Institute of Oceanology

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster’s adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa. The sequencing and assembly of the highly polymorphic oyster genome through a combination of short reads and fosmid pooling, complemented with extensive transcriptome analysis of development and stress response and proteome analysis of the shell, provides new insight into oyster biology and adaptation to a highly changeable environment. Oysters are keystone species in estuarine ecology and among the most important aquaculture species worldwide. The sequencing and assembly of the genome of the Pacific oyster, Crassostrea gigas, are now reported. Comparisons with other genomes reveal an expansion of defence genes as an adaptation to life as a sessile species in the intertidal zone, a surprisingly complex pathway for shell formation and dramatic evolution of genes related to larval development, highlighting their adaptive significance for marine invertebrates.

Abstract Significant climate anomalies persist through the summer (June–August) after El Niño dissipates in spring over the equatorial Pacific. They include the tropical Indian Ocean (TIO) sea surface temperature (SST) warming, increased tropical tropospheric temperature, an anomalous anticyclone over the subtropical northwest Pacific, and increased mei-yu–baiu rainfall over East Asia. The cause of these lingering El Niño effects during summer is investigated using observations and an atmospheric general circulation model (GCM). The results herein indicate that the TIO warming acts like a capacitor anchoring atmospheric anomalies over the Indo–western Pacific Oceans. It causes tropospheric temperature to increase by a moist-adiabatic adjustment in deep convection, emanating a baroclinic Kelvin wave into the Pacific. In the northwest Pacific, this equatorial Kelvin wave induces northeasterly surface wind anomalies, and the resultant divergence in the subtropics triggers suppressed convection and the anomalous anticyclone. The GCM results support this Kelvin wave–induced Ekman divergence mechanism. In response to a prescribed SST increase over the TIO, the model simulates the Kelvin wave with low pressure on the equator as well as suppressed convection and the anomalous anticyclone over the subtropical northwest Pacific. An additional experiment further indicates that the north Indian Ocean warming is most important for the Kelvin wave and northwest Pacific anticyclone, a result corroborated by observations. These results have important implications for the predictability of Indo–western Pacific summer climate: the spatial distribution and magnitude of the TIO warming, rather than simply whether there is an El Niño in the preceding winter, affect summer climate anomalies over the Indo–western Pacific and East Asia.

Abstract Corrosion is a ubiquitous and costly problem for a variety of industries. Understanding and reducing the cost of corrosion remain primary interests for corrosion professionals and relevant asset owners. The present study summarises the findings that arose from the landmark “Study of Corrosion Status and Control Strategies in China”, a key consulting project of the Chinese Academy of Engineering in 2015, which sought to determine the national cost of corrosion and costs associated with representative industries in China. The study estimated that the cost of corrosion in China was approximately 2127.8 billion RMB (~ 310 billion USD), representing about 3.34% of the gross domestic product. The transportation and electronics industries were the two that generated the highest costs among all those surveyed. Based on the survey results, corrosion is a major and significant issue, with several key general strategies to reduce the cost of corrosion also outlined.

Inferences of population genetic structure are of great importance to the fields of ecology and evolutionary biology. The program structure has been widely used to infer population genetic structure. However, previous studies demonstrated that uneven sampling often leads to wrong inferences on hierarchical structure. The most widely used ΔK method tends to identify the uppermost hierarchy of population structure. Recently, four alternative statistics (medmedk, medmeak, maxmedk and maxmeak) were proposed, which appear to be more accurate than the previously used methods for both even and uneven sampling data. However, the lack of easy-to-use software limits the use of these appealing new estimators. Here, we developed a web-based user-friendly software structureselector to calculate the four appealing alternative statistics together with the commonly used Ln Pr(X|K) and ΔK statistics. structureselector accepts the result files of structure, admixture or faststructure as input files. It reports the "best" K for each estimator, and the results are available as HTML or tab separated tables. The program can also generate graphical representations for specific K, which can be easily downloaded from the server. The software is freely available at http://lmme.qdio.ac.cn/StructureSelector/.

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.

The oxidative stress imposed by reactive oxygen species (ROS) plays an important role in many chronic and degenerative diseases. As an important category of phytochemicals, phenolic compounds universally exist in plants, and have been considered to have high antioxidant ability and free radical scavenging capacity, with the mechanism of inhibiting the enzymes responsible for ROS production and reducing highly oxidized ROS. Therefore, phenolic compounds have attracted increasing attention as potential agents for preventing and treating many oxidative stress-related diseases, such as cardiovascular diseases, cancer, ageing, diabetes mellitus and neurodegenerative diseases. This review summarizes current knowledge of natural polyphenols, including resource, bioactivities, bioavailability and potential toxicity.

The El Niño-Southern Oscillation (ENSO), which originates in the Pacific, is the strongest and most well-known mode of tropical climate variability. Its reach is global, and it can force climate variations of the tropical Atlantic and Indian Oceans by perturbing the global atmospheric circulation. Less appreciated is how the tropical Atlantic and Indian Oceans affect the Pacific. Especially noteworthy is the multidecadal Atlantic warming that began in the late 1990s, because recent research suggests that it has influenced Indo-Pacific climate, the character of the ENSO cycle, and the hiatus in global surface warming. Discovery of these pantropical interactions provides a pathway forward for improving predictions of climate variability in the current climate and for refining projections of future climate under different anthropogenic forcing scenarios.

Abstract ENSO induces coherent climate anomalies over the Indo-western Pacific, but these anomalies outlast SST anomalies of the equatorial Pacific by a season, with major effects on the Asian summer monsoon. This review provides historical accounts of major milestones and synthesizes recent advances in the endeavor to understand summer variability over the Indo-Northwest Pacific region. Specifically, a large-scale anomalous anticyclone (AAC) is a recurrent pattern in post-El Ni˜no summers, spanning the tropical Northwest Pacific and North Indian oceans. Regarding the ocean memory that anchors the summer AAC, competing hypotheses emphasize either SST cooling in the easterly trade wind regime of the Northwest Pacific or SST warming in the westerly monsoon regime of the North Indian Ocean. Our synthesis reveals a coupled ocean–atmosphere mode that builds on both mechanisms in a two-stage evolution. In spring, when the northeast trades prevail, the AAC and Northwest Pacific cooling are coupled via wind–evaporation–SST feedback. The Northwest Pacific cooling persists to trigger a summer feedback that arises from the interaction of the AAC and North Indian Ocean warming, enabled by the westerly monsoon wind regime. This Indo-western Pacific ocean capacitor (IPOC) effect explains why El Ni˜no stages its last act over the monsoonal Indo-Northwest Pacific and casts the Indian Ocean warming and AAC in leading roles. The IPOC displays interdecadal modulations by the ENSO variance cycle, significantly correlated with ENSO at the turn of the 20th century and after the 1970s, but not in between. Outstanding issues, including future climate projections, are also discussed.

Advances in revolutionary technologies pose new challenges for human life; in response to them, global responsibility is pushing modern technologies toward greener pathways. Molecular imprinting technology (MIT) is a multidisciplinary mimic technology simulating the specific binding principle of enzymes to substrates or antigens to antibodies; along with its rapid progress and wide applications, MIT faces the challenge of complying with green sustainable development requirements. With the identification of environmental risks associated with unsustainable MIT, a new aspect of MIT, termed green MIT, has emerged and developed. However, so far, no clear definition has been provided to appraise green MIT. Herein, the implementation process of green chemistry in MIT is demonstrated and a mnemonic device in the form of an acronym, GREENIFICATION, is proposed to present the green MIT principles. The entire greenificated imprinting process is surveyed, including element choice, polymerization implementation, energy input, imprinting strategies, waste treatment, and recovery, as well as the impacts of these processes on operator health and the environment. Moreover, assistance of upgraded instrumentation in deploying greener goals is considered. Finally, future perspectives are presented to provide a more complete picture of the greenificated MIT road map and to pave the way for further development.

The outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 virus continually lead to worldwide human infections and deaths. Currently, there is no specific viral protein-targeted therapeutics. Viral nucleocapsid protein is a potential antiviral drug target, serving multiple critical functions during the viral life cycle. However, the structural information of SARS-CoV-2 nucleocapsid protein remains unclear. Herein, we have determined the 2.7 Å crystal structure of the N-terminal RNA binding domain of SARS-CoV-2 nucleocapsid protein. Although the overall structure is similar as other reported coronavirus nucleocapsid protein N-terminal domain, the surface electrostatic potential characteristics between them are distinct. Further comparison with mild virus type HCoV-OC43 equivalent domain demonstrates a unique potential RNA binding pocket alongside the β-sheet core. Complemented by in vitro binding studies, our data provide several atomic resolution features of SARS-CoV-2 nucleocapsid protein N-terminal domain, guiding the design of novel antiviral agents specific targeting to SARS-CoV-2.

Abstract Combined analyses of deep tow magnetic anomalies and International Ocean Discovery Program Expedition 349 cores show that initial seafloor spreading started around 33 Ma in the northeastern South China Sea (SCS), but varied slightly by 1–2 Myr along the northern continent‐ocean boundary (COB). A southward ridge jump of ∼20 km occurred around 23.6 Ma in the East Subbasin; this timing also slightly varied along the ridge and was coeval to the onset of seafloor spreading in the Southwest Subbasin, which propagated for about 400 km southwestward from ∼23.6 to ∼21.5 Ma. The terminal age of seafloor spreading is ∼15 Ma in the East Subbasin and ∼16 Ma in the Southwest Subbasin. The full spreading rate in the East Subbasin varied largely from ∼20 to ∼80 km/Myr, but mostly decreased with time except for the period between ∼26.0 Ma and the ridge jump (∼23.6 Ma), within which the rate was the fastest at ∼70 km/Myr on average. The spreading rates are not correlated, in most cases, to magnetic anomaly amplitudes that reflect basement magnetization contrasts. Shipboard magnetic measurements reveal at least one magnetic reversal in the top 100 m of basaltic layers, in addition to large vertical intensity variations. These complexities are caused by late‐stage lava flows that are magnetized in a different polarity from the primary basaltic layer emplaced during the main phase of crustal accretion. Deep tow magnetic modeling also reveals this smearing in basement magnetizations by incorporating a contamination coefficient of 0.5, which partly alleviates the problem of assuming a magnetic blocking model of constant thickness and uniform magnetization. The primary contribution to magnetic anomalies of the SCS is not in the top 100 m of the igneous basement.

Seasonal and interannual variations of summer upwelling off the South Vietnam coast and the offshore spread of cold water are investigated using a suite of new satellite measurements. In summer, as the southwesterly winds impinge on Annam Cordillera (a north‐south running mountain range on the east coast of Indochina) a strong wind jet occurs at its southern tip offshore east of Saigon, resulting in strong wind curls that are important for ocean upwelling off the coast. In July and August an anticyclonic ocean eddy develops to the southeast, advecting the cold coastal water offshore into the open South China Sea (SCS). The center of this cold filament is located consistently north of the wind speed maximum, indicating that open‐ocean upwelling helps to cool the ocean surface. Corroborating evidence for the cold filament is found in ocean color observations that reveal a collocated tongue of high chlorophyll concentration. The development of this cold filament disrupts the summer warming of the SCS and causes a pronounced semi‐annual cycle in SST. Moreover, the cold filament is an important player in interannual variability in the summer SCS. In 1998, the cold filament and mid‐summer cooling never took place, giving rise to a strong basin‐wide surface warming. Interannual SST variance has a local maximum over the climatological cold filament, and is much greater than the variance over the adjacent Indian and western Pacific Oceans. A cold filament index is constructed, which displays significant lagged correlation with SST in the eastern equatorial Pacific and Indian Oceans, indicative of a teleconnection from El Nino.

Time series of environmental measurements are essential for detecting, measuring and understanding changes in the Earth system and its biological communities. Observational series have accumulated over the past 2-5 decades from measurements across the world's estuaries, bays, lagoons, inland seas and shelf waters influenced by runoff. We synthesize information contained in these time series to develop a global view of changes occurring in marine systems influenced by connectivity to land. Our review is organized around four themes: (i) human activities as drivers of change; (ii) variability of the climate system as a driver of change; (iii) successes, disappointments and challenges of managing change at the sea-land interface; and (iv) discoveries made from observations over time. Multidecadal time series reveal that many of the world's estuarine-coastal ecosystems are in a continuing state of change, and the pace of change is faster than we could have imagined a decade ago. Some have been transformed into novel ecosystems with habitats, biogeochemistry and biological communities outside the natural range of variability. Change takes many forms including linear and nonlinear trends, abrupt state changes and oscillations. The challenge of managing change is daunting in the coastal zone where diverse human pressures are concentrated and intersect with different responses to climate variability over land and over ocean basins. The pace of change in estuarine-coastal ecosystems will likely accelerate as the human population and economies continue to grow and as global climate change accelerates. Wise stewardship of the resources upon which we depend is critically dependent upon a continuing flow of information from observations to measure, understand and anticipate future changes along the world's coastlines.

Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering ~1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture.

Abstract Errors of coupled general circulation models (CGCMs) limit their utility for climate prediction and projection. Origins of and feedback for tropical biases are investigated in the historical climate simulations of 18 CGCMs from phase 5 of the Coupled Model Intercomparison Project (CMIP5), together with the available Atmospheric Model Intercomparison Project (AMIP) simulations. Based on an intermodel empirical orthogonal function (EOF) analysis of tropical Pacific precipitation, the excessive equatorial Pacific cold tongue and double intertropical convergence zone (ITCZ) stand out as the most prominent errors of the current generation of CGCMs. The comparison of CMIP–AMIP pairs enables us to identify whether a given type of errors originates from atmospheric models. The equatorial Pacific cold tongue bias is associated with deficient precipitation and surface easterly wind biases in the western half of the basin in CGCMs, but these errors are absent in atmosphere-only models, indicating that the errors arise from the interaction with the ocean via Bjerknes feedback. For the double ITCZ problem, excessive precipitation south of the equator correlates well with excessive downward solar radiation in the Southern Hemisphere (SH) midlatitudes, an error traced back to atmospheric model simulations of cloud during austral spring and summer. This extratropical forcing of the ITCZ displacements is mediated by tropical ocean–atmosphere interaction and is consistent with recent studies of ocean–atmospheric energy transport balance.

Abstract El Niño induces a basin-wide increase in tropical Indian Ocean (TIO) sea surface temperature (SST) with a lag of one season. The north IO (NIO), in particular, displays a peculiar double-peak warming with the second peak larger in magnitude and persisting well through the summer. Motivated by recent studies suggesting the importance of the TIO warming for the Northwest Pacific and East Asian summer monsoons, the present study investigates the mechanisms for the second peak of the NIO warming using observations and general circulation models. This analysis reveals that internal air–sea interaction within the TIO is key to sustaining the TIO warming through summer. During El Niño, anticyclonic wind curl anomalies force a downwelling Rossby wave in the south TIO through Walker circulation adjustments, causing a sustained SST warming in the tropical southwest IO (SWIO) where the mean thermocline is shallow. During the spring and early summer following El Niño, this SWIO warming sustains an antisymmetric pattern of atmospheric anomalies with northeasterly (northwesterly) wind anomalies north (south) of the equator. Over the NIO as the mean winds turn into southwesterly in May, the northeasterly anomalies force the second SST peak that persists through summer by reducing the wind speed and surface evaporation. Atmospheric general circulation model experiments show that the antisymmetric atmospheric pattern is a response to the TIO warming, suggestive of their mutual interaction. Thus, ocean dynamics and Rossby waves in particular are important for the warming not only locally in SWIO but also on the basin-scale north of the equator, a result with important implications for climate predictability and prediction.

Reconstructing the genomes of bilaterian ancestors is central to our understanding of animal evolution, where knowledge from ancient and/or slow-evolving bilaterian lineages is critical. Here we report a high-quality, chromosome-anchored reference genome for the scallop Patinopecten yessoensis, a bivalve mollusc that has a slow-evolving genome with many ancestral features. Chromosome-based macrosynteny analysis reveals a striking correspondence between the 19 scallop chromosomes and the 17 presumed ancestral bilaterian linkage groups at a level of conservation previously unseen, suggesting that the scallop may have a karyotype close to that of the bilaterian ancestor. Scallop Hox gene expression follows a new mode of subcluster temporal co-linearity that is possibly ancestral and may provide great potential in supporting diverse bilaterian body plans. Transcriptome analysis of scallop mantle eyes finds unexpected diversity in phototransduction cascades and a potentially ancient Pax2/5/8-dependent pathway for noncephalic eyes. The outstanding preservation of ancestral karyotype and developmental control makes the scallop genome a valuable resource for understanding early bilaterian evolution and biology.

The application of biochar in the remediation of heavy metal contaminated soil has received increasing global attention during the past decade. Although there has been some review work on the mechanism of heavy metals stabilization by biochar, the effects and mechanisms of interaction between biochar and functional microbes such as heavy metal tolerant, adsorption and transformation microbial strains remains unclear. In this paper, maize biochar and a heavy metal-tolerant strain Pseudomonas sp. NT-2 were selected to investigate the dynamic effects and potential mechanisms of biochar and bacteria loaded biochar on the stabilization of Cd and Cu mixed contaminated soil by a 75-day pot experiment. The results showed that, compared to the single biochar amendment, the application of biochar inoculated with NT-2 strain at the rate of 5% significantly increased the soil pH at the initial stage of incubation, and followed by a slight decline to a neutral-alkaline range during the reaction. The addition of NT-2 loaded biochar could also significantly increase the proportion of residual fraction of Cd and Cu, thus reduce the proportion of exchangeable and carbonate bound species in the soil, which lead to the decreasing of plant and human bioavailability of the metal in the soil indicated by DTPA and simulated human gastric solution extraction (UBM), respectively. Finally, the application of bacterial loaded biochar also markedly enhanced soil urease and catalase activities during the later stage of the incubation, and improved soil microbial community at the end of incubation, which indicates a recovery of soil function after the metal stabilization. The research results may provide some new insights into the development of functional materials and technologies for the green and sustainable remediation of heavy metal contaminated soil by the combination of biochar and functional microorganisms.

Abstract Shifting electrochemical oxygen reduction reaction (ORR) via two‐electron pathway becomes increasingly crucial as an alternative/green method for hydrogen peroxide (H 2 O 2 ) generation. Here, the development of 2e − ORR catalysts in recent years is reviewed, in aspects of reaction mechanism exploration, types of high‐performance catalysts, factors to influence catalytic performance, and potential applications of 2e − ORR. Based on the previous theoretical and experimental studies, the underlying 2e − ORR catalytic mechanism is firstly unveiled, in aspect of reaction pathway, thermodynamic free energy diagram, limiting potential, and volcano plots. Then, various types of efficient catalysts for producing H 2 O 2 via 2e − ORR pathway are summarized. Additionally, the catalytic active sites and factors to influence catalysts’ performance, such as electronic structure, carbon defect, functional groups (O, N, B, S, F etc.), synergistic effect, and others (pH, pore structure, steric hindrance effect, etc.) are discussed. The H 2 O 2 electrogeneration via 2e − ORR also has various potential applications in wastewater treatment, disinfection, organics degradation, and energy storage. Finally, potential future directions and prospects in 2e − ORR catalysts for electrochemically producing H 2 O 2 are examined. These insights may help develop highly active/selective 2e − ORR catalysts and shape the potential application of this electrochemical H 2 O 2 producing method.

Abstract Two questions motivated this study: 1) Will meteorological droughts become more frequent and severe during the twenty-first century? 2) Given the projected global temperature rise, to what extent does the inclusion of temperature (in addition to precipitation) in drought indicators play a role in future meteorological droughts? To answer, we analyzed the changes in drought frequency, severity, and historically undocumented extreme droughts over 1981–2100, using the standardized precipitation index (SPI; including precipitation only) and standardized precipitation-evapotranspiration index (SPEI; indirectly including temperature), and under two representative concentration pathways (RCP4.5 and RCP8.5). As input data, we employed 103 high-resolution (0.44°) simulations from the Coordinated Regional Climate Downscaling Experiment (CORDEX), based on a combination of 16 global circulation models (GCMs) and 20 regional circulation models (RCMs). This is the first study on global drought projections including RCMs based on such a large ensemble of RCMs. Based on precipitation only, ~15% of the global land is likely to experience more frequent and severe droughts during 2071–2100 versus 1981–2010 for both scenarios. This increase is larger (~47% under RCP4.5, ~49% under RCP8.5) when precipitation and temperature are used. Both SPI and SPEI project more frequent and severe droughts, especially under RCP8.5, over southern South America, the Mediterranean region, southern Africa, southeastern China, Japan, and southern Australia. A decrease in drought is projected for high latitudes in Northern Hemisphere and Southeast Asia. If temperature is included, drought characteristics are projected to increase over North America, Amazonia, central Europe and Asia, the Horn of Africa, India, and central Australia; if only precipitation is considered, they are found to decrease over those areas.