Northwest Pacific Ocean Research Articles

Stock Assessment of Chub Mackerel (Scomber japonicus) in the Northwest Pacific Ocean Based on Catch and Resilience Data

This study aimed to evaluate the stock status of chub mackerel (Scomber japonicus) in the Northwest Pacific Ocean. Chub mackerel is a commercially important fish species in South Korea. The fishing grounds of chub mackerel are in the Northwest Pacific Ocean, off South Korea and the neighboring countries of China and Japan. Previous chub mackerel stock assessments have mostly been based on catch data from a single country. However, in this study we used the total catch data on chub mackerel in the Northwest Pacific Ocean to assess the stock status, owing to their migrations and occurrence in the waters of several different countries. We used a catch and maximum sustainable yield model, which is based on catch and resilience data, using the Monte Carlo method. Moreover, sensitivity analysis was conducted according to the availability of catch data by sea area and country. The results showed that the current level of chub mackerel biomass is lower than the biomass required to achieve a maximum sustainable yield based on median values. Furthermore, analysis of all scenarios showed the same results, while the current biomass showed a decreasing trend. These results indicate that improved cooperative resource management is required to prevent further stock status decline.

Three new species and two new records of Echinothuriidae (Echinodermata: Echinothurioida) from seamounts in the Northwest Pacific Ocean: Diversity, phylogeny and biogeography of deep-sea echinothuriids

The soft sea urchins Echinothuriidae Thomson, 1872, constitute the most commonly encountered sea urchins in the bathyal environment. The echinothuriids are common and frequently abundant in the Indo-Pacific, but the species diversity is still not completely known yet. Our examination of echinoid specimens collected from seven seamounts in the Northwest Pacific Ocean revealed three new species and two new records. The three new species are described as Araeosoma cucullatum sp. nov., Araeosoma polyporum sp. nov., and Hygrosoma involucrum sp. nov. The two new records included two species from the genus Araeosoma. They are distinguished from each other and from congeners by the following characteristics: coloring, ambulacrum, interambulacrum, apical system, spines, and pedicellariae. The identities of the five species are well supported by genetic distance and phylogenetic analyses based on the mitochondrial cytochrome oxidase subunit I (COI) and 16S rRNA genes. Based on the distribution data, we explored the distribution patterns of Araeosoma, Calveriosoma, Hapalosoma, Sperosoma, Tromikosoma, and Hygrosoma, the six echinothuriid genera occurring in deep sea, and delineated 10 isolated deep-sea biogeographic provinces all over the world. The Western Pacific harbors higher species diversity of deep-sea echinothuriids than other sea areas worldwide, indicating that the Western Pacific may play an important part in the dispersal and speciation of deep-sea echinothuriids.

A Deep Learning‐Based Bias Correction Method for Predicting Ocean Surface Waves in the Northwest Pacific Ocean

AbstractOcean waves, especially extreme waves, are vital for air‐sea interaction and shipping. However, current wave models still have significant biases. Based on a numerical wave model and a deep learning model, a BU‐Net by adding batch normalization layers to a U‐Net, we accurately predict the significant wave height (SWH) of the Northwest Pacific Ocean. For each day in 2017–2021, we conducted a 3‐day hindcast experiment using WAVEWATCH3 (WW3) to obtain the SWH forecasts at lead times of 24, 48, and 72 hr, forced by GFS real‐time forecast surface winds. After using BU‐Net, the mean Root Mean Squared Errors (RMSEs) of the SWH forecast from WW3 at lead times of 24, 48, and 72 hr are reduced by 40%, 38%, and 30%, respectively. During typhoon passages, the drop percentages of RMSEs all exceed 20% for three lead times. Therefore, combining numerical models and deep learning is very promising in wave forecasting.

Trophic structure of micronekton in the Northwest Pacific Ocean

IntroductionStable isotope analysis has been widely used in the study of the trophic structure of marine micronekton in recent years.MethodsIn this study, the carbon and nitrogen stable isotope values of fish, cephalopod, shrimp and zooplankton species were measured from samples collected in the Northwest Pacific Ocean in March and September 2019 to construct a continuous trophic spectrum and to compare isotope niches among species. In addition, we compared the variation of isotopic niches of micronekton among different groups and among different species, respectively.ResultsSignificant differences of δ13C and δ15N values were detected among fish, cephalopod and shrimp groups with δ13C value ranges of −21.9‰ to −18.7‰, −21.3‰ to −17.7‰ and −20.4‰ to −19.5‰, respectively and the range of δ15N values was 7.0‰ to 12.4‰, 8.2‰ to 12.2‰ and 7.6‰ to 10.6‰, respectively. Using copepods as the baseline for estimating the average trophic level (TL) of micronekton, the TLs ranged from 2.67 to 4.80 and the average TLs for cephalopods, fishes and shrimp were 3.3 ± 0.3, 3.7 ± 0.6 and 4.0 ± 0.3, respectively. Myctophidae and Stomiidae occupied higher TLs. In addition, Oplophorus gracilirostris, Enoploteuthis chunii and Abralia similis had wide isotopic niches.DiscussionOur results show that Myctophidae, Stomiidae, Oplophorus gracilirostris, Enoploteuthis chunii and Abralia similis play important roles in maintaining the stability of the Kuroshio-Oyashio ecosystem in the Northwest Pacific Ocean.

Analysis of Thermal Conditions in the Northwest Pacific Ocean from Satellite Data

Analysis of Thermal Conditions in the Northwest Pacific Ocean from Satellite Data

Further refinements of a continuous radon monitor for surface ocean water measurements

Radon is an excellent natural tracer for studying various geophysical processes. In the past centuries, radon isotopes measurement approaches for marine research have been fully developed but still suffer limitations. Here we present the setup and validation of an improved continuous online measurement system (PIC-ORn) to measure dissolved radon in the surface ocean and other water bodies. We demonstrated that the PIC measurement efficiency is ~2 times higher than a RAD7 and is less affected by relative humidity and produces reliable results. Laboratorial measurements indicated that the new PIC-ORn system responded timely to the change of radon activities in water. The new system was successfully deployed during a cruise to the northwest Pacific Ocean in June 2021. Despite low radon-in-water activities, the results obtained by the new PIC-ORn system matched the traditional measurement systems within the estimated uncertainties. The PIC-ORn detector takes advantage of higher efficiency, lower cost, and power consumption, and is less affected by air moisture. The new system does not rely on drying units, further reducing on-site supervision, which would benefit the researches in submarine groundwater advection and diffusion and ocean-atmosphere gas exchange.

Mesoscale and submesoscale turbulence in the Northwest Pacific Ocean revealed by numerical simulations

As the intermit between geostrophic-balanced mesoscale eddies and three-dimensional dissipation, submesoscale turbulence (1–50 km) plays a key role in the ocean energy cascade. Based on the output of 1/48° MITgcm llc4320 simulation, mesoscale and submesoscale turbulence in the upper ocean and kinetic energy (KE) cascade between them are investigated in two different mesoscale dynamical regimes. When the timing of mesoscale seasonality varies with the mesoscale dynamical regimes, the timing of submesoscale seasonality is almost uniform. In this 1/48o simulation, the inverse KE cascade, through which mesoscale KE is transferred from small scales to larger scales in altimeter observation, expands farther into the submesoscale range, with a minimum of about 15 km. The inversely transferred submesoscale KE is 1–2 orders of magnitude larger than that transferred forward. Both the inverse and forward KE cascades vary seasonally. While the amplitude of the forward KE cascade changes synchronously with the mixed layer depth, the amplitude of the inverse KE cascade lags behind them by ∼1-month This is due to nonlinear interactions between submesoscale processes and more slowly evolving mesoscale eddies which takes a little longer than direct dissipation. The inverse KE cascade leads to the mesoscale seasonality in the Kuroshio Extension, which is invisible in conventional altimeter observation. In terms of depth dependency, both the eddy kinetic energy (EKE) and normalized vertical vorticity (ξ/f) decrease rapidly with depth in the upper ocean, while the EKE-containing scale increases with depth and the ξ-containing scale has a large core in the mixed layer. It indicates that the upper ocean is full of mesoscale eddies on a relatively small scale which are accompanied by active submesoscale turbulence. The submesoscale seasonality is still significant at 300–400 m, and shows vertically consistency in the whole upper ocean, so there may be downward development in the nonlinear evolution of submesoscale turbulence.

Inter‐Model Spread of the Simulated Winter Surface Air Temperature Over the Eurasian Continent and the Physical Linkage to the Jet Streams From the CMIP6 Models

AbstractThe model uncertainty, one of the major sources of projection uncertainty, is still a challenge in the climate simulation. In this study, we investigated the inter‐model spread of the simulated winter surface air temperature (SAT) over the Eurasian continent and the physical link to the upper‐level jet streams from the Coupled Model Inter‐comparison Project Phase 6 models. Extracted by the inter‐model empirical orthogonal function analysis, the leading inter‐model spread of SAT over the Eurasian continent is characterized by a cold pattern, particularly over high latitudes, which is closely associated with the out‐of‐phase variation in the intensity of the East Asian polar front jet (EAPJ) and East Asian subtropical jet (EASJ). The weakened‐EAPJ‐enhanced‐EASJ pattern is linked to the intensified Siberian high, the strengthened Aleutian low, and the deepened East Asian trough. All the variations would benefit the cold air invasion, resulting in the leading inter‐model spread of the SAT. The possible mechanism for the inter‐model uncertainty in the out‐of‐phase variation in the intensity of the two jets would be traced to the cooling over the Northwest Pacific oceans, which has reduced (enhanced) the meridional temperature gradient over high (low) latitudes and thereby contributed to the out of phase variation in the two jets. Our findings would help provide a potential metric for understanding the winter SAT change over the Eurasian continent.

Investigating the Effects of Super Typhoon HAGIBIS in the Northwest Pacific Ocean Using Multiple Observational Data

Various multi-source observational platforms have enabled the exploration of ocean dynamics in the Northwest Pacific Ocean (NPO). This study investigated daily oceanic variables in response to the combined effect of the 2019 super typhoon HAGIBIS and the Kuroshio current meander (KCM), which has caused economic, ecological, and climatic changes in the NPO since August 2017. During HAGIBIS, the six-hourly wind speed data estimated a wind stress power (Pw) which strengthened around the right and left semicircles of the typhoon, and an Ekman pumping velocity (EPV) which intensified at the center of the typhoon track. As a result, firstly, the sea temperature (ST) decreased along a boundary with a high EPV and a strong cyclonic eddy area, and the mixed layer depth (MLD) was shallow. Secondly, a low sea salinity (SS) concentration showed another area where heavy rain fell on the left side of the typhoon track. Phytoplankton bloom (PB) occurred with a large concentration of chlorophyll a (0.641 mg/m3) over a wide extent (56,615 km2; above 0.5 mg/m3) after one day of HAGIBIS. An analysis of a favorable environment of the PB’s growth determined the cause of the PB, and a shift of the subsurface chlorophyll maximum layer (SCML; above 0.7 mg/m3) was estimated by comprehensive impact analysis. This study may contribute to understanding different individually-estimated physical and biological mechanisms and predicting the recurrence of ocean anomalies.

Using habitat classification and large-scale spatial planning model to identify environmental areas: A case study in the area of the Northwest Pacific Ocean

The deep sea refers to the parts of the oceans with a depth of more than 200 m, and it comprises the largest habitat on earth with the most abundant and diverse marine life. Human activities, such as deep-sea mining, fishing, and shipping, can have severe impacts on deep-sea species and habitats. With the development of the related equipment and technology, interest in deep-sea mining continues to rise; therefore, protecting the unique and fragile deep-sea marine ecosystem has become a global focus. Given the fragility of the deep-sea habitats and the growing demand for deep-sea resources, the United Nations established the International Seabed Authority (the ISA) in 1972, which represents everyone worldwide, to manage the mineral resources in the international seabed area (also known as “the Area”) while fulfilling environmental protection obligations. The most important objective of the regional environmental management plan (REMP) in the Area initiated by the ISA is to balance deep-sea mining and environment protection, and the ISA has considered numerous types of area-based management tools (ABMTs) in the development of the REMPs (Table 1). Using the different ABMTs, several key environmental areas or sites have been identified in various regions, such as the areas of particular environmental interest (APEIs), sites in need of protection (SINPs), or areas in need of protection (AINPs). Additionally, deep-sea mining is prohibited in these sites/areas to avoid its irrecoverable impact on the environment in the Area. The designation these environmental areas or sites can improve the function and resilience of the ecosystem and avoid the unrecoverable impact of deep-sea mining. In this study, we selected the international areas of the Northwest Pacific Ocean for a case study. In order to protect representative species and habitats, such as cold-water corals and seamounts, we utilized environmental factors to classify the study area into eight types of habitats. We then used the appropriate criteria to identify candidate AINPs in two scenarios with a large-scale spatial planning model and analyzed the differences in the protected proportion of the eight types of habitats. The results indicate that identifying the candidate AINPs can reach the protection target of approximately 30% of the area, and each representative species and habitat can be protected. The results obtained in this study can provide technical references for the implementation of REMPs and the designation of AINPs in the study area.

The particle fluxes in sediment traps from Niulang Guyot area in the Northwest Pacific Ocean

The particle fluxes in sediment traps from Niulang Guyot area in the Northwest Pacific Ocean

Genetic population structure and demographic history of the endemic fish Paralichthys olivaceus of the Northwest Pacific Ocean.

The Northwest Pacific marginal waters comprising the South China Sea, East China Sea, Yellow Sea, and the Sea of Japan have unique geomorphic features. The Japanese flounder Paralichthys olivaceus, which is endemic to the Northwest Pacific, has high nutritional, economic, and ecological value. To allow the examination of the demographic history and population structure of the most common P. olivaceus species range over the five marginal seas (East China Sea, Yellow Sea, Bohai Sea, Northwest Pacific Ocean, and the Sea of Japan), the mitochondrial DNA control region of 91 individuals from six populations in China was sequenced. These sequences were combined with 233 sequences from four populations distributed in the Northwestern Pacific Ocean for analysis. Higher levels of nucleotide diversity (0.032 ± 0.016) and haplotype diversity (0.996 ± 0.001) were observed. The peripheral Fuqing population in the East China Sea had the relatively lowest genetic diversity and highest differentiation. Furthermore, when the results of the isolation by distance test, spatial analysis of molecular variation and geographic barrier analysis are also considered, there is a clear need to prioritize resource conservation and enhancement measures in this area. The phylogenetic trees, structure assignment test, and haplotypes network revealed no significant differences in the genealogical structure among ten populations. Mismatch distribution analysis, Bayesian skyline plots, and neutrality tests suggested that P. olivaceus experienced population expansion during the Pleistocene. Ocean currents and climate change play important roles in shaping the geographical distribution and genetic population structure of P. olivaceus.

Insignificant effects of eddies and typhoons on the biogeochemistry of the tropical northwest Pacific Ocean

We investigated the effects of eddies and typhoons on the biogeochemistry of the tropical northwest Pacific by examining the distribution of nutrients, dissolved oxygen (DO), chlorophyll-a (Chl-a), gross primary production (GPP), dissolved organic carbon (DOC), and fluorescent dissolved organic matter (FDOM). Water samples were collected from anticyclonic and cyclonic eddies in September 2019 and 2020, and before and after the passage of a Category 2 typhoon in 2019. The study region was characterized by a deep nitracline (~150 m), which was deeper than both the pycnocline (~50 m) and the FDOM-depleted layer (~75 m). A subsurface chlorophyll maximum layer was observed at 100–150 m depth. No clear differences in Chl-a, DO, GPP, DOC, and FDOM were observed for the anticyclonic and cyclonic eddies, indicating that the eddies did not have a significant influence on biological production. Similarly, there were no discernable changes in Chl-a concentrations or other biogeochemical parameters after the passage of the typhoon, which induced water mixing to a depth of ~60 m. We conjecture that the nutrient-depleted layer was too deep for any eddy- or typhoon-induced vertical mixing to cause upwelling of nutrients to the euphotic zone. Our results imply that the disturbances caused by mesoscale processes in the upper layer of the highly oligotrophic northwest Pacific may have a smaller effect than in oceans in other parts of the world.

A new mesoscale eddy tracking methodology based on fast normalized cross-correlation and its validation in the Northwest Pacific

Most mesoscale eddy tracking methodologies used prior to this study evaluated eddy features using a distance-based proximity relationship, rather than considering similarities between eddies. This study applies a fast normalized cross-correlation methodology in the field of image registration to propose a novel mesoscale eddy tracking methodology that can rapidly and comprehensively calculate the similarities between two eddies and judge their relationship through the correlation coefficient, thus facilitating a more accurate mesoscale eddy trajectory tracking. The sea level anomaly data field is employed to identify the positions of eddies over time. The tracking methodology is then used to track the mesoscale eddy trajectories. After comparing the local nearest neighbor methodology (LNN) with our proposed new methodology in the Northwest Pacific Ocean, we conclude that the proposed methodology can address issues of discontinuity in tracking; especially in cases involving eddies with long lifespans. The tracking trajectories utilized in the proposed methodology achieve superior continuity and integrity and a higher degree of characterization than LNN, with the tracking results showing greater consistency with real eddy motion. The new methodology proposed in this paper has great significance for more widespread use.

Decadal Changes in the Annual Growth of Two Commercial Ommastrephid Species in the Pacific Ocean

Neon flying squid Ommastrephes bartramii and jumbo flying squid Dosidicus gigas are two important commercial ommastrephid species in the Pacific Ocean. As short-lived marine species, squids are highly susceptible to changes in climate and marine environments. According to samples collected from the northwest and southeast Pacific Ocean in different years, we explored the growth characteristics of these two squids in terms of their mantle length (ML) distribution and the relationship between mantle length and body weight (LWR), also considering the relative condition factors (Kn), and explored the effects of the El Niño and Southern Oscillation (ENSO) on their growth. The results showed that the ML for O. bartramii and D. gigas had significant differences among different years and different sexes (p < 0.01), and the size of females was larger than that of males. LWR showed that both squids demonstrated a positive allometric growth pattern (b > 3), and parameters a and b were influenced by year and sex. Furthermore, there were significant differences in Kn in both squids for different years and different sexes (p < 0.01), and their interannual fluctuations were quite significant. In conclusion, the alterations in the marine environment caused by climate change had a significant impact on the growth of O. bartramii and D. gigas in this study. ENSO events had opposite effects on the growth of both squid species.

Small and Abundant but Understudied Ribbed Sculpin Triglops pingelii (Cottidae, Teleostei) from the Kara Sea (Siberian Arctic): Distribution, Biology, and Comparison with Congeners

The features of the spatial and vertical distributions, and size–age and size–sex structures of the ribbed sculpin Triglops pingelii of the Kara Sea are presented. In September 2019, this species was recorded at depths from 18 to 235 m at a bottom temperature from −1.5 to +1.6 °C. The densest concentrations were recorded northeastward of the Yamal Peninsula, at the outlet of the Gulf of Ob at a depth of 18–21 m and a bottom temperature from −1.5 to −1.0 °C. Individuals with a length of 46–126 mm and a body weight of 0.35–15.60 g aged 1+ to 4+ years were recorded in trawl catches. However, fish with a length of 51–90 mm and a body weight < 6 g aged 1+–2+ years dominated. Among fish > 71 mm long, the proportion of females increased sharply, reaching 100% with a length of 120 mm. The individual fecundity of female ribbed sculpins in the Kara Sea with a length of 89–123 mm varied from 100 to 316 (on average 215 ± 15) eggs. It is shown that this species is a necto-bentho-ichthyophage whose main prey are benthic and bentho-pelagic crustaceans (mainly amphipods and mysids), as well as juveniles of various fish, the total proportion of which is >99% of the food weight. In this sculpin, age-related changes in the diet composition are well expressed, i.e., as the size increases, the relative importance of the former prey group decreases sharply, and that of the latter two groups, on the contrary, increases. A comparative analysis of data on the biology and distribution of the six most abundant or common Triglops spp. makes it possible to attribute the ribbed sculpin to medium-sized representatives of the genus, whose maximum length is similar to those of T. jordani from the North Pacific, as well as T. murrayi and T. nibelyni from the Arctic. The lifespan of the ribbed sculpin is within the same limits as reported for other Triglops spp. Its individual fecundity in the Arctic seas is comparable to that of other Triglops species living here, but is significantly lower than that of individuals of this species and other congeners from the northwest Pacific Ocean.

(104) Request for a binding decision on whether the names Actinostephanos Khursevich (Bacillariophyta) and Actinostephanus F. Wen & al. (Gesneriaceae) are sufficiently alike to be confused

(104) Actinostephanos Khursevich (1989) [Algae] Actinostephanus F. Wen & al. (2022) [Angiosp.: Gesner.] The genus Actinostephanos was established by phycologist Galina K. Khursevich, Republic of Belarus (in Bot. Zhurn. 74: 487. 1989) to accommodate a single extinct marine and brackish-water planktonic species, Actinostephanos matrensis (Pant.) Khursevich (≡ Stephanodiscus matrensis Pant. in Beitr. Foss. Bacill. Ung. 2: 114. 1889). Later Khursevich & Tsoj added a second, new species, Actinostephanos rudis Khursevich & Tsoj (in Algologiya 2: 106–107. 1992) from the Kuril-Kamchatka Trench (North-West Pacific Ocean), and Kozyrenko (in Bot. Zhurn. 88(11): 126. 2003) published the new combination A. podolicus (Missuna) Kozyr., based on a variety of A. matrensis. Currently the genus Actinostephanos Khursevich includes only three species names. The generic name Actinostephanos consists of two parts, both derived from the Greek. The first part, “Actino-”, is derived from ἀκτίς (aktís, “ray”, “beam”), meaning radiating; the second half, “-stephanos”, is a masculine given name derived from the Greek word στέφανος (stéphanos), meaning “wreath”, “crown”. As a result of morphological and phylogenetic analysis, the new monotypic genus Actinostephanus F. Wen, Y.G. Wei & L.F. Fu was established (Wen & al. in PhytoKeys 193: 95. 2022) from China with the type A. enpingensis F. Wen & al. (l.c.: 96). Currently, the genus Actinostephanus F. Wen & al. is an endemic to China with a single species. The generic name Actinostephanus consists of two parts, both derived from the Greek as with Actinostephanos, i.e., ἀκτίς (aktís, “ray”, “beam”) and στέφανος (stéphanos, “wreath”, “crown”). In my opinion, the two names are sufficiently alike to cause confusion despite belonging to different groups and geographical regions. For example, Khursevich & Tsoj (l.c.), mentioned “Actinostephanus” as a keyword when describing the new species Actinostephanos rudis. In addition, Oreshkina (in Kuznetsova & Muzylov, Quest. Micropaleontol. 31: 138. 1996) referred to “Actinostephanus rudis sp. n.”. Therefore, I am requesting a binding decision under the Art. 53.2 of the Shenzhen Code (Turland & al. in Regnum Veg. 159. 2018) as to whether the generic names Actinostephanos Khursevich and Actinostephanus F. Wen & al. are sufficiently alike to be confused and thus should be treated as homonyms. I believe that nomenclatural stability would be best served by a decision to treat them as confusable names. If a decision is made to treat them as homonyms, the later-published name, Actinostephanus F. Wen & al., would have to be given a new name in accordance with the Code. UBD, https://orcid.org/0000-0002-7489-7645 I am grateful to Management authorities and the Principal Dr. M. Subhas and the Head Dr. M.B. Shende of the Department of Botany, Janata Mahavidyalaya, Chandrapur for providing facilities. I am grateful to John McNeill and John Wiersema for editorial comments and improving the manuscript.

Variability of Chl a Concentration of Priority Marine Regions of the Northwest of Mexico

Priority Marine Regions (PMR) are important areas for biodiversity conservation in the Northwest Pacific Ocean in Mexico. The oceanographic dynamics of these regions are very important to understand their variability, generate analyses, and predict climate change trends by generating an adequate management of marine resources and their ecological characterization. Chlorophyll a (Chl a) is important to quantify phytoplankton biomass, consider the main basis of the trophic web in marine ecosystems, and determine the primary productivity levels and trends of change. The objective of this research is to analyze the oceanographic variability of 24 PMR through monthly 1-km satellite image resolution Chl a data from September 1997 to October 2018. A cluster analysis of Chl a data yielded 18 regions with clear seasonal variability in the Chl a concentration in the South-Californian Pacific (maximum values in spring-summer and minimum ones in autumn-winter) and Gulf of California (maximum values in winter-spring and minimum ones in summer-autumn). Significant differences (p < 0.05) were observed in Chl a concentration analyses for each one of the regions when climate patterns—El Niño/La Niña Southern Oscillation (ENSO) and normal events—were compared for all the seasons of the year (spring, summer, autumn, and winter).

Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

BackgroundDNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life.ResultsWe reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark.ConclusionsOverall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome.DugvPVxjq4uxwMDSRMxarRVideo

Evaluating the impacts of mesoscale eddies on abundance and distribution of neon flying squid in the Northwest Pacific Ocean

Mesoscale eddies are ubiquitous in global oceans yielding significant impacts on marine life. As a short-lived pelagic squid species, the population of neon flying squid (Ommastrephes bartramii) is extremely sensitive to changes in ambient oceanic variables. However, a comprehensive understanding of how mesoscale eddies affect the O. bartramii population in the Northwest Pacific Ocean is still lacking. In this study, a 10-year squid fisheries dataset with eddy tracking and high-resolution reanalysis ocean reanalysis data was used to evaluate the impact of mesoscale eddies and their induced changes in environmental conditions on the abundance and habitat distribution of O. bartramii in the Northwest Pacific Ocean. A weighted-based habitat suitability index (HSI) model was developed with three crucial environmental factors: sea surface temperature (SST), seawater temperature at 50-m depth (T50m), and chlorophyll-a concentration (Chl-a). During years with an unstable Kuroshio Extension (KE) state, the abundance of O. bartramii was significantly higher in anticyclonic eddies (AEs) than that in cyclonic eddies (CEs). This difference was well explained by the distribution pattern of suitable habitats in eddies derived from the HSI model. Enlarged ranges of the preferred SST, T50m, and Chl-a for O. bartramii within AEs were the main causes of more squids occurring inside the warm-core eddies, whereas highly productive CEs matching with unfavorable thermal conditions tended to form unsuitable habitats for O. bartramii. Our findings suggest that with an unstable KE background, suitable thermal conditions combined with favorable foraging conditions within AEs were the main drivers that yielded the high abundance of O. bartramii in the warm eddies.