Evidence of biogeography in surface ocean bacterioplankton assemblages

Regardless of the importance of bacterial assemblages as essential components of ecosystems, little is known about how their populations are structured. We analyzed the composition and turnover rates, based on 16S rDNA sequences, of surface water oceanic bacterial assemblages of the fraction between 0.1 and 0.8 μm along a latitudinal gradient (45°6′42′′N in the North Atlantic to 15°8′37′′S in the South Pacific) including geographic distance, temperature, chlorophyll a and salinity. Here we show that oceanic bacterial assemblages between 0.1 and 0.8 μm, can be structured by a variety of environmental interactions that include separation by distance and chlorophyll a concentration in temperate North Atlantic coastal samples and temperature in tropical Atlantic and Pacific coastal and open ocean samples. Bacterial phyla composition diverged between temperate and tropical regions. This study suggests that some bacterial assemblages could be structured both by environmental and spatial factors, while others by environmental factors alone.     

Spatial Diversity of Bacterioplankton Communities in Surface Water of Northern South China Sea

The South China Sea is one of the largest marginal seas, with relatively frequent passage of eddies and featuring distinct spatial variation in the western tropical Pacific Ocean. Here, we report a phylogenetic study of bacterial community structures in surface seawater of the northern South China Sea (nSCS). Samples collected from 31 sites across large environmental gradients were used to construct clone libraries and yielded 2,443 sequences grouped into 170 OTUs. Phylogenetic analysis revealed 23 bacterial classes with major components α-, β- and γ-Proteobacteria, as well as Cyanobacteria. At class and genus taxon levels, community structure of coastal waters was distinctively different from that of deep-sea waters and displayed a higher diversity index. Redundancy analyses revealed that bacterial community structures displayed a significant correlation with the water depth of individual sampling sites. Members of α-Proteobacteria were the principal component contributing to the differences of the clone libraries. Furthermore, the bacterial communities exhibited heterogeneity within zones of upwelling and anticyclonic eddies. Our results suggested that surface bacterial communities in nSCS had two-level patterns of spatial distribution structured by ecological types (coastal VS. oceanic zones) and mesoscale physical processes, and also provided evidence for bacterial phylogenetic phyla shaped by ecological preferences.     

Role of planktonic bacteria in productivity and cycling of organic matter in the Eastern Pacific Ocean

Total number, biomass, production, and respiration of bacterioplankton were measured in oligotrophic, mesotrophic and eutrophic waters of the Eastern Pacific. Total number of bacteria in the upper mixed layer and in the upper thermocline boundary layers varied from 30–60.10³ ml^-1 in oligotrophic waters to 100–400.10³ ml^-1 in mesotrophic waters of fronts and divergences, and to 1–2,5.10⁶ ml^-1 in eutrophic waters of coastal upwellings. Wet biomass varied from 5–10 mg l^-1 in oligotrophic waters, to 50–200 mg l^-1 in mesotrophic waters, and to 1–2 g m^-3 in eutrophic waters. Below the layer of maximum temperature gradient i.e. below 35–50 m, bacterioplankton density decreased 5–10 times. P/B coefficients per day were highest in the oligotrophic surface water ( 1), and lowest in the eutrophic ones (0.2–0.4). In mesotrophic waters they were intermediate (0.4–1.0). the stock of labile organic matter (LOM) accessible to microbial action varied from 0.3 to 1.6 mg Cl^-1. Its highest value occurred in the upwelling area. The stock of LOM does not noticeably decrease from the euphotic zone to a depth of 2 000 m. Its turnover time varied from 5 to 45 days in surface waters, and 30–50 years in deep oceanic waters. The role of bacterioplankton in productivity and in cycling of organic matter in surface — and deep oceanic waters is discussed.     

Oceanographic significance of Pacific late miocene calcareous nannoplankton

An analysis of the variability in the composition and distribution of Pacific Late Miocene calcareous nannoplankton about their average biogeography shows that there are primarily two environmental factors causing that variability, climate and dissolution. Climate produces a latitudinal, biogeographic differentiation of the Late Miocene nannoflora, while selective dissolution superimposes a bathymetric differentiation of the nannoflora on that due to climate. Together, these two factors produce three distinct Late Miocene nannofloral assemblages, a high-latitude, temperate assemblage characterized by Reticulofenestra pseudoumbilica and Coccolithus pelagicus, and two tropical assemblages, their differences in composition depending on water depth and surface-water productivity: (1) in shallower water and beneath areas of higher organic production and sedimentation of calcite there is an undissolved assemblage characterized by sphenoliths, small elliptical placoliths and Coccolithus pataecus; (2) in deeper water and areas of lower productivity there is a dissolved assemblage dominated by discoasters.Selective dissolution produces most of the apparent biogeographic variation in Pacific Late Miocene nannoplankton compositions, the variation in compositions observed between the seventeen sites studied. Dissolution preferentially removes the more soluble constituents of the tropical nannoflora so that increasing dissolution tends to give tropical nannoflora a cooler, more temperate aspect. At the same time, selective dissolution shifts the composition of the warmer, tropical component towards its more resistant taxa.Nannoplankton records show a period of greatly decreased calcite dissolution in deep tropical and temperate South Pacific sites between about 8 and 10 m.y. ago. This decrease is strongly correlated with a temporary increase in the ¹³C composition of Pacific deep waters. Calcite dissolution increased during this same period in the deep North Pacific.Nannoplankton records of Late Miocene climate in the tropics are distinctly different from those at higher, south temperate latitudes. Tropical records show a sharp warming in the earliest Late Miocene after a generally cool late Middle Miocene. This was followed by a temporary cooling, nearly to Middle Miocene levels, about 7 m.y. ago. Toward the end of the Late Miocene, the tropical Pacific warmed again and remained warm into the Pliocene. Warming of temperate climates occurred much later. Not until latest Miocene did the southern the Pliocene. Warming of temperate climates occurred much later. Not until latest Miocene did the southern temperate latitudes warm appreciably. Southern subpolar climate cooled continuously through the Late Miocene. We attribute the resulting increases in the latitudinal climatic contrast across the southern Pacific Ocean to the development and migration of a strong subtropical convergence.On the basis of the nannoplankton oceanographic records we postulate that beginning about 10.5 m.y. ago Pacific surface circulation became primarily zonal and the production of deep and bottom waters in the Southern Ocean increased sharply. This produced a northward decrease in calcite preservation, an increase in benthic ¹³C, and a strong climatic gradient across southern latitudes. The period of most vigorous deep Pacific circulation ended 7 m.y. ago in response, we speculate, to the reduced ocean salinities during the Messinian.     

Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus

Ostreococcus is a marine picophytoeukaryote for which culture studies indicate there are ‘high-light'' and ‘low-light'' adapted ecotypes. Representatives of these ecotypes fall within two to three 18S ribosomal DNA (rDNA) clades for the former and one for the latter. However, clade distributions and relationships to this form of niche partitioning are unknown in nature. We developed two quantitative PCR primer-probe sets and enumerated the proposed ecotypes in the Pacific Ocean as well as the subtropical and tropical North Atlantic. Statistical differences in factors such as salinity, temperature and NO₃ indicated the ecophysiological parameters behind clade distributions are more complex than irradiance alone. Clade OII, containing the putatively low-light adapted strains, was detected at warm oligotrophic sites. In contrast, Clade OI, containing high-light adapted strains, was present in cooler mesotrophic and coastal waters. Maximal OI abundance (19 555±37 18S rDNA copies per ml) was detected in mesotrophic waters at 40 m depth, approaching the nutricline. OII was often more abundant at the deep chlorophyll maximum, when nutrient concentrations were significantly higher than at the surface (stratified euphotic zone waters). However, in mixed euphotic-zone water columns, relatively high numbers (for example, 891±107 18S rDNA copies per ml, Sargasso Sea, springtime) were detected at the surface. Both Clades OI and OII were found at multiple euphotic zone depths, but co-occurrence at the same geographical location appeared rare and was detected only in continental slope waters. In situ growth rate estimates using these primer-probes and better comprehension of physiology will enhance ecological understanding of Ostreococcus Clades OII and OI which appear to be oceanic and coastal clades, respectively.     

On the role of dense aggregations of males and juveniles in the functional structure of the range of the blue shark Prionace glauca

Analysis of the quantitative distribution and size composition indicated a high extent of the differentiation of the range of the blue shark Prionace glauca. This most abundant and widely distributed species in the oceanic epipelagial of the entire World Ocean remains for the first years of its life in coastal and neritic waters at depths of 80 m. At the earliest age, at a length under 70 cm, sexes separate into individual schools; females stay nearer to the coast. In the eastern Atlantic, two regions of juvenile habitats are recorded: to the north and to the south of the equator, with a typical gap between them in tropical waters. On reaching a length of 160–190 cm, sharks leave for oceanic waters; immature females follow dense aggregations of adult males situated in oceanic waters where their first mating takes place with a delayed fertilization until reaching sexual maturity. A similar pattern of distribution is traced in the eastern Pacific and other regions of the World Ocean. Under conditions of an increased demand and high prices of shark fins, such aggregations of juveniles and adult males where density exceeds average values dozens of times, can easily lead to overfishing and endanger the species existence and the stability of the structure of the oceanic biota as a whole. The necessity of introducing international protection measures with respect to such aggregations is substantiated.     

Macroecological patterns of archaeal ammonia oxidizers in the Atlantic Ocean

Macroecological patterns are found in animals and plants, but also in micro‐organisms. Macroecological and biogeographic distribution patterns in marine Archaea, however, have not been studied yet. Ammonia‐oxidizing Archaea (AOA) show a bipolar distribution (i.e. similar communities in the northernmost and the southernmost locations, separated by distinct communities in the tropical and gyral regions) throughout the Atlantic, detectable from epipelagic to upper bathypelagic layers (<2000 m depth). This tentatively suggests an influence of the epipelagic conditions of organic matter production on bathypelagic AOA communities. The AOA communities below 2000 m depth showed a less pronounced biogeographic distribution pattern than the upper 2000 m water column. Overall, AOA in the surface and deep Atlantic waters exhibit distance–decay relationships and follow the Rapoport rule in a similar way as bacterial communities and macroorganisms. This indicates a major role of environmental conditions in shaping the community composition and assembly (species sorting) and no, or only weak limits for dispersal in the oceanic thaumarchaeal communities. However, there is indication of a different strength of these relationships between AOA and Bacteria, linked to the intrinsic differences between these two domains.     

Novel lineages of Prochlorococcus and Synechococcus in the global oceans

Picocyanobacteria represented by Prochlorococcus and Synechococcus have an important role in oceanic carbon fixation and nutrient cycling. In this study, we compared the community composition of picocyanobacteria from diverse marine ecosystems ranging from estuary to open oceans, tropical to polar oceans and surface to deep water, based on the sequences of 16S-23S rRNA internal transcribed spacer (ITS). A total of 1339 ITS sequences recovered from 20 samples unveiled diverse and several previously unknown clades of Prochlorococcus and Synechococcus. Six high-light (HL)-adapted Prochlorococcus clades were identified, among which clade HLVI had not been described previously. Prochlorococcus clades HLIII, HLIV and HLV, detected in the Equatorial Pacific samples, could be related to the HNLC clades recently found in the high-nutrient, low-chlorophyll (HNLC), iron-depleted tropical oceans. At least four novel Synechococcus clades (out of six clades in total) in subcluster 5.3 were found in subtropical open oceans and the South China Sea. A niche partitioning with depth was observed in the Synechococcus subcluster 5.3. Members of Synechococcus subcluster 5.2 were dominant in the high-latitude waters (northern Bering Sea and Chukchi Sea), suggesting a possible cold-adaptation of some marine Synechococcus in this subcluster. A distinct shift of the picocyanobacterial community was observed from the Bering Sea to the Chukchi Sea, which reflected the change of water temperature. Our study demonstrates that oceanic systems contain a large pool of diverse picocyanobacteria, and further suggest that new genotypes or ecotypes of picocyanobacteria will continue to emerge, as microbial consortia are explored with advanced sequencing technology.     

The distribution of radiolarian assemblages in the modern and ice-age Pacific

Data on radiolarian abundances from several recent regional studies of the Pacific have been combined with new data from the temperate and tropical area to provide an ocean-wide view of radiolarian distributions. A Q-mode factor analysis of these data identified seven factors which have their areas of dominance in the following regions: tropics, western Pacific, subarctic, Antarctic, transitional zone, temperate regions, and the eastern central water masses. The distributions of these factors tended to follow those of surface water masses and major ocean currents. A more detailed analysis of the temperate and tropical region better delineated the complex flow and counter flow in this area. The relationship between the distribution of modern radiolarian assemblages and the surface circulation of the Pacific can be used to deduce the nature of oceanographic changes which occurred in the past. The modern radiolarian distributions are compared with those mapped at the 18, 000 B.P. level and reveal two major differences in the ice-age Pacific. The Tropical Factor, restricted primarily to the eastern half of the ocean in modern times, ranged across the entire ocean at 18, 000 B.P. and extended into the area of the western boundary currents. The Subarctic Factor, now found mainly in the western subarctic, expanded to the east and south at 18, 000 B.P. and had strong similarities to an assemblage found in the subantarctic area. The expansion of these two dominant assemblages was at the expense of the Western Pacific, Temperate, and Transitional Factors. These differences in the 18, 000 B.P. distributions are thought to be caused by an increase in the influence of arctic air masses in the North Pacific and by a general increase in the wind-driven zonal flow.     

Variability in the Correlation between Asian Dust Storms and Chlorophyll a Concentration from the North to Equatorial Pacific

A long-term record of Asian dust storms showed seven high-occurrence-frequency centers in China. The intrusion of Asian dust into the downwind seas, including the China seas, the Sea of Japan, the subarctic North Pacific, the North Pacific subtropical gyre, and the western and eastern Equatorial Pacific, has been shown to add nutrients to ocean ecosystems and enhance their biological activities. To explore the relationship between the transported dust from various sources to the six seas and oceanic biological activities with different nutrient conditions, the correlation between monthly chlorophyll a concentration in each sea and monthly dust storm occurrence frequencies reaching the sea during 1997–2007 was examined in this study. No correlations were observed between dust and chlorophyll a concentration in the <50 m China seas because atmospheric deposition is commonly believed to exert less impact on coastal seas. Significant correlations existed between dust sources and many sea areas, suggesting a link between dust and chlorophyll a concentration in those seas. However, the correlation coefficients were highly variable. In general, the correlation coefficients (0.54–0.63) for the Sea of Japan were highest, except for that between the subarctic Pacific and the Taklimakan Desert, where it was as high as 0.7. For the >50 m China seas and the North Pacific subtropical gyre, the correlation coefficients were in the range 0.32–0.57. The correlation coefficients for the western and eastern Equatorial Pacific were relatively low (<0.36). These correlation coefficients were further interpreted in terms of the geographical distributions of dust sources, the transport pathways, the dust deposition, the nutrient conditions of oceans, and the probability of dust storms reaching the seas.     

Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments

Methane (CH₄) emitted from high-latitude lakes accounts for 2–6% of the global atmospheric CH₄ budget. Methanotrophs in lake sediments and water columns mitigate the amount of CH₄ that enters the atmosphere, yet their identity and activity in arctic and subarctic lakes are poorly understood. We used stable isotope probing (SIP), quantitative PCR (Q-PCR), pyrosequencing and enrichment cultures to determine the identity and diversity of active aerobic methanotrophs in the water columns and sediments (0–25 cm) from an arctic tundra lake (Lake Qalluuraq) on the north slope of Alaska and a subarctic taiga lake (Lake Killarney) in Alaska''s interior. The water column CH₄ oxidation potential for these shallow (∼2 m deep) lakes was greatest in hypoxic bottom water from the subarctic lake. The type II methanotroph, Methylocystis, was prevalent in enrichment cultures of planktonic methanotrophs from the water columns. In the sediments, type I methanotrophs (Methylobacter, Methylosoma and Methylomonas) at the sediment-water interface (0–1 cm) were most active in assimilating CH₄, whereas the type I methanotroph Methylobacter and/or type II methanotroph Methylocystis contributed substantially to carbon acquisition in the deeper (15–20 cm) sediments. In addition to methanotrophs, an unexpectedly high abundance of methylotrophs also actively utilized CH₄-derived carbon. This study provides new insight into the identity and activity of methanotrophs in the sediments and water from high-latitude lakes.     

Larvae of Pterothrissus gissu (Albilidae) in temperate waters of the northwestern part of the Pacific Ocean

According to results of trawl and oceanological surveys, the distribution and numbers of leptocephalic larvae of Japanese gissu Pterothrissus gissu in June–July 2010–2011 in temperate waters of the northwestern part of the Pacific Ocean in connection with water circulation and distribution of thermohaline characteristics are considered. Larvae of Japanese gissu in the water area of the survey were characterized by high occurrence and numbers; all of them were caught in a layer of 0–30 m mainly in the dark hours of the day at the temperature of the surface water layer of 2.8–8.7°C. Their distribution in waters of the western subarctic circulation is related to both constant and wind currents.     

First Autonomous Bio-Optical Profiling Float in the Gulf of Mexico Reveals Dynamic Biogeochemistry in Deep Waters

Profiling floats equipped with bio-optical sensors well complement ship-based and satellite ocean color measurements by providing highly-resolved time-series data on the vertical structure of biogeochemical processes in oceanic waters. This is the first study to employ an autonomous profiling (APEX) float in the Gulf of Mexico for measuring spatiotemporal variability in bio-optics and hydrography. During the 17-month deployment (July 2011 to December 2012), the float mission collected profiles of temperature, salinity, chlorophyll fluorescence, particulate backscattering (b_bp), and colored dissolved organic matter (CDOM) fluorescence from the ocean surface to a depth of 1,500 m. Biogeochemical variability was characterized by distinct depth trends and local “hot spots”, including impacts from mesoscale processes associated with each of the water masses sampled, from ambient deep waters over the Florida Plain, into the Loop Current, up the Florida Canyon, and eventually into the Florida Straits. A deep chlorophyll maximum (DCM) occurred between 30 and 120 m, with the DCM depth significantly related to the unique density layer ρ = 1023.6 (R² = 0.62). Particulate backscattering, b_bp, demonstrated multiple peaks throughout the water column, including from phytoplankton, deep scattering layers, and resuspension. The bio-optical relationship developed between b_bp and chlorophyll (R² = 0.49) was compared to a global relationship and could significantly improve regional ocean-color algorithms. Photooxidation and autochthonous production contributed to CDOM distributions in the upper water column, whereas in deep water, CDOM behaved as a semi-conservative tracer of water masses, demonstrating a tight relationship with density (R² = 0.87). In the wake of the Deepwater Horizon oil spill, this research lends support to the use of autonomous drifting profilers as a powerful tool for consideration in the design of an expanded and integrated observing network for the Gulf of Mexico.     

Shell Condition and Survival of Puget Sound Pteropods Are Impaired by Ocean Acidification Conditions

We tested whether the thecosome pteropod Limacina helicina from Puget Sound, an urbanized estuary in the northwest continental US, experiences shell dissolution and altered mortality rates when exposed to the high CO₂, low aragonite saturation state (Ω_a) conditions that occur in Puget Sound and the northeast Pacific Ocean. Five, week-long experiments were conducted in which we incubated pteropods collected from Puget Sound in four carbon chemistry conditions: current summer surface (∼460–500 µatm CO₂, Ω_a≈1.59), current deep water or surface conditions during upwelling (∼760 and ∼1600–1700 µatm CO₂, Ω_a≈1.17 and 0.56), and future deep water or surface conditions during upwelling (∼2800–3400 µatm CO₂, Ω_a≈0.28). We measured shell condition using a scoring regime of five shell characteristics that capture different aspects of shell dissolution. We characterized carbon chemistry conditions in statistical analyses with Ω_a, and conducted analyses considering Ω_a both as a continuous dataset and as discrete treatments. Shell dissolution increased linearly as aragonite saturation state decreased. Discrete treatment comparisons indicate that shell dissolution was greater in undersaturated treatments compared to oversaturated treatments. Survival increased linearly with aragonite saturation state, though discrete treatment comparisons indicated that survival was similar in all but the lowest saturation state treatment. These results indicate that, under starvation conditions, pteropod survival may not be greatly affected by current and expected near-future aragonite saturation state in the NE Pacific, but shell dissolution may. Given that subsurface waters in Puget Sound’s main basin are undersaturated with respect to aragonite in the winter and can be undersaturated in the summer, the condition and persistence of the species in this estuary warrants further study.     

Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years

Microbial activities that affect global oceanographic and atmospheric processes happen throughout the water column, yet the long-term ecological dynamics of microbes have been studied largely in the euphotic zone and adjacent seasonally mixed depths. We investigated temporal patterns in the community structure of free-living bacteria, by sampling approximately monthly from 5 m, the deep chlorophyll maximum (∼15–40 m), 150, 500 and 890 m, in San Pedro Channel (maximum depth 900 m, hypoxic below ∼500 m), off the coast of Southern California. Community structure and biodiversity (inverse Simpson index) showed seasonal patterns near the surface and bottom of the water column, but not at intermediate depths. Inverse Simpson''s index was highest in the winter in surface waters and in the spring at 890 m, and varied interannually at all depths. Biodiversity appeared to be driven partially by exchange of microbes between depths and was highest when communities were changing slowly over time. Meanwhile, communities from the surface through 500 m varied interannually. After accounting for seasonality, several environmental parameters co-varied with community structure at the surface and 890 m, but not at the intermediate depths. Abundant and seasonally variable groups included, at 890 m, Nitrospina, Flavobacteria and Marine Group A. Seasonality at 890 m is likely driven by variability in sinking particles, which originate in surface waters, pass transiently through the middle water column and accumulate on the seafloor where they alter the chemical environment. Seasonal subeuphotic groups are likely those whose ecology is strongly influenced by these particles. This surface-to-bottom, decade-long, study identifies seasonality and interannual variability not only of overall community structure, but also of numerous taxonomic groups and near-species level operational taxonomic units.     

The Ecuadorian Artisanal Fishery for Large Pelagics: Species Composition and Spatio-Temporal Dynamics

The artisanal fisheries of Ecuador operate within one of the most dynamic and productive marine ecosystems of the world. This study investigates the catch composition of the Ecuadorian artisanal fishery for large pelagic fishes, including aspects of its spatio-temporal dynamics. The analyses of this study are based on the most extensive dataset available to date for this fishery: a total of 106,963 trip-landing inspection records collected at its five principal ports during 2008 ‒ 2012. Ecuadorian artisanal fisheries remove a substantial amount of biomass from the upper trophic-level predatory fish community of the eastern tropical Pacific Ocean. It is estimated that at least 135 thousand metric tons (mt) (about 15.5 million fish) were landed in the five principal ports during the study period. The great novelty of Ecuadorian artisanal fisheries is the “oceanic-artisanal” fleet component, which consists of mother-ship (nodriza) boats with their towed fiber-glass skiffs (fibras) operating with pelagic longlines. This fleet has fully expanded into oceanic waters as far offshore as 100°W, west of the Galapagos Archipelago. It is estimated that nodriza operations produce as much as 80% of the total catches of the artisanal fishery. The remainder is produced by independent fibras operating in inshore waters with pelagic longlines and/or surface gillnets. A multivariate regression tree analysis was used to investigate spatio-environmental effects on the nodriza fleet (n = 6,821 trips). The catch species composition of the nodriza fleet is strongly influenced by the northwesterly circulation of the Humboldt Current along the coast of Peru and its associated cold waters masses. The target species and longline gear-type used by nodrizas change seasonally with the incursion of cool waters (< 25°C) from the south and offshore. During this season, dolphinfish (Coryphaena hippurus) dominates the catches. However, in warmer waters, the fishery changes to tuna-billfish-shark longline gear and the catch composition becomes much more diverse.     

Identifying Pelagic Habitat Hotspots of Neon Flying Squid in the Temperate Waters of the Central North Pacific

We identified the pelagic habitat hotspots of the neon flying squid (Ommastrephes bartramii) in the central North Pacific from May to July and characterized the spatial patterns of squid aggregations in relation to oceanographic features such as mesoscale oceanic eddies and the Transition Zone Chlorophyll-a Front (TZCF). The data used for the habitat model construction and analyses were squid fishery information, remotely-sensed and numerical model-derived environmental data from May to July 1999–2010. Squid habitat hotspots were deduced from the monthly Maximum Entropy (MaxEnt) models and were identified as regions of persistent high suitable habitat across the 12-year period. The distribution of predicted squid habitat hotspots in central North Pacific revealed interesting spatial and temporal patterns likely linked with the presence and dynamics of oceanographic features in squid’s putative foraging grounds from late spring to summer. From May to June, the inferred patches of squid habitat hotspots developed within the Kuroshio-Oyashio transition zone (KOTZ; 37–40°N) and further expanded north towards the subarctic frontal zone (SAFZ; 40–44°N) in July. The squid habitat hotspots within the KOTZ and areas west of the dateline (160°W-180°) were likely influenced and associated with the highly dynamic and transient oceanic eddies and could possibly account for lower squid suitable habitat persistence obtained from these regions. However, predicted squid habitat hotspots located in regions east of the dateline (180°-160°W) from June to July, showed predominantly higher squid habitat persistence presumably due to their proximity to the mean position of the seasonally-shifting TZCF and consequent utilization of the highly productive waters of the SAFZ.     

The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology

Bacteria and their viruses (phage) are fundamental drivers of many ecosystem processes including global biogeochemistry and horizontal gene transfer. While databases and resources for studying function in uncultured bacterial communities are relatively advanced, many fewer exist for their viral counterparts. The issue is largely technical in that the majority (often 90%) of viral sequences are functionally ‘unknown’ making viruses a virtually untapped resource of functional and physiological information. Here, we provide a community resource that organizes this unknown sequence space into 27 K high confidence protein clusters using 32 viral metagenomes from four biogeographic regions in the Pacific Ocean that vary by season, depth, and proximity to land, and include some of the first deep pelagic ocean viral metagenomes. These protein clusters more than double currently available viral protein clusters, including those from environmental datasets. Further, a protein cluster guided analysis of functional diversity revealed that richness decreased (i) from deep to surface waters, (ii) from winter to summer, (iii) and with distance from shore in surface waters only. These data provide a framework from which to draw on for future metadata-enabled functional inquiries of the vast viral unknown.     

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.Subject terms: Biogeochemistry, Limnology, Microbial ecology, Freshwater ecology