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Virioplankton are a key component of the marine biosphere in maintaining diversity of microorganisms and stabilizing ecosystems. They also contribute greatly to nutrient cycles/cycling by releasing organic matter after lysis of hosts. In this study, we constructed the first global viral oceanography database (gVOD) by collecting 10 931 viral abundance (VA) data and 727 viral production (VP) data, along with host and relevant oceanographic parameters when available. Most VA data were obtained in the North Atlantic (32 %) and North Pacific (29 %) oceans, while the southeast Pacific and Indian oceans were quite undersampled. The VA in the global ocean was 1.17(±3.31)×107 particles mL−1. The lytic and lysogenic VP in the global ocean was 9.87(±24.16)×105 and 2.53(±8.64)×105 particlesmL-1h-1, respectively. Average VA in coastal oceans was higher than that in surface open oceans (3.61(±6.30)×107 versus 0.73(±1.24)×107 particles mL−1), while average VP in coastal and surface open oceans was close. Vertically, VA, lytic VP and lysogenic VP deceased from surface to deep oceans by about 1 order of magnitude. The total number of viruses in the global ocean estimated by bin-averaging and the random forest method was 1.56×1030 and 1.49×1030 particles, leading to an estimate of global ocean viral biomass at 35.9 and 34.4 Tg C, respectively. We expect that the gVOD will be a fundamental and very useful database for laboratory, field and modeling studies in marine ecology and biogeochemistry. The full gVOD database (Xie et al., 2020) is stored in PANGAEA (https://doi.org/10.1594/PANGAEA.915758).

The niche differentiation of ammonia and nitrite oxidizers is controversial because they display disparate patterns in estuarine, coastal, and oceanic regimes. We analyzed diversity and abundance of ammonia-oxidizing archaea (AOA) and β-proteobacteria (AOB), nitrite-oxidizing bacteria (NOB), and nitrification rates to identify their niche differentiation along a salinity gradient from the Pearl River estuary to the South China Sea. AOA were generally more abundant than β-AOB; however, AOB more clearly attached to particles compared with AOA in the upper reaches of the Pearl River estuary. The NOB Nitrospira had higher abundances in the upper and middle reaches of the Pearl River estuary, while Nitrospina was dominant in the lower estuary. In addition, AOB and Nitrospira could be more active than AOA and Nitrospina since significantly positive correlations were observed between their gene abundance and the nitrification rate in the Pearl River estuary. There is a significant positive correlation between ammonia and nitrite oxidizer abundances in the hypoxic waters of the estuary, suggesting a possible coupling through metabolic interactions between them. Phylogenetic analysis further revealed that the AOA and NOB Nitrospina subgroups can be separated into different niches based on their adaptations to substrate levels. Water mass mixing is apparently crucial in regulating the distribution of nitrifiers from the estuary to open ocean. However, when eliminating water mass effect, the substrate availability and the nitrifiers' adaptations to substrate availability via their ecological strategies essentially determine their niche differentiation.

Corners play an important role on image processing, while it is difficult to detect reliable and repeatable corners in SAR images due to the complex property of SAR sensors. In this paper, we propose a fast and novel corner detection method for SAR imagery. First, a local processing window is constructed for each point. We use the local mean of a 3 x 3 mask to represent a single point, which is weighted by a Gaussian template. Then the candidate point is compared with 16 surrounding points in the processing window. Considering the multiplicative property of speckle noise, the similarity measure between the center point and the surrounding points is calculated by the ratio of their local means. If there exist more than M continuous points are different from the center point, then the candidate point is labelled as a corner point. Finally, a selection strategy is implemented by ranking the corner score and employing the non-maxima suppression method. Extreme situations such as isolated bright points are also removed. Experimental results on both simulated and real-world SAR images show that the proposed detector has a high repeatability and a low localization error, compared with other state-of-the-art detectors.

This paper reviews progress on understanding biological carbon sequestration in the ocean with special reference to the microbial formation and transformation of recalcitrant dissolved organic carbon (RDOC), the microbial carbon pump (MCP). We propose that RDOC is a concept with a wide continuum of recalcitrance. Most RDOC compounds maintain their levels of recalcitrance only in a specific environmental context (RDOCt). The ocean RDOC pool also contains compounds that may be inaccessible to microbes due to their extremely low concentration (RDOCc). This differentiation allows us to appreciate the linkage between microbial source and RDOC composition on a range of temporal and spatial scales. Analyses of biomarkers and isotopic records show intensive MCP processes in the Proterozoic oceans when the MCP could have played a significant role in regulating climate. Understanding the dynamics of the MCP in conjunction with the better constrained biological pump (BP) over geological timescales could help to predict future climate trends. Integration of the MCP and the BP will require new research approaches and opportunities. Major goals include understanding the interactions between particulate organic carbon (POC) and RDOC that contribute to sequestration efficiency, and the concurrent determination of the chemical composition of organic carbon, microbial community composition and enzymatic activity. Molecular biomarkers and isotopic tracers should be employed to link water column processes to sediment records, as well as to link present-day observations to paleo-evolution. Ecosystem models need to be developed based on empirical relationships derived from bioassay experiments and field investigations in order to predict the dynamics of carbon cycling along the stability continuum of POC and RDOC under potential global change scenarios. We propose that inorganic nutrient input to coastal waters may reduce the capacity for carbon sequestration as RDOC. The nutrient regime enabling maximum carbon storage from combined POC flux and RDOC formation should therefore be sought.

Carbon sequestration in the ocean is of great concern with respect to the mitigation of global warming. How to hold the fixed organic carbon in the presence of tremendous numbers of heterotrophic microorganisms in marine environments is the central issue. We previously hypothesized that excessive nutrients would ultimately decrease the storage of organic carbon in marine environments. To test this, a series of in situ nutrient enrichment incubation experiments were conducted at a site (17.59° N, 127.00° E) within the western Pacific oligotrophic gyre. Five treatments were employed: glucose (Glu), algal exudation organic material (EOM), nitrate (N) and phosphate (P), N and P in combination with glucose and a control with no added nutrients. The results showed that the dissolved organic carbon consumption rates and bacterial community specific growth rates were enhanced by inorganic nutrient enrichment treatments during the initial 48 h incubation. At the end of 14 days of incubation, about one-third (average 3.3 μmol C kg−1) more organic carbon was respired in the glucose-enriched incubation with the addition of inorganic nutrients compared to that without. In contrast, when nutrients were limiting, glucose could not be efficiently used by the bacteria and thus it remained in the environment. These results suggest that repletion of inorganic nutrients could facilitate microbial consumption of organic carbon and thus has a significant impact on carbon cycling in the environment.

Although respiration-based oxidation of reduced carbon releases CO2 into the environment, it provides an ecosystem with the metabolic energy for essential biogeochemical processes, including the newly proposed microbial carbon pump (MCP). The efficiency of MCP in heterotrophic microorganisms is related to the mechanisms of energy transduction employed and hence is related to the form of respiration utilized. Anaerobic organisms typically have lower efficiencies of energy transduction and hence lower efficiencies of energy-dependent carbon transformation. This leads to a lower MCP efficiency on a per-cell basis. Substantial input of terrigenous nutrients and organic matter into estuarine ecosystems typically results in elevated heterotrophic respiration that rapidly consumes dissolved oxygen, potentially producing hypoxic and anoxic zones in the water column. The lowered availability of dissolved oxygen and the excessive supply of nutrients such as nitrate from river discharge lead to enhanced anaerobic respiration processes such as denitrification and dissimilatory nitrate reduction to ammonium. Thus, some nutrients may be consumed through anaerobic heterotrophs, instead of being utilized by phytoplankton for autotrophic carbon fixation. In this manner, eutrophied estuarine ecosystems become largely fueled by anaerobic respiratory pathways and their efficiency is less due to lowered ecosystem productivity when compared to healthy and balanced estuarine ecosystems. This situation may have a negative impact on the ecological function and efficiency of the MCP which depends on the supply of both organic carbon and metabolic energy. This review presents our current understanding of the MCP mechanisms from the view point of ecosystem energy transduction efficiency, which has not been discussed in previous literature.

The causes for a productive upwelling region to be a source of CO2 are usually referred to the excess CO2 supplied via upwelling of high dissolved inorganic carbon (DIC) from deep water. Furthermore, we hypothesize that microbial activity plays a significant role on top of that. To test this hypothesis, multiple biogeochemical parameters were investigated at two cyclonic-eddy-induced upwelling sites, CE1 and CE2, in the western South China Sea. The data showed that upwelling can exert significant influences on biological activities in the euphotic zone and can also impact on particulate organic carbon (POC) export flux depending on upwelling conditions, such as the magnitude, timing, and duration of nutrient input and consequent microbial activities. At CE2, the increase of phytoplankton biomass caused by the upwelled nutrients resulted in increase of POC export flux compared to non-eddy reference sites, while at CE1 the microbial respiration of organic carbon stimulated by the upwelled nutrients significantly contributed to the attenuation of POC export flux. These results suggest that on top of upwelled DIC, microbial activities stimulated by upwelled nutrients and labile organic carbon produced by phytoplankton can play a critical role for an upwelling area to be outgassing or uptaking CO2. We point out that even though an upwelling region is outgassing CO2, carbon sequestration still takes place through the POC-based biological pump as well as the refractory dissolved organic carbon (RDOC)-based microbial carbon pump.

As the most abundant biological entities in the ocean, viruses influence host mortality and nutrient recycling mainly through lytic infection. Yet, the ecological characteristics of virioplankton and viral impacts on host mortality and biogeochemical cycling in the deep sea are largely unknown. In the present study, viral abundance and lytic infection were investigated throughout the water column in the western Pacific Ocean. Both the prokaryotic and viral abundance and production showed a significantly decreasing trend from epipelagic to meso- and bathypelagic waters. Viral abundance decreased from 0.36–1.05 × 1010 particles L−1 to 0.43–0.80 × 109 particles L−1, while the virus : prokaryote ratio varied from 7.21 to 16.23 to 2.45–23.40, at the surface and 2000 m, respectively. Lytic viral production rates in surface and 2000 m waters were, on average, 1.03 × 1010 L−1 day−1 and 5.74 × 108 L−1 day−1. Relatively high percentages of prokaryotic cells lysed by viruses at 1000 and 2000 m were observed, suggesting a significant contribution of viruses to prokaryotic mortality in the deep ocean. The carbon released by viral lysis in deep western Pacific Ocean waters was from 0.03 to 2.32 μg C L−1 day−1. Our findings demonstrated a highly dynamic and active viral population in these deep waters and suggested that virioplankton play an important role in the microbial loop and subsequently biogeochemical cycling in deep oceans.

Coupled nitrification–denitrification plays a critical role in the removal of excess nitrogen, which is chiefly caused by humans, to mitigate estuary and coastal eutrophication. Despite its obvious importance, limited information about the relationships between nitrifying and denitrifying microbial communities in estuaries, and their controlling factors have been documented. We investigated the nitrifying and denitrifying microbial communities in the estuary of turbid subtropical Yangtze River (YRE), the largest river in Asia, by analyzing the ammonia monooxygenase gene amoA, including archaeal and bacterial amoA, and the dissimilatory nitrite reductase gene nirS using clone libraries and quantitative PCR (qPCR). The diversity indices and rarefaction analysis revealed a quite low diversity for both β-proteobacterial and archaeal amoA genes, but qPCR data showed significantly higher amoA gene copy numbers for archaea than β-proteobacteria. Compared with the amoA gene, a significantly higher level of diversity but lower gene copy numbers were found for the nirS gene. Nitrification and denitrification rates based on 15N incubation experiments supported gene abundance data as denitrification rates were below detection limit, suggesting lower denitrification than nitrification potential. In general, the abundances of the amoA and nirS genes were significantly higher in the bottom samples than the surface ones, and in the high-turbidity river mouth, were significantly higher in the particle-associated (> 3 μm) than the free-living (0.2 ~ 3 μm) communities. Notably, positive correlations between the amoA and nirS gene abundances suggested potential gene-based coupling between nitrification and denitrification, especially for the particle-associated assemblages. Statistical analysis of correlations between the community structure, gene abundances and environmental variables further revealed that dissolved oxygen and total suspended material might be the key factors controlling community spatial structure and regulating nitrification and denitrification potentials in the YRE ecosystem.

Prochlorococcus, the smallest but most abundant marine primary producer, plays an important role in carbon cycling of the global ocean. As a phototroph, Prochlorococcus is thought to be confined to the euphotic zone, with commonly observed maximum depths of ~ 150–200 m, but here we show for the first time the substantial presence of Prochlorococcus populations in the dark ocean ("deep Prochlorococcus" hereafter). Intensive studies at the Luzon Strait in the western Pacific Ocean show that the deep Prochlorococcus populations are exported from the euphotic zone. Multiple physical processes including internal solitary waves could be responsible for the transportation. These findings reveal a novel mechanism for picoplankton carbon export other than the known mechanisms such as sinking of phytodetritus and aggregates or grazing-mediated transportation.

In order to test the influences of ocean acidification on the ocean pelagic ecosystem, so far the largest CO2 manipulation mesocosm study (European Project on Ocean Acidification, EPOCA) was performed in Kings Bay (Kongsfjorden), Spitsbergen. During a 30 day incubation, bacterial diversity was investigated using DNA fingerprinting and clone library analysis of bacterioplankton samples. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the PCR amplicons of the 16S rRNA genes revealed that general bacterial diversity, taxonomic richness and community structure were influenced by the variation of productivity during the time of incubation, but not the degree of ocean acidification. A BIOENV analysis suggested a complex control of bacterial community structure by various biological and chemical environmental parameters. The maximum apparent diversity of bacterioplankton (i.e., the number of T-RFs) in high and low pCO2 treatments differed significantly. A negative relationship between the relative abundance of Bacteroidetes and pCO2 levels was observed for samples at the end of the experiment by the combination of T-RFLP and clone library analysis. Our study suggests that ocean acidification affects the development of bacterial assemblages and potentially impacts the ecological function of the bacterioplankton in the marine ecosystem.

Using first-principles calculations within the framework of density-functional theory, we studied the modulation effect of hydrogen/fluorine chemical decoration on the surface work function of BN sheets. We found that the difference in the work function (ΔWBN) between two surfaces of the chair structure varies with the different decoration. Geometric distortion and chemical effects cause opposite modulation effects, and the chemical effect plays a leading role by inducing charge redistribution in the system.

No abstract available.