high-fluorescence viruses, which may be related to differences in their biological characteristics, such as the density of packaged nucleic acid materials. Our study provided experimental evidence for the responses of natural viral communities to changes in global environmental factors (e.g., temperature and solar radiation).

Carbon sequestration processes and mechanisms in coastal mariculture environments in China

China is the global leader in mariculture production. Increasing sequestered marine carbon (also known as blue carbon) via mariculture activities is a promising approach for mitigating climate change and promoting the development of a low-carbon economy. Mariculture blue carbon is also considered an important component of China’s “sea granary”. In addition to shellfish and macroalgae yields, which represent carbon removed from mariculture environment, blue carbon also includes other important components, which have been largely neglected in the past, such as the carbon transformed by microbes, dissolved organic carbon (mainly referred to as recalcitrant dissolved organic carbon), and sedimentary particulate carbon. Hence, from different aspects, a comprehensive study on the formation processes and mechanisms of carbon sequestration is of great significance for comprehensively unveiling the carbon sequestration capability in coastal mariculture environment, which will contribute to the sustainable development of the fishery economy and construction of an ecological civilization. Moreover, it may add significant economic benefits to the future carbon-trading market.

Distributions and relationships of virio- and picoplankton in the epi-, meso- and bathypelagic zones of the Western Pacific Ocean

&NA; Virio‐ and picoplankton mediate important biogeochemical processes and the environmental factors that regulate their dynamics, and the virus–host interactions are incompletely known, especially in the deep sea. Here we report on their distributions and relationships with environmental factors at 21 stations covering a latitudinal range (2–23° N) in the Western Pacific Ocean. This region is characterized by a complex western boundary current system. Synechococcus, autotrophic picoeukaryotes, heterotrophic prokaryotes and virus‐like particles (VLPs) were high (<2.4 × 102–6.3 × 104, <34–2.8 × 103, 3.9 × 104–1.3 × 106 cells mL−1 and 5.1 × 105–2.7 × 107 mL−1, respectively), and Prochlorococcus were low (<2.3 × 102–1.0 × 105 cells mL−1) in the Luzon Strait and the four most southerly stations, where upwelling occurs. Covariations in the abundances of VLPs with heterotrophic and autotrophic picoplankton, and their correlation (i.e. r2 = 0.63 and 0.52, respectively) suggested a strong host dependence in the epi‐ and mesopelagic zones. In the bathypelagic zone, only abiotic factors significantly influenced VLPs abundance variation (r2 = 0.12). This study shows that the dynamics of virio‐ and picoplankton in this Western Pacific are controlled by suite of complex and depth‐dependent relationship among physical and biological factors that in turn link the physical hydrography of the western boundary current system with microbial‐mediated biogeochemical processes.

Carbon pools and fluxes in the China Seas and adjacent oceans

The China Seas include the South China Sea, East China Sea, Yellow Sea, and Bohai Sea. Located off the Northwestern Pacific margin, covering 4700000 km2 from tropical to northern temperate zones, and including a variety of continental margins/basins and depths, the China Seas provide typical cases for carbon budget studies. The South China Sea being a deep basin and part of the Western Pacific Warm Pool is characterized by oceanic features; the East China Sea with a wide continental shelf, enormous terrestrial discharges and open margins to the West Pacific, is featured by strong cross-shelf materials transport; the Yellow Sea is featured by the confluence of cold and warm waters; and the Bohai Sea is a shallow semi-closed gulf with strong impacts of human activities. Three large rivers, the Yangtze River, Yellow River, and Pearl River, flow into the East China Sea, the Bohai Sea, and the South China Sea, respectively. The Kuroshio Current at the outer margin of the Chinese continental shelf is one of the two major western boundary currents of the world oceans and its strength and position directly affect the regional climate of China. These characteristics make the China Seas a typical case of marginal seas to study carbon storage and fluxes. This paper systematically analyzes the literature data on the carbon pools and fluxes of the Bohai Sea, Yellow Sea, East China Sea, and South China Sea, including different interfaces (land-sea, sea-air, sediment-water, and marginal sea-open ocean) and different ecosystems (mangroves, wetland, seagrass beds, macroalgae mariculture, coral reefs, euphotic zones, and water column). Among the four seas, the Bohai Sea and South China Sea are acting as CO2 sources, releasing about 0.22 and 13.86–33.60 Tg C yr−1 into the atmosphere, respectively, whereas the Yellow Sea and East China Sea are acting as carbon sinks, absorbing about 1.15 and 6.92–23.30 Tg C yr−1 of atmospheric CO2, respectively. Overall, if only the CO2 exchange at the sea-air interface is considered, the Chinese marginal seas appear to be a source of atmospheric CO2, with a net release of 6.01–9.33 Tg C yr−1, mainly from the inputs of rivers and adjacent oceans. The riverine dissolved inorganic carbon (DIC) input into the Bohai Sea and Yellow Sea, East China Sea, and South China Sea are 5.04, 14.60, and 40.14 Tg C yr−1, respectively. The DIC input from adjacent oceans is as high as 144.81 Tg C yr−1, significantly exceeding the carbon released from the seas to the atmosphere. In terms of output, the depositional fluxes of organic carbon in the Bohai Sea, Yellow Sea, East China Sea, and South China Sea are 2.00, 3.60, 7.40, and 5.92 Tg C yr−1, respectively. The fluxes of organic carbon from the East China Sea and South China Sea to the adjacent oceans are 15.25–36.70 and 43.93 Tg C yr−1, respectively. The annual carbon storage of mangroves, wetlands, and seagrass in Chinese coastal waters is 0.36–1.75 Tg C yr−1, with a dissolved organic carbon (DOC) output from seagrass beds of up to 0.59 Tg C yr−1. Removable organic carbon flux by Chinese macroalgae mariculture account for 0.68 Tg C yr−1 and the associated POC depositional and DOC releasing fluxes are 0.14 and 0.82 Tg C yr−1, respectively. Thus, in total, the annual output of organic carbon, which is mainly DOC, in the China Seas is 81.72–104.56 Tg C yr−1. The DOC efflux from the East China Sea to the adjacent oceans is 15.00–35.00 Tg C yr−1. The DOC efflux from the South China Sea is 31.39 Tg C yr−1. Although the marginal China Seas seem to be a source of atmospheric CO2 based on the CO2 flux at the sea-air interface, the combined effects of the riverine input in the area, oceanic input, depositional export, and microbial carbon pump (DOC conversion and output) indicate that the China Seas represent an important carbon storage area.

Impacts of maricultural activities on characteristics of dissolved organic carbon and nutrients in a typical raft-culture area of the Yellow Sea, North China

Ailian Bay is an integrated multi-trophic aquaculture bay with approximately 60 years maricultural activities in North China. The floating raft culture of kelp and shellfish is the unique mariculture mode. In this study, the impacts of intensive mariculture activities on seasonal carbon and nutrient dynamics in Ailian Bay were systematically analysed via seasonal surveys between 2015 and 2016. The dissolved inorganic nitrogen and silicon reached the maximum concentrations during summer, which were mainly attributed to the release of shellfish metabolic by-products and their filter-feeding effects on diatoms. Dissolved organic carbon (DOC) concentrations were significantly elevated when kelps were rotting in summer and kelp seeding were occurring in winter. Meanwhile, the fluorescence intensity of humic-like chromophoric dissolved organic matter was relatively high in kelp mariculture zone. As most humic-like DOC are potentially refractory substances, we propose that kelp mariculture would contribute importantly to the increase of refractory DOC pool in oceans.

Insight Into the Pico- and Nano-Phytoplankton Communities in the Deepest Biosphere, the Mariana Trench

As photoautotrophs, phytoplankton are generally present in the euphotic zone of the ocean, however, recently healthy phytoplankton cells were found to be also ubiquitous in the dark deep sea, i.e., at water depths between 2000 and 4000 m. The distributions of phytoplankton communities in much deeper waters, such as the hadal zone, are unclear. In this study, the vertical distribution of the pico- and nano-phytoplankton (PN) communities from the surface to 8320 m, including the epipelagic, mesopelagic, bathypelagic, and hadal zones, were investigated via both 18S and p23S rRNA gene analysis in the Challenger Deep of the Mariana Trench. The results showed that Dinoflagellata, Chrysophyceae, Haptophyta, Chlorophyta, Prochloraceae, Pseudanabaenaceae, Synechococcaceae, and Eustigmatophyceae, etc., were the predominant PN in the Mariana Trench. Redundancy analyses revealed that depth, followed by temperature, was the most important environmental factors correlated with vertical distribution of PN community. In the hadal zone, the PN community structure was considerably different from those in the shallower zones. Some PN communities, e.g., Eustigmatophyceae and Chrysophyceae, which have the heterotrophic characteristics, were sparse in shallower waters, while they were identified with high relative abundance (94.1% and 20.1%, respectively) at the depth of 8320 m. However, the dinoflagellates and Prochloraceae Prochlorococcus were detected throughout the entire water column. We proposed that vertical sinking, heterotrophic metabolism, and/or the transition to resting stage of phytoplankton might contribute to the presence of phytoplankton in the hadal zone. This study provided insight into the PN community in the Mariana Trench, implied the significance of phytoplankton in exporting organic matters from the euphotic to the hadal zone, and also hinted the possible existence of some undetermined energy metabolism (e.g., heterotrophy) of phytoplankton making themselves adapt and survive in the hadal environment.

Stellar populations of local infrared-selected galaxies

The stellar populations of 849 local infrared-selected galaxies from SDSS and IRAS (including 419 star-forming galaxies, 326 composite galaxies, 35 Seyfert 2s, and 69 LINERs in 4 spectral classes) are studied by using STARLIGHT. Among the 4 spectral classes, the importance of young populations decreases from star-forming, composite, Seyfert 2 to LINER; and Seyfert 2 and LINER are more metal-rich; ULIGs (ultra luminous infrared galaxies) & LIGs present the youngest populations among 3 infrared luminosity bins; and normal galaxies are more metal-rich. The dominant contributors to masses are all old populations.