ALBERT

Description: The sinking of particulate matter from the upper ocean dominates the export and sequestration of organic carbon by the biological pump, a critical component of the Earth's carbon cycle. Controls on carbon export are thought to be driven by ecological processes that produce and repackage sinking biogenic particles. Here, we present observations during the demise of the Northeast Atlantic Ocean spring bloom illustrating the importance of storm-induced turbulence on the dynamics of sinking particles. A sequence of four large storms caused upper layer mean turbulence levels to vary by more than three orders of magnitude. Large particle (>0.1 to 10 mm) abundance and size changed accordingly: increasing via shear coagulation when turbulence was moderate and decreasing rapidly when turbulence was intense due to shear disaggregation. Particle export was also tied to storm forcing as large particles were mixed to depth during mixed layer deepening. After the mixed layer shoaled, these particles, now isolated from intense surface mixing, grew larger and subsequently sank. This sequence of events matched the timing of sinking particle flux observations. Particle export was influenced by increases in aggregate abundance and porosity, which appeared to be enhanced by the repeated creation and destruction of aggregates. Last, particle transit efficiency through the mesopelagic zone was reduced by presumably biotic processes that created small particles (〈0.5 mm) from larger ones. Our results demonstrate that ocean turbulence significantly impacts the nature and dynamics of sinking particles, strongly influencing particle export and the efficiency of the biological pump.

Description: Warmer temperatures and higher sea level than today characterized the Last Interglacial interval [Pleistocene, 128 to 116 thousand years ago (ka)]. This period is a remarkable deep-time analog for temperature and sea-level conditions as projected for 2100 AD, yet there has been no evidence of fossil assemblages in the equatorial Atlantic. Here, we report foraminifer, metazoan (mollusks, bony fish, bryozoans, decapods, and sharks among others), and plant communities of coastal tropical marine and mangrove affinities, dating precisely from a ca. 130 to 115 ka time interval near the Equator, at Kourou, in French Guiana. These communities include ca. 230 recent species, some being endangered today and/or first recorded as fossils. The hyperdiverse Kourou mollusk assemblage suggests stronger affinities between Guianese and Caribbean coastal waters by the Last Interglacial than today, questioning the structuring role of the Amazon Plume on tropical Western Atlantic communities at the time. Grassland-dominated pollen, phytoliths, and charcoals from younger deposits in the same sections attest to a marine retreat and dryer conditions during the onset of the last glacial (ca. 110 to 50 ka), with a savanna-dominated landscape and episodes of fire. Charcoals from the last millennia suggest human presence in a mosaic of modern-like continental habitats. Our results provide key information about the ecology and biogeography of pristine Pleistocene tropical coastal ecosystems, especially relevant regarding the—widely anthropogenic—ongoing global warming.

Description: The South Shetland Trough, Antarctica, is an underexplored region for microbiological and biotechnological exploitation. Herein, we describe the isolation and characterization of the novel bacterium Lacinutrix shetlandiensis sp. nov. WUR7 from a deep-sea environment. We explored its chemical diversity via a metabologenomics approach, wherein the OSMAC strategy was strategically employed to upregulate cryptic genes for secondary metabolite production. Based on hybrid de novo whole genome sequencing and digital DNA–DNA hybridization, isolate WUR7 was identified as a novel species from the Gram-negative genus Lacinutrix. Its genome was mined for the presence of biosynthetic gene clusters with limited results. However, extensive investigation of its metabolism uncovered an unusual tryptophan decarboxylase with high sequence homology and conserved structure of the active site as compared to ZP_02040762, a highly specific tryptophan decarboxylase from Ruminococcus gnavus. Therefore, WUR7's metabolism was directed toward indole-based alkaloid biosynthesis by feeding it with L-tryptophan. As expected, its metabolome profile changed dramatically, by triggering the extracellular accumulation of a massive array of metabolites unexpressed in the absence of tryptophan. Untargeted LC-MS/MS coupled with molecular networking, followed along with chemoinformatic dereplication, allowed for the annotation of 10 indole alkaloids, belonging to β-carboline, bisindole, and monoindole classes, alongside several unknown alkaloids. These findings guided us to the isolation of a new natural bisindole alkaloid 8,9-dihydrocoscinamide B (1), as the first alkaloid from the genus Lacinutrix, whose structure was elucidated on the basis of extensive 1D and 2D NMR and HR-ESIMS experiments. This comprehensive strategy allowed us to unlock the previously unexploited metabolome of L. shetlandiensis sp. nov. WUR7.

Description: Significance Assessing change in Southern Ocean ecosystems is challenging due to its remoteness. Large-scale datasets that allow comparison between present-day conditions and those prior to large-scale ecosystem disturbances caused by humans (e.g., fishing/whaling) are rare. We infer the contemporary offshore foraging distribution of a marine predator, southern right whales (n = 1,002), using a customized stable isotope-based assignment approach based on biogeochemical models of the Southern Ocean. We then compare the contemporary distributions during the late austral summer and autumn to whaling catch data representing historical distributions during the same seasons. We show remarkable consistency of mid-latitude distribution across four centuries but shifts in foraging grounds in the past 30 y, particularly in the high latitudes that are likely driven by climate-associated alterations in prey availability. Abstract Assessing environmental changes in Southern Ocean ecosystems is difficult due to its remoteness and data sparsity. Monitoring marine predators that respond rapidly to environmental variation may enable us to track anthropogenic effects on ecosystems. Yet, many long-term datasets of marine predators are incomplete because they are spatially constrained and/or track ecosystems already modified by industrial fishing and whaling in the latter half of the 20th century. Here, we assess the contemporary offshore distribution of a wide-ranging marine predator, the southern right whale (SRW, Eubalaena australis), that forages on copepods and krill from ~30°S to the Antarctic ice edge (〉60°S). We analyzed carbon and nitrogen isotope values of 1,002 skin samples from six genetically distinct SRW populations using a customized assignment approach that accounts for temporal and spatial variation in the Southern Ocean phytoplankton isoscape. Over the past three decades, SRWs increased their use of mid-latitude foraging grounds in the south Atlantic and southwest (SW) Indian oceans in the late austral summer and autumn and slightly increased their use of high-latitude (〉60°S) foraging grounds in the SW Pacific, coincident with observed changes in prey distribution and abundance on a circumpolar scale. Comparing foraging assignments with whaling records since the 18th century showed remarkable stability in use of mid-latitude foraging areas. We attribute this consistency across four centuries to the physical stability of ocean fronts and resulting productivity in mid-latitude ecosystems of the Southern Ocean compared with polar regions that may be more influenced by recent climate change.

Description: Prochlorococcus is a key member of open-ocean primary producer communities. Despite its importance, little is known about the predators that consume this cyanobacterium and make its biomass available to higher trophic levels. We identify potential predators along a gradient wherein Prochlorococcus abundance increased from near detection limits (coastal California) to 〉200,000 cells mL-1 (subtropical North Pacific Gyre). A replicated RNA-Stable Isotope Probing experiment involving the in situ community, and labeled Prochlorococcus as prey, revealed choanoflagellates as the most active predators of Prochlorococcus, alongside a radiolarian, chrysophytes, dictyochophytes, and specific MAST lineages. These predators were not appropriately highlighted in multiyear conventional 18S rRNA gene amplicon surveys where dinoflagellates and other taxa had highest relative amplicon abundances across the gradient. In identifying direct consumers of Prochlorococcus, we reveal food-web linkages of individual protistan taxa and resolve routes of carbon transfer from the base of marine food webs.

Description: Significance Oceans represent 70% of our planet’s surface, housing a large spectrum of microorganisms that interact with the above atmosphere. Ocean microorganisms were proposed in the late 80’s to be at the center of a climate feedback loop involving dimethyl sulfide (DMS) that would form aerosols and modify cloud properties (CLAW hypothesis). In the present paper, we report observational evidence from semicontrolled experiments in the South Pacific that nitrate ions, yet hitherto not considered, is a key species involved in aerosol nucleation in the pristine marine atmosphere and which precursors are coemitted with DMS. Our results further indicate that nitrate ion formation would be related to short-term microbial processes, sensitive to environmental stressors, therefore potentially “closing the loop”. Abstract Our understanding of ocean–cloud interactions and their effect on climate lacks insight into a key pathway: do biogenic marine emissions form new particles in the open ocean atmosphere? Using measurements collected in ship-borne air–sea interface tanks deployed in the Southwestern Pacific Ocean, we identified new particle formation (NPF) during nighttime that was related to plankton community composition. We show that nitrate ions are the only species for which abundance could support NPF rates in our semicontrolled experiments. Nitrate ions also prevailed in the natural pristine marine atmosphere and were elevated under higher sub-10 nm particle concentrations. We hypothesize that these nucleation events were fueled by complex, short-term biogeochemical cycling involving the microbial loop. These findings suggest a new perspective with a previously unidentified role of nitrate of marine biogeochemical origin in aerosol nucleation.

Description: Significance A substantial component of the global nitrogen cycle is the production of biologically inaccessible dinitrogen attributed to anaerobic denitrification by prokaryotes. Recent evidence identified a eukaryote, foraminifera, as new key players in this “loss” of bioavailable nitrogen. The evolution of denitrification in eukaryotes is a rare event, and the genetic mechanisms of the denitrification pathway in foraminifera are just starting to be elucidated. We present large-scale sequencing analyses of 10 denitrifying foraminiferal species, which reveals the high conservation of the foraminiferal denitrification pathway. We further find evidence for a complementation of denitrification by the foraminiferal microbiome. Together, these findings provide insights into the early evolution of a previously overlooked component in the marine nitrogen cycle. Abstract: Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown, and the missing denitrification pathway components are elusive. Analyzing transcriptomes and metagenomes of 10 foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteraceae, which harbor genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success in oxygen depleted habitats.

Description: Significance: Adaptive radiation, the evolutionary process whereby a lineage diversifies over a short period of time, often occurs in geographically isolated or newly formed habitats where colonizing species encounter unoccupied niches and reduced selective pressures. Rapid radiations may also occur in diverse and complex environments, but these cases are less well documented. Here, we show that the hamlets, a group of Caribbean reef fishes, radiated within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. Genomic analysis suggests that color pattern diversity is generated by different combinations of alleles at a few genes with large effect. Such a modular genomic architecture of diversification is emerging as a common denominator to a variety of radiations. Abstract: Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth’s diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in a highly diverse marine habitat. The hamlets, a group of reef fishes from the wider Caribbean, have radiated into a stunning diversity of color patterns but show low divergence across other ecological axes. Although the hamlet lineage is ∼26 My old, the radiation appears to have occurred within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. As such, the hamlets provide a compelling backdrop to uncover the genomic elements associated with phenotypic diversification and an excellent opportunity to build a broader comparative framework for understanding the drivers of adaptive radiation. The analysis of 170 genomes suggests that color pattern diversity is generated by different combinations of alleles at a few large-effect loci. Such a modular genomic architecture of diversification has been documented before in Heliconius butterflies, capuchino finches, and munia finches, three other tropical radiations that took place in highly diverse and complex environments. The hamlet radiation also occurred in a context of high effective population size, which is typical of marine populations. This allows for the accumulation of new variants through mutation and the retention of ancestral genetic variation, both of which appear to be important in this radiation.

Description: Significance Resilience to global change will require adaptation to multiple concurrent environmental changes. However, it is unclear if adaptations to multiple stressors can be predicted from the sum of single-stressor adaptation. To answer this question, we experimentally evolved a marine copepod to warming, acidification, and their combination, finding that copepods were able to adapt to all conditions over 25 generations. Warming was a much stronger selective pressure than acidification alone and under multiple-stressor conditions. Nevertheless, the multiple-stressor response to selection was synergistic and unique from either single stressor. Thus, adaptation to single stressors may not reveal adaptive potential or mechanisms of adaptation under multiple stressors, demonstrating the complexity of predicting adaptive responses under multifaceted environmental change. Abstract Metazoan adaptation to global change relies on selection of standing genetic variation. Determining the extent to which this variation exists in natural populations, particularly for responses to simultaneous stressors, is essential to make accurate predictions for persistence in future conditions. Here, we identified the genetic variation enabling the copepod Acartia tonsa to adapt to experimental ocean warming, acidification, and combined ocean warming and acidification (OWA) over 25 generations of continual selection. Replicate populations showed a consistent polygenic response to each condition, targeting an array of adaptive mechanisms including cellular homeostasis, development, and stress response. We used a genome-wide covariance approach to partition the allelic changes into three categories: selection, drift and replicate-specific selection, and laboratory adaptation responses. The majority of allele frequency change in warming (57%) and OWA (63%) was driven by shared selection pressures across replicates, but this effect was weaker under acidification alone (20%). OWA and warming shared 37% of their response to selection but OWA and acidification shared just 1%, indicating that warming is the dominant driver of selection in OWA. Despite the dominance of warming, the interaction with acidification was still critical as the OWA selection response was highly synergistic with 47% of the allelic selection response unique from either individual treatment. These results disentangle how genomic targets of selection differ between single and multiple stressors and demonstrate the complexity that nonadditive multiple stressors will contribute to predictions of adaptation to complex environmental shifts caused by global change.

Description: Orbital cyclicity is a fundamental pacemaker of Earth’s climate system. The Newark–Hartford Basin (NHB) lake sediment record of eastern North America contains compelling geologic expressions of this cyclicity, reflecting variations of climatic conditions in tropical Pangea during the Late Triassic and earliest Jurassic (~233 to 199 Ma). Climate modeling enables a deeper mechanistic understanding of Earth system modulation during this unique greenhouse and supercontinent period. We link major features of the NHB record to the combined climatic effects of orbital forcing, paleogeographic changes, and atmospheric p CO 2 variations. An ensemble of transient, orbitally driven climate simulations is assessed for nine time slices, three atmospheric p CO 2 values, and two paleogeographic reconstructions. Climatic transitions from tropical humid to more seasonal and ultimately semiarid are associated with tectonic drift of the NHB from ~ 5 ° N to 20 ° N . The modeled orbital modulation of the precipitation–evaporation balance is most pronounced during the 220 to 200 Ma interval, whereas it is limited by weak seasonality and increasing aridity before and after this interval. Lower p CO 2 at around 205 Ma contributes to drier climates and could have led to the observed damping of sediment cyclicity. Eccentricity-modulated precession dominates the orbitally driven climate response in the NHB region. High obliquity further amplifies summer precipitation through the seasonal shifts in the tropical rainfall belt. Regions with other proxy records are also assessed, providing guidance toward an integrated picture of global astronomical climate forcing in the Late Triassic and ultimately of other periods in Earth history.

Description: During the last ice age, the Northern Hemisphere experienced a series of abrupt millennial-scale climatic changes linked to variations in the strength of the Atlantic Meridional Overturning Circulation and sea-ice extent. However, our understanding of their impacts on decadal-scale climate variability in central Europe has been limited by the lack of high-resolution continental archives. Here, we present a near annual-resolution climate proxy record of central European temperature reconstructed from the Eifel maar lakes of Holzmaar and Auel in Germany, spanning the past 60,000 years. The lake sediments reveal a series of previously undocumented multidecadal climate cycles of around 20 to 150 years that persisted through the last glacial cycle. The periodicity of these cycles suggests that they are related to the Atlantic multidecadal climate oscillations found in the instrumental record and in other climate archives during the Holocene. Our record shows that multidecadal variability in central Europe was strong during all warm interstadials, but was substantially muted during all cold stadial periods. We suggest that this decrease in multidecadal variability was the result of the atmospheric circulation changes associated with the weakening of the Atlantic Meridional Overturning Circulation and the expansion of North Atlantic sea-ice cover during the coldest parts of the last ice age.

Description: During the last glacial interval, marine sediments recorded reduced current ventilation within the ocean interior below water depths of approximately 〉1,500 m [B. A. Hoogakker et al., Nat. Geosci. 8, 40–43 (2015)]. The degree of the associated oxygen depletion in the different ocean basins, however, is still poorly constrained. Here, we present sedimentary records of redox-sensitive metals from the southwest African margin. These records show evidence of continuous bottom water anoxia in the eastern South Atlantic during the last glaciation that led to enhanced carbon burial over a prolonged period of time. Our geochemical data indicate that upwelling-related productivity and the associated oxygen minimum zone in the eastern South Atlantic shifted far seaward during the last glacial period and only slowly retreated during deglaciation times. While increased productivity during the last ice age may have contributed to oxygen depletion in bottom waters, especially on the upper slope, slow-down of the Late Quaternary deep water circulation pattern [Rutberg et al., Nature 405, 935–938 (2000)] appears to be the ultimate driver of anoxic conditions in deep waters.

Description: Animal gastrointestinal tracts harbor a microbiome that is integral to host function, yet species from diverse phyla have evolved a reduced digestive system or lost it completely. Whether such changes are associated with alterations in the diversity and/or abundance of the microbiome remains an untested hypothesis in evolutionary symbiosis. Here, using the life history transition from planktotrophy (feeding) to lecithotrophy (nonfeeding) in the sea urchin Heliocidaris, we demonstrate that the lack of a functional gut corresponds with a reduction in microbial community diversity and abundance as well as the association with a diet-specific microbiome. We also determine that the lecithotroph vertically transmits a Rickettsiales that may complement host nutrition through amino acid biosynthesis and influence host reproduction. Our results indicate that the evolutionary loss of a functional gut correlates with a reduction in the microbiome and the association with an endosymbiont. Symbiotic transitions can therefore accompany life history transitions in the evolution of developmental strategies.

Description: Significance: A central goal in invasion genomics is to identify and determine the mechanisms that underlie the successful colonization, establishment, and subsequent range expansion of invasive populations of nonindigenous species. Using a whole-genome approach, we evaluate the importance of genetic diversity for the successful establishment of nonindigenous species. Our study shows that genetic diversity per se is not the major factor driving invasions, since we observed all possible scenarios with invasive populations showing reduced, similar but also increased, genetic diversity relative to the native population. Using coalescent methods, we reconstruct the demographic history of the invasion and infer the source population of each invasion event, which shows that propagule pressure and multiple introductions play an important role in determining invasion success. Abstract: Invasion rates have increased in the past 100 y irrespective of international conventions. What characterizes a successful invasion event? And how does genetic diversity translate into invasion success? Employing a whole-genome perspective using one of the most successful marine invasive species world-wide as a model, we resolve temporal invasion dynamics during independent invasion events in Eurasia. We reveal complex regionally independent invasion histories including cases of recurrent translocations, time-limited translocations, and stepping-stone range expansions with severe bottlenecks within the same species. Irrespective of these different invasion dynamics, which lead to contrasting patterns of genetic diversity, all nonindigenous populations are similarly successful. This illustrates that genetic diversity, per se, is not necessarily the driving force behind invasion success. Other factors such as propagule pressure and repeated introductions are an important contribution to facilitate successful invasions. This calls into question the dominant paradigm of the genetic paradox of invasions, i.e., the successful establishment of nonindigenous populations with low levels of genetic diversity.

Description: With over 18,000 species, the Acanthomorpha, or spiny-rayed fishes, form the largest and arguably most diverse radiation of vertebrates. One of the key novelties that contributed to their evolutionary success are the spiny rays in their fins that serve as a defense mechanism. We investigated the patterning mechanisms underlying the differentiation of median fin Anlagen into discrete spiny and soft rayed domains during the ontogeny of the direct-developing cichlid fish Astatotilapia burtoni. Distinct transcription factor signatures characterize these two fin domains, whereby mutually exclusive expression of hoxa13a/b with alx4a/b and tbx2b marks the spine to soft-ray boundary. The soft-ray domain is established by BMP inhibition via gremlin1b, which synergizes in the posterior fin with shh secreted from a zone of polarizing activity. Modulation of BMP signaling by chemical inhibition or gremlin1b CRISPR/Cas9 knockout induces homeotic transformations of spines into soft rays and vice versa. The expression of spine and soft-ray genes in nonacanthomorph fins indicates that a combination of exaptation and posterior expansion of an ancestral developmental program for the anterior fin margin allowed the evolution of robustly individuated spiny and soft-rayed domains. We propose that a repeated exaptation of such pattern might underly the convergent evolution of anterior spiny fin elements across fishes.

Description: The Trans-European Suture Zone (TESZ) is the transition zone from the Precambrian East European Craton in the north and east to the younger Phanerozoic mobile belts to the south and west. It is the most prominent lithospheric tectonic feature of Europe. The term Trans-European Suture Zone was only adapted around year 2000 during the Pan-European EUROPROBE program of the European Science Foundation. Until then, parts of the zone were termed Teisseyre-Tornquist Zone, Sorgenfrei-Tornquist Zone, Trans-European Fault, and Tornquist Fan.

Description: Habitat heterogeneity and species diversity are often linked. On the deep seafloor, sediment variability and hard-substrate availability influence geographic patterns of species richness and turnover. The assumption of a generally homogeneous, sedimented abyssal seafloor is at odds with the fact that the faunal diversity in some abyssal regions exceeds that of shallow-water environments. Here we show, using a ground-truthed analysis of multibeam sonar data, that the deep seafloor may be much rockier than previously assumed. A combination of bathymetry data, ruggedness, and backscatter from a trans-Atlantic corridor along the Vema Fracture Zone, covering crustal ages from 0 to 100 Ma, show rock exposures occurring at all crustal ages. Extrapolating to the whole Atlantic, over 260,000 km2 of rock habitats potentially occur along Atlantic fracture zones alone, significantly increasing our knowledge about abyssal habitat heterogeneity. This implies that sampling campaigns need to be considerably more sophisticated than at present to capture the full deep-sea habitat heterogeneity and biodiversity.

Description: The impact of the ongoing anthropogenic warming on the Arctic Ocean sea ice is ascertained and closely monitored. However, its long-term fate remains an open question as its natural variability on centennial to millennial timescales is not well documented. Here, we use marine sedimentary records to reconstruct Arctic sea-ice fluctuations. Cores collected along the Lomonosov Ridge that extends across the Arctic Ocean from northern Greenland to the Laptev Sea were radiocarbon dated and analyzed for their micropaleontological and palynological contents, both bearing information on the past sea-ice cover. Results demonstrate that multiyear pack ice remained a robust feature of the western and central Lomonosov Ridge and that perennial sea ice remained present throughout the present interglacial, even during the climate optimum of the middle Holocene that globally peaked ∼6,500 y ago. In contradistinction, the southeastern Lomonosov Ridge area experienced seasonally sea-ice-free conditions, at least, sporadically, until about 4,000 y ago. They were marked by relatively high phytoplanktonic productivity and organic carbon fluxes at the seafloor resulting in low biogenic carbonate preservation. These results point to contrasted west–east surface ocean conditions in the Arctic Ocean, not unlike those of the Arctic dipole linked to the recent loss of Arctic sea ice. Hence, our data suggest that seasonally ice-free conditions in the southeastern Arctic Ocean with a dominant Arctic dipolar pattern, may be a recurrent feature under “warm world” climate.

Description: A fundamental problem for the evolution of pregnancy, the most specialized form of parental investment among vertebrates, is the rejection of the nonself-embryo. Mammals achieve immunological tolerance by down-regulating both major histocompatibility complex pathways (MHC I and II). Although pregnancy has evolved multiple times independently among vertebrates, knowledge of associated immune system adjustments is restricted to mammals. All of them (except monotremata) display full internal pregnancy, making evolutionary reconstructions within the class mammalia meaningless. Here, we study the seahorse and pipefish family (syngnathids) that have evolved male pregnancy across a gradient from external oviparity to internal gestation. We assess how immunological tolerance is achieved by reconstruction of the immune gene repertoire in a comprehensive sample of 12 seahorse and pipefish genomes along the “male pregnancy” gradient together with expression patterns of key immune and pregnancy genes in reproductive tissues. We found that the evolution of pregnancy coincided with a modification of the adaptive immune system. Divergent genomic rearrangements of the MHC II pathway among fully pregnant species were identified in both genera of the syngnathids: The pipefishes (Syngnathus) displayed loss of several genes of the MHC II pathway while seahorses (Hippocampus) featured a highly divergent invariant chain (CD74). Our findings suggest that a trade-off between immunological tolerance and embryo rejection accompanied the evolution of unique male pregnancy. That pipefishes survive in an ocean of microbes without one arm of the adaptive immune defense suggests a high degree of immunological flexibility among vertebrates, which may advance our understanding of immune-deficiency diseases.

Description: Assessment of the global budget of the greenhouse gas nitrous oxide ([Formula: see text]O) is limited by poor knowledge of the oceanic [Formula: see text]O flux to the atmosphere, of which the magnitude, spatial distribution, and temporal variability remain highly uncertain. Here, we reconstruct climatological [Formula: see text]O emissions from the ocean by training a supervised learning algorithm with over 158,000 [Formula: see text]O measurements from the surface ocean-the largest synthesis to date. The reconstruction captures observed latitudinal gradients and coastal hot spots of [Formula: see text]O flux and reveals a vigorous global seasonal cycle. We estimate an annual mean [Formula: see text]O flux of 4.2 ± 1.0 Tg N[Formula: see text], 64% of which occurs in the tropics, and 20% in coastal upwelling systems that occupy less than 3% of the ocean area. This [Formula: see text]O flux ranges from a low of 3.3 ± 1.3 Tg N[Formula: see text] in the boreal spring to a high of 5.5 ± 2.0 Tg N[Formula: see text] in the boreal summer. Much of the seasonal variations in global [Formula: see text]O emissions can be traced to seasonal upwelling in the tropical ocean and winter mixing in the Southern Ocean. The dominant contribution to seasonality by productive, low-oxygen tropical upwelling systems (〉75%) suggests a sensitivity of the global [Formula: see text]O flux to El Niño-Southern Oscillation and anthropogenic stratification of the low latitude ocean. This ocean flux estimate is consistent with the range adopted by the Intergovernmental Panel on Climate Change, but reduces its uncertainty by more than fivefold, enabling more precise determination of other terms in the atmospheric [Formula: see text]O budget.

Description: Climate-driven depletion of ocean oxygen strongly impacts the global cycles of carbon and nutrients as well as the survival of many animal species. One of the main uncertainties in predicting changes to marine oxygen levels is the regulation of the biological respiration demand associated with the biological pump. Derived from the Redfield ratio, the molar ratio of oxygen to organic carbon consumed during respiration (i.e., the respiration quotient, r−O2:C) is consistently assumed constant but rarely, if ever, measured. Using a prognostic Earth system model, we show that a 0.1 increase in the respiration quotient from 1.0 leads to a 2.3% decline in global oxygen, a large expansion of low-oxygen zones, additional water column denitrification of 38 Tg N/y, and the loss of fixed nitrogen and carbon production in the ocean. We then present direct chemical measurements of r−O2:C using a Pacific Ocean meridional transect crossing all major surface biome types. The observed r−O2:C has a positive correlation with temperature, and regional mean values differ significantly from Redfield proportions. Finally, an independent global inverse model analysis constrained with nutrients, oxygen, and carbon concentrations supports a positive temperature dependence of r−O2:C in exported organic matter. We provide evidence against the common assumption of a static biological link between the respiration of organic carbon and the consumption of oxygen. Furthermore, the model simulations suggest that a changing respiration quotient will impact multiple biogeochemical cycles and that future warming can lead to more intense deoxygenation than previously anticipated.

Description: The ocean is our planet’s largest life-support system. It stabilizes climate; stores carbon; produces oxygen; nurtures biodiversity; directly supports human well-being through food, mineral, and energy resources; and provides cultural and recreational services. The value of the ocean economy speaks to its importance: The Organization for Economic Cooperation and Development (OECD) estimates that by 2030, $3 trillion USD will be generated annually from ocean sectors such as transportation, fishing, tourism, and energy (1). Unsustainable resource extraction, pollution, climate change, and habitat destruction are on the rise and affecting many parts of the world’s oceans (2). The ocean is rapidly changing, and yet the ways in which these changes will play out are not yet clear.

Description: Plastid endosymbiosis has been a major force in the evolution of eukaryotic cellular complexity, but how endosymbionts are integrated is still poorly understood at a mechanistic level. Dinoflagellates, an ecologically important protist lineage, represent a unique model to study this process because dinoflagellate plastids have repeatedly been reduced, lost, and replaced by new plastids, leading to a spectrum of ages and integration levels. Here we describe deep-transcriptomic analyses of the Antarctic Ross Sea dinoflagellate (RSD), which harbors long-term but temporary kleptoplasts stolen from haptophyte prey, and is closely related to dinoflagellates with fully integrated plastids derived from different haptophytes. In some members of this lineage, called the Kareniaceae, their tertiary haptophyte plastids have crossed a tipping point to stable integration, but RSD has not, and may therefore reveal the order of events leading up to endosymbiotic integration. We show that RSD has retained its ancestral secondary plastid and has partitioned functions between this plastid and the kleptoplast. It has also obtained genes for kleptoplast-targeted proteins via horizontal gene transfer (HGT) that are not derived from the kleptoplast lineage. Importantly, many of these HGTs are also found in the related species with fully integrated plastids, which provides direct evidence that genetic integration preceded organelle fixation. Finally, we find that expression of kleptoplast-targeted genes is unaffected by environmental parameters, unlike prey-encoded homologs, suggesting that kleptoplast-targeted HGTs have adapted to posttranscriptional regulation mechanisms of the host.

Description: Significance: Although viruses are well-characterized regulators of eukaryotic algae, little is known about those infecting unicellular predators in oceans. We report the largest marine virus genome yet discovered, found in a wild predatory choanoflagellate sorted away from other Pacific microbes and pursued using integration of cultivation-independent and laboratory methods. The giant virus encodes nearly 900 proteins, many unlike known proteins, others related to cellular metabolism and organic matter degradation, and 3 type-1 rhodopsins. The viral rhodopsin that is most abundant in ocean metagenomes, and also present in an algal virus, pumps protons when illuminated, akin to cellular rhodopsins that generate a proton-motive force. Giant viruses likely provision multiple host species with photoheterotrophic capacities, including predatory unicellular relatives of animals. Abstract: Giant viruses are remarkable for their large genomes, often rivaling those of small bacteria, and for having genes thought exclusive to cellular life. Most isolated to date infect nonmarine protists, leaving their strategies and prevalence in marine environments largely unknown. Using eukaryotic single-cell metagenomics in the Pacific, we discovered a Mimiviridae lineage of giant viruses, which infects choanoflagellates, widespread protistan predators related to metazoans. The ChoanoVirus genomes are the largest yet from pelagic ecosystems, with 442 of 862 predicted proteins lacking known homologs. They are enriched in enzymes for modifying organic compounds, including degradation of chitin, an abundant polysaccharide in oceans, and they encode 3 divergent type-1 rhodopsins (VirR) with distinct evolutionary histories from those that capture sunlight in cellular organisms. One (VirRDTS) is similar to the only other putative rhodopsin from a virus (PgV) with a known host (a marine alga). Unlike the algal virus, ChoanoViruses encode the entire pigment biosynthesis pathway and cleavage enzyme for producing the required chromophore, retinal. We demonstrate that the rhodopsin shared by ChoanoViruses and PgV binds retinal and pumps protons. Moreover, our 1.65-Å resolved VirRDTS crystal structure and mutational analyses exposed differences from previously characterized type-1 rhodopsins, all of which come from cellular organisms. Multiple VirR types are present in metagenomes from across surface oceans, where they are correlated with and nearly as abundant as a canonical marker gene from Mimiviridae. Our findings indicate that light-dependent energy transfer systems are likely common components of giant viruses of photosynthetic and phagotrophic unicellular marine eukaryotes.

Description: Benthic foraminifera populate a diverse range of marine habitats. Their ability to use alternative electron acceptors—nitrate (NO3−) or oxygen (O2)—makes them important mediators of benthic nitrogen cycling. Nevertheless, the metabolic scaling of the two alternative respiration pathways and the environmental determinants of foraminiferal denitrification rates are yet unknown. We measured denitrification and O2 respiration rates for 10 benthic foraminifer species sampled in the Peruvian oxygen minimum zone (OMZ). Denitrification and O2 respiration rates significantly scale sublinearly with the cell volume. The scaling is lower for O2 respiration than for denitrification, indicating that NO3− metabolism during denitrification is more efficient than O2 metabolism during aerobic respiration in foraminifera from the Peruvian OMZ. The negative correlation of the O2 respiration rate with the surface/volume ratio is steeper than for the denitrification rate. This is likely explained by the presence of an intracellular NO3− storage in denitrifying foraminifera. Furthermore, we observe an increasing mean cell volume of the Peruvian foraminifera, under higher NO3− availability. This suggests that the cell size of denitrifying foraminifera is not limited by O2 but rather by NO3− availability. Based on our findings, we develop a mathematical formulation of foraminiferal cell volume as a predictor of respiration and denitrification rates, which can further constrain foraminiferal biogeochemical cycling in biogeochemical models. Our findings show that NO3− is the preferred electron acceptor in foraminifera from the OMZ, where the foraminiferal contribution to denitrification is governed by the ratio between NO3− and O2.

Description: Significance During the Holocene (11,600 y ago to present), northern peatlands accumulated significant C stocks over millennia. However, virtually nothing is known about peatlands that are no longer in the landscape, including ones formed prior to the Holocene: Where were they, when did they form, and why did they disappear? We used records of peatlands buried by mineral sediments for a reconstruction of peat-forming wetlands for the past 130,000 y. Northern peatlands expanded across high latitudes during warm periods and were buried during periods of glacial advance in northern latitudes. Thus, peat accumulation and burial represent a key long-term C storage mechanism in the Earth system. Abstract Glacial−interglacial variations in CO2 and methane in polar ice cores have been attributed, in part, to changes in global wetland extent, but the wetland distribution before the Last Glacial Maximum (LGM, 21 ka to 18 ka) remains virtually unknown. We present a study of global peatland extent and carbon (C) stocks through the last glacial cycle (130 ka to present) using a newly compiled database of 1,063 detailed stratigraphic records of peat deposits buried by mineral sediments, as well as a global peatland model. Quantitative agreement between modeling and observations shows extensive peat accumulation before the LGM in northern latitudes (〉40°N), particularly during warmer periods including the last interglacial (130 ka to 116 ka, MIS 5e) and the interstadial (57 ka to 29 ka, MIS 3). During cooling periods of glacial advance and permafrost formation, the burial of northern peatlands by glaciers and mineral sediments decreased active peatland extent, thickness, and modeled C stocks by 70 to 90% from warmer times. Tropical peatland extent and C stocks show little temporal variation throughout the study period. While the increased burial of northern peats was correlated with cooling periods, the burial of tropical peat was predominately driven by changes in sea level and regional hydrology. Peat burial by mineral sediments represents a mechanism for long-term terrestrial C storage in the Earth system. These results show that northern peatlands accumulate significant C stocks during warmer times, indicating their potential for C sequestration during the warming Anthropocene.

Description: Ocean acidification (OA) is considered an important threat to coral reef ecosystems, because it reduces the availability of carbonate ions that reef-building corals need to produce their skeletons. However, while theory predicts that coral calcification rates decline as carbonate ion concentrations decrease, this prediction is not consistently borne out in laboratory manipulation experiments or in studies of corals inhabiting naturally low-pH reefs today. The skeletal growth of corals consists of two distinct processes: extension (upward growth) and densification (lateral thickening). Here, we show that skeletal density is directly sensitive to changes in seawater carbonate ion concentration and thus, to OA, whereas extension is not. We present a numerical model of Porites skeletal growth that links skeletal density with the external seawater environment via its influence on the chemistry of coral calcifying fluid. We validate the model using existing coral skeletal datasets from six Porites species collected across five reef sites and use this framework to project the impact of 21st century OA on Porites skeletal density across the global tropics. Our model predicts that OA alone will drive up to 20.3 ± 5.4% decline in the skeletal density of reef-building Porites corals.

Description: The Pacific hosts the largest oxygen minimum zones (OMZs) in the world ocean, which are thought to intensify and expand under future climate change, with significant consequences for marine ecosystems, biogeochemical cycles, and fisheries. At present, no deep ventilation occurs in the North Pacific due to a persistent halocline, but relatively better-oxygenated subsurface North Pacific Intermediate Water (NPIW) mitigates OMZ development in lower latitudes. Over the past decades, instrumental data show decreasing oxygenation in NPIW; however, long-term variations in middepth ventilation are potentially large, obscuring anthropogenic influences against millennial-scale natural background shifts. Here, we use paleoceanographic proxy evidence from the Okhotsk Sea, the foremost North Pacific ventilation region, to show that its modern oxygenated pattern is a relatively recent feature, with little to no ventilation before six thousand years ago, constituting an apparent Early–Middle Holocene (EMH) threshold or “tipping point.” Complementary paleomodeling results likewise indicate a warmer, saltier EMH NPIW, different from its modern conditions. During the EMH, the Okhotsk Sea switched from a modern oxygenation source to a sink, through a combination of sea ice loss, higher water temperatures, and remineralization rates, inhibiting ventilation. We estimate a strongly decreased EMH NPIW oxygenation of ∼30 to 50%, and increased middepth Pacific nutrient concentrations and carbon storage. Our results (i) imply that under past or future warmer-than-present conditions, oceanic biogeochemical feedback mechanisms may change or even switch direction, and (ii) provide constraints on the high-latitude North Pacific’s influence on mesopelagic ventilation dynamics, with consequences for large oceanic regions.

Description: Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms. Here, we synthesize the powerful paradigm emerging from these two patterns, connecting the roles of function, functional redundancy and taxonomy in microbial systems. We conclude that both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.

Description: Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15–46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800–1066 CE) and subsequent medieval (1066–1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.

Description: Recognition that evolution operates on the same timescale as ecological processes has motivated growing interest in eco-evolutionary dynamics. Nonetheless, generating sufficient data to test predictions about eco-evolutionary dynamics has proved challenging, particularly in natural contexts. Here we argue that genomic data can be integrated into the study of eco-evolutionary dynamics in ways that deepen our understanding of the interplay between ecology and evolution. Specifically, we outline five major questions in the study of eco-evolutionary dynamics for which genomic data may provide answers. Although genomic data alone will not be sufficient to resolve these challenges, integrating genomic data can provide a more mechanistic understanding of the causes of phenotypic change, help elucidate the mechanisms driving eco-evolutionary dynamics, and lead to more accurate evolutionary predictions of eco-evolutionary dynamics in nature.

Description: Although nearly all 2 °C scenarios use negative CO2 emission technologies, only relatively small investments are being made in them, and concerns are being raised regarding their large-scale use. If no explicit policy decisions are taken soon, however, their use will simply be forced on us to meet the Paris climate targets.

Description: Continued warming of the Arctic Ocean in coming decades is projected to trigger the release of teragrams (1 Tg = 10(6) tons) of methane from thawing subsea permafrost on shallow continental shelves and dissociation of methane hydrate on upper continental slopes. On the shallow shelves (〈100 m water depth), methane released from the seafloor may reach the atmosphere and potentially amplify global warming. On the other hand, biological uptake of carbon dioxide (CO2) has the potential to offset the positive warming potential of emitted methane, a process that has not received detailed consideration for these settings. Continuous sea-air gas flux data collected over a shallow ebullitive methane seep field on the Svalbard margin reveal atmospheric CO2 uptake rates (-33,300 ± 7,900 μmol m(-2)⋅d(-1)) twice that of surrounding waters and ∼1,900 times greater than the diffusive sea-air methane efflux (17.3 ± 4.8 μmol m(-2)⋅d(-1)). The negative radiative forcing expected from this CO2 uptake is up to 231 times greater than the positive radiative forcing from the methane emissions. Surface water characteristics (e.g., high dissolved oxygen, high pH, and enrichment of (13)C in CO2) indicate that upwelling of cold, nutrient-rich water from near the seafloor accompanies methane emissions and stimulates CO2 consumption by photosynthesizing phytoplankton. These findings challenge the widely held perception that areas characterized by shallow-water methane seeps and/or strongly elevated sea-air methane flux always increase the global atmospheric greenhouse gas burden.

Description: Marine microscopic plastic (microplastic) debris is a modern societal issue, illustrating the challenge of balancing the convenience of plastic in daily life with the prospect of causing ecological harm by careless disposal. Here we develop the concept of microplastic as a complex, dynamic mixture of polymers and additives, to which organic material and contaminants can successively bind to form an ‘ecocorona’, increasing the density and surface charge of particles and changing their bioavailability and toxicity. Chronic exposure to microplastic is rarely lethal, but can adversely affect individual animals, reducing feeding and depleting energy stores, with knock-on effects for fecundity and growth. We explore the extent to which ecological processes could be impacted, including altered behaviours, bioturbation and impacts on carbon flux to the deep ocean. We discuss how microplastic compares with other anthropogenic pollutants in terms of ecological risk, and consider the role of science and society in tackling this global issue in the future.

Description: Autophagy is a mechanism by which cellular material is delivered to lysosomes for degradation, leading to the basal turnover of cell components and providing energy and macromolecular precursors. Autophagy has opposing, context-dependent roles in cancer, and interventions to both stimulate and inhibit autophagy have been proposed as cancer therapies. This has led to the therapeutic targeting of autophagy in cancer to be sometimes viewed as controversial. In this Review, we suggest a way forwards for the effective targeting of autophagy by understanding the context-dependent roles of autophagy and by capitalizing on modern approaches to clinical trial design.

Description: Connections between glaciation, chemical weathering, and the global carbon cycle could steer the evolution of global climate over geologic time, but even the directionality of feedbacks in this system remain to be resolved. Here, we assemble a compilation of hydrochemical data from glacierized catchments, use this data to evaluate the dominant chemical reactions associated with glacial weathering, and explore the implications for long-term geochemical cycles. Weathering yields from catchments in our compilation are higher than the global average, which results, in part, from higher runoff in glaciated catchments. Our analysis supports the theory that glacial weathering is characterized predominantly by weathering of trace sulfide and carbonate minerals. To evaluate the effects of glacial weathering on atmospheric pCO2, we use a solute mixing model to predict the ratio of alkalinity to dissolved inorganic carbon (DIC) generated by weathering reactions. Compared with nonglacial weathering, glacial weathering is more likely to yield alkalinity/DIC ratios less than 1, suggesting that enhanced sulfide oxidation as a result of glaciation may act as a source of CO2 to the atmosphere. Back-of-the-envelope calculations indicate that oxidative fluxes could change ocean–atmosphere CO2 equilibrium by 25 ppm or more over 10 ky. Over longer timescales, CO2 release could act as a negative feedback, limiting progress of glaciation, dependent on lithology and the concentration of atmospheric O2. Future work on glaciation–weathering–carbon cycle feedbacks should consider weathering of trace sulfide minerals in addition to silicate minerals.

Description: Significance: Cold and dry glacial-state climate conditions persisted in the Southern Hemisphere until approximately 17.7 ka, when paleoclimate records show a largely unexplained sharp, nearly synchronous acceleration in deglaciation. Detailed measurements in Antarctic ice cores document exactly at that time a unique, ∼192-y series of massive halogen-rich volcanic eruptions geochemically attributed to Mount Takahe in West Antarctica. Rather than a coincidence, we postulate that halogen-catalyzed stratospheric ozone depletion over Antarctica triggered large-scale atmospheric circulation and hydroclimate changes similar to the modern Antarctic ozone hole, explaining the synchronicity and abruptness of accelerated Southern Hemisphere deglaciation. Abstract: Glacial-state greenhouse gas concentrations and Southern Hemisphere climate conditions persisted until ∼17.7 ka, when a nearly synchronous acceleration in deglaciation was recorded in paleoclimate proxies in large parts of the Southern Hemisphere, with many changes ascribed to a sudden poleward shift in the Southern Hemisphere westerlies and subsequent climate impacts. We used high-resolution chemical measurements in the West Antarctic Ice Sheet Divide, Byrd, and other ice cores to document a unique, ∼192-y series of halogen-rich volcanic eruptions exactly at the start of accelerated deglaciation, with tephra identifying the nearby Mount Takahe volcano as the source. Extensive fallout from these massive eruptions has been found 〉2,800 km from Mount Takahe. Sulfur isotope anomalies and marked decreases in ice core bromine consistent with increased surface UV radiation indicate that the eruptions led to stratospheric ozone depletion. Rather than a highly improbable coincidence, circulation and climate changes extending from the Antarctic Peninsula to the subtropics—similar to those associated with modern stratospheric ozone depletion over Antarctica—plausibly link the Mount Takahe eruptions to the onset of accelerated Southern Hemisphere deglaciation ∼17.7 ka.

Description: Phytoplankton photosynthesis is a critical flux in the carbon cycle, accounting for approximately 40% of the carbon dioxide fixed globally on an annual basis and fuelling the productivity of aquatic food webs. However, rapid evolutionary responses of phytoplankton to warming remain largely unexplored, particularly outside the laboratory, where multiple selection pressures can modify adaptation to environmental change. Here, we use a decade-long experiment in outdoor mesocosms to investigate mechanisms of adaptation to warming (+4 °C above ambient temperature) in the green alga Chlamydomonas reinhardtii, in naturally assembled communities. Isolates from warmed mesocosms had higher optimal growth temperatures than their counterparts from ambient treatments. Consequently, warm-adapted isolates were stronger competitors at elevated temperature and experienced a decline in competitive fitness in ambient conditions, indicating adaptation to local thermal regimes. Higher competitive fitness in the warmed isolates was linked to greater photosynthetic capacity and reduced susceptibility to photoinhibition. These findings suggest that adaptive responses to warming in phytoplankton could help to mitigate projected declines in aquatic net primary production by increasing rates of cellular net photosynthesis.

Description: Nitrogen fixation — the reduction of dinitrogen (N2) gas to biologically available nitrogen (N) — is an important source of N for terrestrial and aquatic ecosystems. In terrestrial environments, N2-fixing symbioses involve multicellular plants, but in the marine environment these symbioses occur with unicellular planktonic algae. An unusual symbiosis between an uncultivated unicellular cyanobacterium (UCYN-A) and a haptophyte picoplankton alga was recently discovered in oligotrophic oceans. UCYN-A has a highly reduced genome, and exchanges fixed N for fixed carbon with its host. This symbiosis bears some resemblance to symbioses found in freshwater ecosystems. UCYN-A shares many core genes with the 'spheroid bodies' of Epithemia turgida and the endosymbionts of the amoeba Paulinella chromatophora. UCYN-A is widely distributed, and has diversified into a number of sublineages that could be ecotypes. Many questions remain regarding the physical and genetic mechanisms of the association, but UCYN-A is an intriguing model for contemplating the evolution of N2-fixing organelles.

Description: A major percentage of fixed nitrogen (N) loss in the oceans occurs within nitrite-rich oxygen minimum zones (OMZs) via denitrification and anammox. It remains unclear to what extent ammonium and nitrite oxidation co-occur, either supplying or competing for substrates involved in nitrogen loss in the OMZ core. Assessment of the oxygen (O2) sensitivity of these processes down to the O2 concentrations present in the OMZ core (〈10 nmol⋅L−1) is therefore essential for understanding and modeling nitrogen loss in OMZs. We determined rates of ammonium and nitrite oxidation in the seasonal OMZ off Concepcion, Chile at manipulated O2 levels between 5 nmol⋅L−1 and 20 μmol⋅L−1. Rates of both processes were detectable in the low nanomolar range (5–33 nmol⋅L−1 O2), but demonstrated a strong dependence on O2 concentrations with apparent half-saturation constants (Kms) of 333 ± 130 nmol⋅L−1 O2 for ammonium oxidation and 778 ± 168 nmol⋅L−1 O2 for nitrite oxidation assuming one-component Michaelis–Menten kinetics. Nitrite oxidation rates, however, were better described with a two-component Michaelis–Menten model, indicating a high-affinity component with a Km of just a few nanomolar. As the communities of ammonium and nitrite oxidizers were similar to other OMZs, these kinetics should apply across OMZ systems. The high O2 affinities imply that ammonium and nitrite oxidation can occur within the OMZ core whenever O2 is supplied, for example, by episodic intrusions. These processes therefore compete with anammox and denitrification for ammonium and nitrite, thereby exerting an important control over nitrogen loss.

Description: The isotopic diversity of oceanic island basalts (OIB) is usually attributed to the influence, in their sources, of ancient material recycled into the mantle, although the nature, age, and quantities of this material remain controversial. The unradiogenic Pb isotope signature of the enriched mantle I (EM I) source of basalts from, for example, Pitcairn or Walvis Ridge has been variously attributed to recycled pelagic sediments, lower continental crust, or recycled subcontinental lithosphere. Our study helps resolve this debate by showing that Pitcairn lavas contain sulfides whose sulfur isotopic compositions are affected by mass-independent fractionation (S-MIF down to Δ33S = −0.8), something which is thought to have occurred on Earth only before 2.45 Ga, constraining the youngest possible age of the EM I source component. With this independent age constraint and a Monte Carlo refinement modeling of lead isotopes, we place the likely Pitcairn source age at 2.5 Ga to 2.6 Ga. The Pb, Sr, Nd, and Hf isotopic mixing arrays show that the Archean EM I material was poor in trace elements, resembling Archean sediment. After subduction, this Archean sediment apparently remained stored in the deep Earth for billions of years before returning to the surface as Pitcairn´s characteristic EM I signature. The presence of negative S-MIF in the deep mantle may also help resolve the problem of an apparent deficit of negative Δ33S anomalies so far found in surface reservoirs.

Description: Members of the archaeal phylum Bathyarchaeota are widespread and abundant in the energy-deficient marine subsurface sediments. However, their life strategies have remained largely elusive. Here, we provide genetic evidence that some lineages of Bathyarchaeota are acetogens, being capable of homoacetogenesis, a metabolism so far restricted to the domain Bacteria. Metabolic reconstruction based on genomic bins assembled from the metagenome of deep-sea subsurface sediments shows that the metabolism of some lineages of Bathyarchaeota is similar to that of bona fide bacterial homoacetogens, by having pathways for acetogenesis and for the fermentative utilization of a variety of organic substrates. Heterologous expression and activity assay of the acetate kinase gene ack from Bathyarchaeota, demonstrate further the capability of these Bathyarchaeota to grow as acetogens. The presence and expression of bathyarchaeotal genes indicative of active acetogenesis was also confirmed in Peru Margin subsurface sediments where Bathyarchaeota are abundant. The analyses reveal that this ubiquitous and abundant subsurface archaeal group has adopted a versatile life strategy to make a living under energy-limiting conditions. These findings further expand the metabolic potential of Archaea and argue for a revision of the role of Archaea in the carbon cycle of marine sediments.

Description: The biological carbon pump, which transports particulate organic carbon (POC) from the surface to the deep ocean, plays an important role in regulating atmospheric carbon dioxide (CO2) concentrations. We know very little about geographical variability in the remineralization depth of this sinking material and less about what controls such variability. Here we present previously unpublished profiles of mesopelagic POC flux derived from neutrally buoyant sediment traps deployed in the North Atlantic, from which we calculate the remineralization length scale for each site. Combining these results with corresponding data from the North Pacific, we show that the observed variability in attenuation of vertical POC flux can largely be explained by temperature, with shallower remineralization occurring in warmer waters. This is seemingly inconsistent with conclusions drawn from earlier analyses of deep-sea sediment trap and export flux data, which suggest lowest transfer efficiency at high latitudes. However, the two patterns can be reconciled by considering relatively intense remineralization of a labile fraction of material in warm waters, followed by efficient downward transfer of the remaining refractory fraction, while in cold environments, a larger labile fraction undergoes slower remineralization that continues over a longer length scale. Based on the observed relationship, future increases in ocean temperature will likely lead to shallower remineralization of POC and hence reduced storage of CO2 by the ocean.

Description: Theoretical studies predict that competition for limited resources reduces biodiversity to the point of ecological instability, whereas strong predator/prey interactions enhance the number of coexisting species and limit fluctuations in abundances. In open ocean ecosystems, competition for low availability of essential nutrients results in relatively few abundant microbial species. The remarkable stability in overall cell abundance of the dominant photosynthetic cyanobacterium Prochlorococcus is assumed to reflect a simple food web structure strongly controlled by grazers and/or viruses. This hypothesized link between stability and ecological interactions, however, has been difficult to test with open ocean microbes because sampling methods commonly have poor temporal and spatial resolution. Here we use continuous techniques on two different winter-time cruises to show that Prochlorococcus cell production and mortality rates are tightly synchronized to the day/night cycle across the subtropical Pacific Ocean. In warmer waters, we observed harmonic oscillations in cell production and mortality rates, with a peak in mortality rate consistently occurring ∼6 h after the peak in cell production. Essentially no cell mortality was observed during daylight. Our results are best explained as a synchronized two-component trophic interaction with the per-capita rates of Prochlorococcus consumption driven either directly by the day/night cycle or indirectly by Prochlorococcus cell production. Light-driven synchrony of food web dynamics in which most of the newly produced Prochlorococcus cells are consumed each night likely enforces ecosystem stability across vast expanses of the open ocean. © 2015, National Academy of Sciences. All rights reserved.

Description: No records exist to evaluate long-term pH dynamics in high-latitude oceans, which have the greatest probability of rapid acidification from anthropogenic CO2 emissions. We reconstructed both seasonal variability and anthropogenic change in seawater pH and temperature by using laser ablation high-resolution 2D images of stable boron isotopes (δ11B) on a long-lived coralline alga that grew continuously through the 20th century. Analyses focused on four multiannual growth segments. We show a long-term decline of 0.08 ± 0.01 pH units between the end of the 19th and 20th century, which is consistent with atmospheric CO2 records. Additionally, a strong seasonal cycle (∼0.22 pH units) is observed and interpreted as episodic annual pH increases caused by the consumption of CO2 during strong algal (kelp) growth in spring and summer. The rate of acidification intensifies from –0.006 ± 0.007 pH units per decade (between 1920s and 1960s) to –0.019 ± 0.009 pH units per decade (between 1960s and 1990s), and the episodic pH increases show a continuous shift to earlier times of the year throughout the centennial record. This is indicative of ecosystem shifts in shallow water algal productivity in this high-latitude habitat resulting from warming and acidification.

Description: Inorganic nitrogen depletion restricts productivity in much of the low-latitude oceans, generating a selective advantage for diazotrophic organisms capable of fixing atmospheric dinitrogen (N2). However, the abundance and activity of diazotrophs can in turn be controlled by the availability of other potentially limiting nutrients, including phosphorus (P) and iron (Fe). Here we present high-resolution data (∼0.3°) for dissolved iron, aluminum, and inorganic phosphorus that confirm the existence of a sharp north–south biogeochemical boundary in the surface nutrient concentrations of the (sub)tropical Atlantic Ocean. Combining satellite-based precipitation data with results from a previous study, we here demonstrate that wet deposition in the region of the intertropical convergence zone acts as the major dissolved iron source to surface waters. Moreover, corresponding observations of N2 fixation and the distribution of diazotrophic Trichodesmium spp. indicate that movement in the region of elevated dissolved iron as a result of the seasonal migration of the intertropical convergence zone drives a shift in the latitudinal distribution of diazotrophy and corresponding dissolved inorganic phosphorus depletion. These conclusions are consistent with the results of an idealized numerical model of the system. The boundary between the distinct biogeochemical systems of the (sub)tropical Atlantic thus appears to be defined by the diazotrophic response to spatial–temporal variability in external Fe inputs. Consequently, in addition to demonstrating a unique seasonal cycle forced by atmospheric nutrient inputs, we suggest that the underlying biogeochemical mechanisms would likely characterize the response of oligotrophic systems to altered environmental forcing over longer timescales.

Description: Phytochrome photosensors control a vast gene network in streptophyte plants, acting as master regulators of diverse growth and developmental processes throughout the life cycle. In contrast with their absence in known chlorophyte algal genomes and most sequenced prasinophyte algal genomes, a phytochrome is found in Micromonas pusilla , a widely distributed marine picoprasinophyte (〈2 μm cell diameter). Together with phytochromes identified from other prasinophyte lineages, we establish that prasinophyte and streptophyte phytochromes share core lightinput and signaling-output domain architectures except for the loss of C-terminal response regulator receiver domains in the streptophyte phytochrome lineage. Phylogenetic reconstructions robustly support the presence of phytochrome in the common progenitor of green algae and land plants. These analyses reveal a monophyletic clade containing streptophyte, prasinophyte, cryptophyte, and glaucophyte phytochromes implying an origin in the eukaryotic ancestor of the Archaeplastida. Transcriptomic measurements reveal diurnal regulation of phytochrome and bilin chromophore biosynthetic genes in Micromonas. Expression of these genes precedes both light-mediated phytochrome redistribution from the cytoplasm to the nucleus and increased expression of photo-synthesis-associated genes. Prasinophyte phytochromes perceive wavelengths of light transmitted farther through seawater than the red/far-red light sensed by land plant phytochromes. Prasinophyte phytochromes also retain light-regulated histidine kinase activity lost in the streptophyte phytochrome lineage. Our studies demonstrate that light-mediated nuclear translocation of phytochrome predates the emergence of land plants and likely represents a widespread signaling mechanism in unicellular algae.

Description: Plant phytochromes are photoswitchable red/far-red photoreceptors that allow competition with neighboring plants for photosynthetically active red light. In aquatic environments, red and far-red light are rapidly attenuated with depth; therefore, photosynthetic species must use shorter wavelengths of light. Nevertheless, phytochrome-related proteins are found in recently sequenced genomes of many eukaryotic algae from aquatic environments. We examined the photosensory properties of seven phytochromes from diverse algae: four prasinophyte (green algal) species, the heterokont (brown algal) Ectocarpus siliculosus, and two glaucophyte species. We demonstrate that algal phytochromes are not limited to red and far-red responses. Instead, different algal phytochromes can sense orange, green, and even blue light. Characterization of these previously undescribed photosensors using CD spectroscopy supports a structurally heterogeneous chromophore in the far-red-absorbing photostate. Our study thus demonstrates that extensive spectral tuning of phytochromes has evolved in phylogenetically distinct lineages of aquatic photosynthetic eukaryotes.

Description: In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity. This review examines how a growing knowledge of the vast range of animal-bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology. Specifically, we highlight recent technological and intellectual advances that have changed our thinking about five questions: how have bacteria facilitated the origin and evolution of animals; how do animals and bacteria affect each other's genomes; how does normal animal development depend on bacterial partners; how is homeostasis maintained between animals and their symbionts; and how can ecological approaches deepen our understanding of the multiple levels of animal-bacterial interaction. As answers to these fundamental questions emerge, all biologists will be challenged to broaden their appreciation of these interactions and to include investigations of the relationships between and among bacteria and their animal partners as we seek a better understanding of the natural world.

Description: Long-term observations of the reactive chemical composition of the tropical marine boundary layer (MBL) are rare, despite its crucial role for the chemical stability of the atmosphere. Recent observations of reactive bromine species in the tropical MBL showed unexpectedly high levels that could potentially have an impact on the ozone budget. Uncertainties in the ozone budget are amplified by our poor understanding of the fate of NOx (= NO + NO2), particularly the importance of nighttime chemical NOx sinks. Here, we present year-round observations of the multiisotopic composition of atmospheric nitrate in the tropical MBL at the Cape Verde Atmospheric Observatory. We show that the observed oxygen isotope ratios of nitrate are compatible with nitrate formation chemistry, which includes the BrNO3 sink at a level of ca. 20 ± 10% of nitrate formation pathways. The results also suggest that the N2O5 pathway is a negligible NOx sink in this environment. Observations further indicate a possible link between the NO2/NOx ratio and the nitrogen isotopic content of nitrate in this low NOx environment, possibly reflecting the seasonal change in the photochemical equilibrium among NOx species. This study demonstrates the relevance of using the stable isotopes of oxygen and nitrogen of atmospheric nitrate in association with concentration measurements to identify and constrain chemical processes occurring in the MBL.

Description: Northern Hemisphere sea ice has been declining sharply over the past decades and 2012 exhibited the lowest Arctic summer sea-ice cover in historic times. Whereas ongoing changes are closely monitored through satellite observations, we have only limited data of past Arctic sea-ice cover derived from short historical records, indirect terrestrial proxies, and low-resolution marine sediment cores. A multicentury time series from extremely long-lived annual increment-forming crustose coralline algal buildups now provides the first high-resolution in situ marine proxy for sea-ice cover. Growth and Mg/Ca ratios of these Arctic-wide occurring calcified algae are sensitive to changes in both temperature and solar radiation. Growth sharply declines with increasing sea-ice blockage of light from the benthic algal habitat. The 646-y multisite record from the Canadian Arctic indicates that during the Little Ice Age, sea ice was extensive but highly variable on subdecadal time scales and coincided with an expansion of ice-dependent Thule/Labrador Inuit sea mammal hunters in the region. The past 150 y instead have been characterized by sea ice exhibiting multidecadal variability with a long-term decline distinctly steeper than at any time since the 14th century.

Description: Diatoms of the iron-replete continental margins and North Atlantic are key exporters of organic carbon. In contrast, diatoms of the iron-limited Antarctic Circumpolar Current sequester silicon, but comparatively little carbon, in the underlying deep ocean and sediments. Because the Southern Ocean is the major hub of oceanic nutrient distribution, selective silicon sequestration there limits diatom blooms elsewhere and consequently the biotic carbon sequestration potential of the entire ocean. We investigated this paradox in an in situ iron fertilization experiment by comparing accumulation and sinking of diatom populations inside and outside the iron-fertilized patch over 5 wk. A bloom comprising various thin- and thick-shelled diatom species developed inside the patch despite the presence of large grazer populations. After the third week, most of the thinner-shelled diatom species underwent mass mortality, formed large, mucous aggregates, and sank out en masse (carbon sinkers). In contrast, thicker-shelled species, in particular Fragilariopsis kerguelensis, persisted in the surface layers, sank mainly empty shells continuously, and reduced silicate concentrations to similar levels both inside and outside the patch (silica sinkers). These patterns imply that thick-shelled, hence grazer-protected, diatom species evolved in response to heavy copepod grazing pressure in the presence of an abundant silicate supply. The ecology of these silica-sinking species decouples silicon and carbon cycles in the iron-limited Southern Ocean, whereas carbon-sinking species, when stimulated by iron fertilization, export more carbon per silicon. Our results suggest that large-scale iron fertilization of the silicate-rich Southern Ocean will not change silicon sequestration but will add carbon to the sinking silica flux.

Description: Insects with complex life-cycles should optimize age and size at maturity during larval development. When inhabiting seasonal environments, organisms have limited reproductive periods and face fundamental decisions: individuals that reach maturity late in season have to either reproduce at a small size or increase their growth rates. Increasing growth rates is costly in insects because of higher juvenile mortality, decreased adult survival or increased susceptibility to parasitism by bacteria and viruses via compromised immune function. Environmental changes such as seasonality can also alter the quantitative genetic architecture. Here, we explore the quantitative genetics of life history and immunity traits under two experimentally induced seasonal environments in the cricket Gryllus bimaculatus. Seasonality affected the life history but not the immune phenotypes. Individuals under decreasing day length developed slower and grew to a bigger size. We found ample additive genetic variance and heritability for components of immunity (haemocyte densities, proPhenoloxidase activity, resistance against Serratia marcescens), and for the life history traits, age and size at maturity. Despite genetic covariance among traits, the structure of G was inconsistent with genetically based trade-off between life history and immune traits (for example, a strong positive genetic correlation between growth rate and haemocyte density was estimated). However, conditional evolvabilities support the idea that genetic covariance structure limits the capacity of individual traits to evolve independently. We found no evidence for G × E interactions arising from the experimentally induced seasonality.

Description: Calcifying echinoid larvae respond to changes in seawater carbonate chemistry with reduced growth and developmental delay. To date, no information exists on how ocean acidification acts on pH homeostasis in echinoderm larvae. Understanding acid–base regulatory capacities is important because intracellular formation and maintenance of the calcium carbonate skeleton is dependent on pH homeostasis. Using H+-selective microelectrodes and the pH-sensitive fluorescent dye BCECF, we conducted in vivo measurements of extracellular and intracellular pH (pHe and pHi) in echinoderm larvae. We exposed pluteus larvae to a range of seawater CO2 conditions and demonstrated that the extracellular compartment surrounding the calcifying primary mesenchyme cells (PMCs) conforms to the surrounding seawater with respect to pH during exposure to elevated seawater pCO2. Using FITC dextran conjugates, we demonstrate that sea urchin larvae have a leaky integument. PMCs and spicules are therefore directly exposed to strong changes in pHe whenever seawater pH changes. However, measurements of pHi demonstrated that PMCs are able to fully compensate an induced intracellular acidosis. This was highly dependent on Na+ and HCO3−, suggesting a bicarbonate buffer mechanism involving secondary active Na+-dependent membrane transport proteins. We suggest that, under ocean acidification, maintained pHi enables calcification to proceed despite decreased pHe. However, this probably causes enhanced costs. Increased costs for calcification or cellular homeostasis can be one of the main factors leading to modifications in energy partitioning, which then impacts growth and, ultimately, results in increased mortality of echinoid larvae during the pelagic life stage.

Description: Coccolithophores are an important component of the Earth system, and, as calcifiers, their possible susceptibility to ocean acidification is of major concern. Laboratory studies at enhanced pCO2 levels have produced divergent results without overall consensus. However, it has been predicted from these studies that, although calcification may not be depressed in all species, acidification will produce "a transition in dominance from more to less heavily calcified coccolithophores"Ridgwell A, et al., (2009) Biogeosciences 6:2611-2623. A recent observational study Beaufort L, et al., (2011) Nature 476:80-83 also suggested that coccolithophores are less calcified in more acidic conditions.We present the results of a large observational study of coccolithophore morphology in the Bay of Biscay. Samples were collected once a month for over a year, along a 1,000-km-long transect. Our data clearly show that there is a pronounced seasonality in the morphotypes of Emiliania huxleyi, the most abundant coccolithophore species. Whereas pH and CaCO 3saturation are lowest in winter, the E. huxleyi population shifts from 〈10% (summer) to >90% (winter) of the heavily calcified form. However, it is unlikely that the shifts in carbonate chemistry alone caused the morphotype shift. Our finding that the most heavily calcified morphotype dominates when conditions are most acidic is contrary to the earlier predictions and raises further questions about the fate of coccolithophores in a high-CO2 world.

Description: Cell-based therapies, such as adoptive immunotherapy and stem-cell therapy, have received considerable attention as novel therapeutics in oncological research and clinical practice. The development of effective therapeutic strategies using tumor-targeted cells requires the ability to determine in vivo the location, distribution, and long-term viability of the therapeutic cell populations as well as their biological fate with respect to cell activation and differentiation. In conjunction with various noninvasive imaging modalities, cell-labeling methods, such as exogenous labeling or transfection with a reporter gene, allow visualization of labeled cells in vivo in real time, as well as monitoring and quantifying cell accumulation and function. Such cell-tracking methods also have an important role in basic cancer research, where they serve to elucidate novel biological mechanisms. In this Review, we describe the basic principles of cell-tracking methods, explain various approaches to cell tracking, and highlight recent examples for the application of such methods in animals and humans.

Description: Microbial degradation of substrates to terminal products is commonly understood as a unidirectional process. In individual enzymatic reactions, however, reversibility (reverse reaction and product back flux) is common. Hence, it is possible that entire pathways of microbial degradation are associated with back flux from the accumulating product pool through intracellular intermediates into the substrate pool. We investigated carbon and sulfur back flux during the anaerobic oxidation of methane (AOM) with sulfate, one of the least exergonic microbial catabolic processes known. The involved enzymes must operate not far from the thermodynamic equilibrium. Such an energetic situation is likely to favor product back flux. Indeed, cultures of highly enriched archaeal–bacterial consortia, performing net AOM with unlabeled methane and sulfate, converted label from 14C-bicarbonate and 35S-sulfide to 14C-methane and 35S-sulfate, respectively. Back fluxes reached 5% and 13%, respectively, of the net AOM rate. The existence of catabolic back fluxes in the reverse direction of net reactions has implications for biogeochemical isotope studies. In environments where biochemical processes are close to thermodynamic equilibrium, measured fluxes of labeled substrates to products are not equal to microbial net rates. Detection of a reaction in situ by labeling may not even indicate a net reaction occurring in the direction of label conversion but may reflect the reverse component of a so far unrecognized net reaction. Furthermore, the natural isotopic composition of the substrate and product pool will be determined by both the forward and back flux. This finding may have to be considered in the interpretation of stable isotope records.

Description: Large-scale transcription profiling via direct cDNA sequencing provides important insights as to how foundation species cope with increasing climatic extremes predicted under global warming. Species distributed along a thermal cline, such as the ecologically important seagrass Zostera marina, provide an opportunity to assess temperature effects on gene expression as a function of their long-term adaptation to heat stress. We exposed a southern and northern European population of Zostera marina from contrasting thermal environments to a realistic heat wave in a common-stress garden. In a fully crossed experiment, eight cDNA libraries, each comprising ∼125 000 reads, were obtained during and after a simulated heat wave, along with nonstressed control treatments. Although gene-expression patterns during stress were similar in both populations and were dominated by classical heat-shock proteins, transcription profiles diverged after the heat wave. Gene-expression patterns in southern genotypes returned to control values immediately, but genotypes from the northern site failed to recover and revealed the induction of genes involved in protein degradation, indicating failed metabolic compensation to high sea-surface temperature. We conclude that the return of gene-expression patterns during recovery provides critical information on thermal adaptation in aquatic habitats under climatic stress. As a unifying concept for ecological genomics, we propose transcriptomic resilience, analogous to ecological resilience, as an important measure to predict the tolerance of individuals and hence the fate of local populations in the face of global warming.

Description: The use of molecular methods is altering our understanding of the microbial biosphere and the complexity of the tree of life. Here, we report a newly discovered uncultured plastid-bearing eukaryotic lineage named the rappemonads. Phylogenies using near-complete plastid ribosomal DNA (rDNA) operons demonstrate that this group represents an evolutionarily distinct lineage branching with haptophyte and cryptophyte algae. Environmental DNA sequencing revealed extensive diversity at North Atlantic, North Pacific, and European freshwater sites, suggesting a broad ecophysiology and wide habitat distribution. Quantitative PCR analyses demonstrate that the rappemonads are often rare but can form transient blooms in the Sargasso Sea, where high 16S rRNA gene copies mL-1 were detected in late winter. This pattern is consistent with these microbes being a member of the rare biosphere, whose constituents have been proposed to play important roles under ecosystem change. Fluorescence in situ hybridization revealed that cells from this unique lineage were 6.6 ± 1.2 x 5.7 ± 1.0 μm, larger than numerically dominant open-ocean phytoplankton, and appear to contain two to four plastids. The rappemonads are unique, widespread, putatively photosynthetic algae that are absent from present-day ecosystem models and current versions of the tree of life.

Description: A threat of irreversible damage should prompt action to mitigate climate change, according to the United Nations Framework Convention on Climate Change, which serves as a basis for international climate policy. CO2-induced climate change is known to be largely irreversible on timescales of many centuries1, as simulated global mean temperature remains approximately constant for such periods following a complete cessation of carbon dioxide emissions while thermosteric sea level continues to rise1,2,3,4,5,6. Here we use simulations with the Canadian Earth System Model to show that ongoing regional changes in temperature and precipitation are significant, following a complete cessation of carbon dioxide emissions in 2100, despite almost constant global mean temperatures. Moreover, our projections show warming at intermediate depths in the Southern Ocean that is many times larger by the year 3000 than that realized in 2100. We suggest that a warming of the intermediate-depth ocean around Antarctica at the scale simulated for the year 3000 could lead to the collapse of the West Antarctic Ice Sheet, which would be associated with a rise in sea level of several metres2,7,8.

Description: Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. The isolation of Candidatus “Nitrosopumilus maritimus” strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. Here we report the 1,645,259-bp closed genome of strain SCM1, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria. Consistent with in situ isotopic studies of marine archaea, the genome sequence indicates N. maritimus grows autotrophically using a variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon assimilation, while maintaining limited capacity for assimilation of organic carbon. This unique instance of archaeal biosynthesis of the osmoprotectant ectoine and an unprecedented enrichment of multicopper oxidases, thioredoxin-like proteins, and transcriptional regulators points to an organism responsive to environmental cues and adapted to handling reactive copper and nitrogen species that likely derive from its distinctive biochemistry. The conservation of N. maritimus gene content and organization within marine metagenomes indicates that the unique physiology of these specialized oligophiles may play a significant role in the biogeochemical cycles of carbon and nitrogen.

Description: Among eukaryotes, four major phytoplankton lineages are responsible for marine photosynthesis; prymnesiophytes, alveolates, stramenopiles, and prasinophytes. Contributions by individual taxa, however, are not well known, and genomes have been analyzed fromonly the latter two lineages. Tiny "picoplanktonic" members of the prymnesiophyte lineage have long been inferred to be ecologically important but remain poorly characterized. Here, we examine pico-prymnesiophyte evolutionary history and ecology using cultivation-independent methods. 18S rRNA gene analysis showed picoprymnesiophytes belonged to broadly distributed uncultivated taxa. Therefore, we used targeted metagenomics to analyze uncultured pico-prymnesiophytes sorted by flow cytometry from subtropical North Atlantic waters. The data reveal a composite nuclear-encoded gene repertoire with strong green-lineage affiliations, which contrasts with the evolutionary history indicated by the plastid genome. Measured pico-prymnesiophyte growth rates were rapid in this region, resulting in primary production contributions similar to the cyanobacterium Prochlorococcus. On average, pico-prymnesiophytes formed 25 of global picophytoplankton biomass, with differing contributions in five biogeographical provinces spanning tropical to subpolar systems. Elements likely contributing to success include high gene density and genes potentially involved in defense and nutrient uptake. Our findings have implications reaching beyond pico-prymnesiophytes, to the prasinophytes and stramenopiles. For example, prevalence of putative Ni-containing superoxide dismutases (SODs), instead of Fe-containing SODs, seems to be a common adaptation among eukaryotic phytoplankton for reducing Fe quotas in low-Fe modern oceans. Moreover, highly mosaic gene repertoires, although compositionally distinct for each major eukaryotic lineage, now seem to be an underlying facet of successful marine phytoplankton.

Description: The exquisite preservation of soft-bodied animals in Burgess Shale-type deposits provides important clues into the early evolution of body plans that emerged during the Cambrian explosion1. Until now, such deposits have remained silent regarding the early evolution of extant molluscan lineages—in particular the cephalopods. Nautiloids, traditionally considered basal within the cephalopods, are generally depicted as evolving from a creeping Cambrian ancestor whose dorsal shell afforded protection and buoyancy2. Although nautiloid-like shells occur from the Late Cambrian onwards, the fossil record provides little constraint on this model, or indeed on the early evolution of cephalopods. Here, we reinterpret the problematic Middle Cambrian animal Nectocaris pteryx3,4 as a primitive (that is, stem-group), non-mineralized cephalopod, based on new material from the Burgess Shale. Together with Nectocaris, the problematic Lower Cambrian taxa Petalilium5 and (probably) Vetustovermis6,7 form a distinctive clade, Nectocarididae, characterized by an open axial cavity with paired gills, wide lateral fins, a single pair of long, prehensile tentacles, a pair of non-faceted eyes on short stalks, and a large, flexible anterior funnel. This clade extends the cephalopods’ fossil record2 by over 30 million years, and indicates that primitive cephalopods lacked a mineralized shell, were hyperbenthic, and were presumably carnivorous. The presence of a funnel suggests that jet propulsion evolved in cephalopods before the acquisition of a shell. The explosive diversification of mineralized cephalopods in the Ordovician may have an understated Cambrian ‘fuse’.

Description: Throughout Earth's history, the oceans have played a dominant role in the climate system through the storage and transport of heat and the exchange of water and climate-relevant gases with the atmosphere. The ocean's heat capacity is ≈1,000 times larger than that of the atmosphere, its content of reactive carbon more than 60 times larger. Through a variety of physical, chemical, and biological processes, the ocean acts as a driver of climate variability on time scales ranging from seasonal to interannual to decadal to glacial–interglacial. The same processes will also be involved in future responses of the ocean to global change. Here we assess the responses of the seawater carbonate system and of the ocean's physical and biological carbon pumps to (i) ocean warming and the associated changes in vertical mixing and overturning circulation, and (ii) ocean acidification and carbonation. Our analysis underscores that many of these responses have the potential for significant feedback to the climate system. Because several of the underlying processes are interlinked and nonlinear, the sign and magnitude of the ocean's carbon cycle feedback to climate change is yet unknown. Understanding these processes and their sensitivities to global change will be crucial to our ability to project future climate change.

Description: Understanding the ecological impacts of climate change is a crucial challenge of the twenty-first century. There is a clear lack of general rules regarding the impacts of global warming on biota. Here, we present a metaanalysis of the effect of climate change on body size of ectothermic aquatic organisms (bacteria, phyto- and zooplankton, and fish) from the community to the individual level. Using long-term surveys, experimental data and published results, we show a significant increase in the proportion of small-sized species and young age classes and a decrease in size-at-age. These results are in accordance with the ecological rules dealing with the temperature–size relationships (i.e., Bergmann's rule, James' rule and Temperature–Size Rule). Our study provides evidence that reduced body size is the third universal ecological response to global warming in aquatic systems besides the shift of species ranges toward higher altitudes and latitudes and the seasonal shifts in life cycle events.

Description: The El Niño/Southern Oscillation (ENSO) phenomenon, originating in the Tropical Pacific, is the strongest natural interannual climate signal and has widespread effects on the global climate system and the ecology of the Tropical Pacific. Any strong change in ENSO statistics will therefore have serious climatic and ecological consequences. Most global climate models do simulate ENSO, although large biases exist with respect to its characteristics. The ENSO response to global warming differs strongly from model to model and is thus highly uncertain. Some models simulate an increase in ENSO amplitude, others a decrease, and others virtually no change. Extremely strong changes constituting tipping point behavior are not simulated by any of the models. Nevertheless, some interesting changes in ENSO dynamics can be inferred from observations and model integrations. Although no tipping point behavior is envisaged in the physical climate system, smooth transitions in it may give rise to tipping point behavior in the biological, chemical, and even socioeconomic systems. For example, the simulated weakening of the Pacific zonal sea surface temperature gradient in the Hadley Centre model (with dynamic vegetation included) caused rapid Amazon forest die-back in the mid-twenty-first century, which in turn drove a nonlinear increase in atmospheric CO2, accelerating global warming.

Description: Fisheries can have a large impact on marine ecosystems, because the effects of removing large predatory fish may cascade down the food web. The implications of these cascading processes on system functioning and resilience remain a source of intense scientific debate. By using field data covering a 30-year period, we show for the Baltic Sea that the underlying mechanisms of trophic cascades produced a shift in ecosystem functioning after the collapse of the top predator cod. We identified an ecological threshold, corresponding to a planktivore abundance of ≈17 × 1010 individuals, that separates 2 ecosystem configurations in which zooplankton dynamics are driven by either hydroclimatic forces or predation pressure. Abundances of the planktivore sprat above the threshold decouple zooplankton dynamics from hydrological circumstances. The current strong regulation by sprat of the feeding resources for larval cod may hinder cod recovery and the return of the ecosystem to a prior state. This calls for the inclusion of a food web perspective in management decisions.

Description: The pelagic ocean harbors one of the largest ecosystems on Earth. It is responsible for approximately half of global primary production, sustains worldwide fisheries, and plays an important role in the global carbon cycle. Ocean warming caused by anthropogenic climate change is already starting to impact the marine biota, with possible consequences for ocean productivity and ecosystem services. Because temperature sensitivities of marine autotrophic and heterotrophic processes differ greatly, ocean warming is expected to cause major shifts in the flow of carbon and energy through the pelagic system. Attempts to integrate such biological responses into marine ecosystem and biogeochemical models suffer from a lack of empirical data. Here, we show, using an indoor-mesocosm approach, that rising temperature accelerates respiratory consumption of organic carbon relative to autotrophic production in a natural plankton community. Increasing temperature by 2-6 degrees C hence decreased the biological drawdown of dissolved inorganic carbon in the surface layer by up to 31%. Moreover, warming shifted the partitioning between particulate and dissolved organic carbon toward an enhanced accumulation of dissolved compounds. In line with these findings, the loss of organic carbon through sinking was significantly reduced at elevated temperatures. The observed changes in biogenic carbon flow have the potential to reduce the transfer of primary produced organic matter to higher trophic levels, weaken the ocean's biological carbon pump, and hence provide a positive feedback to rising atmospheric CO2.

Description: Marine primary productivity is iron (Fe)-limited in vast regions of the contemporary oceans, most notably the high nutrient low chlorophyll (HNLC) regions. Diatoms often form large blooms upon the relief of Fe limitation in HNLC regions despite their prebloom low cell density. Although Fe plays an important role in controlling diatom distribution, the mechanisms of Fe uptake and adaptation to low iron availability are largely unknown. Through a combination of nontargeted transcriptomic and metabolomic approaches, we have explored the biochemical strategies preferred by Phaeodactylum tricornutum at growth-limiting levels of dissolved Fe. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport, and nitrate assimilation, were down-regulated. Our results show that this retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electrons by mitochondrial alternative oxidase (AOX) and non-photochemical quenching (NPQ), and augmented Fe-independent oxidative stress responses. Iron limitation leads to the elevated expression of at least three gene clusters absent from the Thalassiosira pseudonana genome that encode for components of iron capture and uptake mechanisms.

Description: By the end of this century, anthropogenic carbon dioxide (CO2) emissions are expected to decrease the surface ocean pH by as much as 0.3 unit. At the same time, the ocean is expected to warm with an associated expansion of the oxygen minimum layer (OML). Thus, there is a growing demand to understand the response of the marine biota to these global changes. We show that ocean acidification will substantially depress metabolic rates (31%) and activity levels (45%) in the jumbo squid, Dosidicus gigas, a top predator in the Eastern Pacific. This effect is exacerbated by high temperature. Reduced aerobic and locomotory scope in warm, high-CO2 surface waters will presumably impair predator–prey interactions with cascading consequences for growth, reproduction, and survival. Moreover, as the OML shoals, squids will have to retreat to these shallower, less hospitable, waters at night to feed and repay any oxygen debt that accumulates during their diel vertical migration into the OML. Thus, we demonstrate that, in the absence of adaptation or horizontal migration, the synergism between ocean acidification, global warming, and expanding hypoxia will compress the habitable depth range of the species. These interactions may ultimately define the long-term fate of this commercially and ecologically important predator.

Description: Increased knowledge of the present global carbon cycle is important for our ability to understand and to predict the future carbon cycle and global climate. Approximately half of the anthropogenic carbon released to the atmosphere from fossil fuel burning is stored in the ocean, although distribution and regional fluxes of the ocean sink are debated. Estimates of anthropogenic carbon (C ant) in the oceans remain prone to error arising from (i) a need to estimate preindustrial reference concentrations of carbon for different oceanic regions, and (ii) differing behavior of transient ocean tracers used to infer C ant. We introduce an empirical approach to estimate C ant that circumvents both problems by using measurement of the decadal change of ocean carbon concentrations and the exponential nature of the atmospheric C ant increase. In contrast to prior approaches, the results are independent of tracer data but are shown to be qualitatively and quantitatively consistent with tracer-derived estimates. The approach reveals more C ant in the deep ocean than prior studies; with possible implications for future carbon uptake and deep ocean carbonate dissolution. Our results suggest that this approachs applied on the unprecedented global data archive provides a means of estimating the C ant for large parts of the world's ocean.

Description: Lytic viral infection and programmed cell death (PCD) are thought to represent two distinct death mechanisms in phytoplankton, unicellular photoautotrophs that drift with ocean currents. Here, we demonstrate an interaction between autocatalytic PCD and lytic viral infection in the cosmopolitan coccolithophorid, Emiliania huxleyi. Successful infection of E. huxleyi strain 374 with a lytic virus, EhV1, resulted in rapid internal degradation of cellular components, a dramatic reduction in the photosynthetic efficiency (F-v/F-m), and an up-regulation of metacaspase protein expression, concomitant with induction of caspase-like activity. Caspase activation was confirmed through in vitro cleavage in cell extracts of the fluorogenic peptide substrate, IETD-AFC, and direct, in vivo staining of cells with the fluorescently labeled irreversible caspase inhibitor, FITC-VAD-FMK. Direct addition of z-VAD-FMK to infected cultures abolished cellular caspase activity and protein expression and severely impaired viral production. The absence of metacaspase protein expression in resistant E. huxleyi strain 373 during EhV1 infection further demonstrated the critical role of these proteases in facilitating viral lysis. Together with the presence of caspase cleavage recognition sequences within virally encoded proteins, we provide experimental evidence that coccolithoviruses induce and actively recruit host metacaspases as part of their replication strategy. These findings reveal a critical role for metacaspases in the turnover of phytoplankton biomass upon infection with viruses and point to coevolution of host-virus interactions in the activation and maintenance of these enzymes in planktonic, unicellular protists.

Description: A unique 16-year time series of deep video surveys in Monterey Bay reveals that the Humboldt squid, Dosidicus gigas, has substantially expanded its perennial geographic range in the eastern North Pacific by invading the waters off central California. This sustained range expansion coincides with changes in climate-linked oceanographic conditions and a reduction in competing top predators. It is also coincident with a decline in the abundance of Pacific hake, the most important commercial groundfish species off western North America. Recognizing the interactive effects of multiple changes in the environment is an issue of growing concern in ocean conservation and sustainability research.

Description: The Younger Dryas cold interval represents a time when much of the Northern Hemisphere cooled from �12.9 to 11.5 kiloyears B.P. The cause of this event, which has long been viewed as the canonical example of abrupt climate change, was initially attributed to the routing of freshwater to the St. Lawrence River with an attendant reduction in Atlantic meridional overturning circulation. However, this mechanism has recently been questioned because current proxies and dating techniques have been unable to confirm that eastward routing with an increase in freshwater flux occurred during the Younger Dryas. Here we use new geochemical proxies (�Mg/Ca, U/Ca, and 87Sr/86Sr) measured in planktonic foraminifera at the mouth of the St. Lawrence estuary as tracers of freshwater sources to further evaluate this question. Our proxies, combined with planktonic �18Oseawater and �13C, confirm that routing of runoff from western Canada to the St. Lawrence River occurred at the start of the Younger Dryas, with an attendant increase in freshwater flux of 0.06 +- 0.02 Sverdrup (1 Sverdrup = 106 m3s-1). This base discharge increase is sufficient to have reduced Atlantic meridional overturning circulation and caused the Younger Dryas cold interval. In addition, our data indicate subsequent fluctuations in the freshwater flux to the St. Lawrence River of ~0.06–0.12 Sverdrup, thus explaining the variability in the overturning circulation and climate during the Younger Dryas.

Description: The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococus tauri (Prasinophyceae), This cosmopolitan marine primary producer is the world's smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C4 photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry. © 2006 by The National Academy of Sciences of the USA.

Description: Contemporary climate change is characterized both by increasing mean temperature and increasing climate variability such as heat waves, storms, and floods. How populations and communities cope with such climatic extremes is a question central to contemporary ecology and biodiversity conservation. Previous work has shown that species diversity can affect ecosystem functioning and resilience. Here, we show that genotypic diversity can replace the role of species diversity in a species-poor coastal ecosystem, and it may buffer against extreme climatic events. In a manipulative field experiment, increasing the genotypic diversity of the cosmopolitan seagrass Zostera marina enhanced biomass production, plant density, and faunal abundance, despite near-lethal water temperatures due to extreme warming across Europe. Net biodiversity effects were explained by genotypic complementarity rather than by selection of particularly robust genotypes. Positive effects on invertebrate fauna suggest that genetic diversity has second-order effects reaching higher trophic levels. Our results highlight the importance of maintaining genetic as well as species diversity to enhance ecosystem resilience in a world of increasing uncertainty.

Description: The deep ocean is home to a group of broad-collared hemichordates—the so-called ‘lophenteropneusts’—that have been photographed gliding on the sea floor1,2,3,4,5,6,7,8 but have not previously been collected. It has been claimed that these worms have collar tentacles and blend morphological features of the two main hemichordate body plans, namely the tentacle-less enteropneusts and the tentacle-bearing pterobranchs. Consequently, lophenteropneusts have been invoked as missing links to suggest that the former evolved into the latter5. The most significant aspect of the lophenteropneust hypothesis is its prediction that the fundamental body plan within a basal phylum of deuterostomes was enteropneust-like. The assumption of such an ancestral state influences ideas about the evolution of the vertebrates from the invertebrates9,10,11,12,13,14. Here we report on the first collected specimen of a broad-collared, deep-sea enteropneust and describe it as a new family, genus and species. The collar, although disproportionately broad, lacks tentacles. In addition, we find no evidence of tentacles in the available deep-sea photographs (published and unpublished) of broad-collared enteropneusts, including those formerly designated as lophenteropneusts. Thus, the lophenteropneust hypothesis was based on misinterpretation of deep-sea photographs of low quality and should no longer be used to support the idea that the enteropneust body plan is basal within the phylum Hemichordata.

Description: The anaerobic oxidation of methane (AOM) is one of the major sinks of this substantial greenhouse gas in marine environments. Recent investigations have shown that diverse communities of anaerobic archaea and sulfate-reducing bacteria are involved in AOM. Most of the relevant archaea are assigned to two distinct phylogenetic clusters, ANME-1 and ANME-2. A suite of specific 13C-depleted lipids demonstrating the presence of consortia mediating AOM in fossil and recent environments has been established. Here we report on substantial differences in the lipid composition of microbial consortia sampled from distinct compartments of AOM-driven carbonate reefs growing in the northwestern Black Sea. Communities in which the dominant archaea are from the ANME-1 cluster yield internally cyclized tetraether lipids typical of thermophiles. Those in which ANME-2 archaea are dominant yield sn-2-hydroxyarchaeol accompanied by crocetane and crocetenes. The bacterial lipids from these communities are also distinct even though the sulfate-reducing bacteria all belong to the Desulfosarcina/Desulfococcus group. Nonisoprenoidal glycerol diethers are predominantly associated with ANME-1-dominated communities. Communities with ANME-2 yield mainly conventional, ester-linked diglycerides. ANME-1 archaea and associated sulfate-reducing bacteria seem to be enabled to use low concentrations of methane and to grow within a broad range of temperatures. Our results offer a tool for the study of recent and especially of fossil methane environments.

Description: Concentrations of biodiversity, or hotspots, represent conservation priorities in terrestrial ecosystems but remain largely unexplored in marine habitats. In the open ocean, many large predators such as tunas, sharks, billfishes, and sea turtles are of current conservation concern because of their vulnerability to overfishing and ecosystem role. Here we use scientific-observer records from pelagic longline fisheries in the Atlantic and Pacific Oceans to show that oceanic predators concentrate in distinct diversity hotspots. Predator diversity consistently peaks at intermediate latitudes (20–30° N and S), where tropical and temperate species ranges overlap. Individual hotspots are found close to prominent habitat features such as reefs, shelf breaks, or seamounts and often coincide with zooplankton and coral reef hotspots. Closed-area models in the northwest Atlantic predict that protection of hotspots outperforms other area closures in safeguarding threatened pelagic predators from ecological extinction. We conclude that the seemingly monotonous landscape of the open ocean shows rich structure in species diversity and that these features should be used to focus future conservation efforts.

Description: Coccolithophores are a group of calcifying unicellular algae that constitute a major fraction of oceanic primary productivity, play an important role in the global carbon cycle, and are key biostratigraphic marker fossils. Their taxonomy is primarily based on the morphology of the minute calcite plates, or coccoliths, covering the cell. These are diverse and include widespread fine scale variation, of which the biological/taxonomic significance is unknown. Do they represent phenotypic plasticity, genetic polymorphisms, or species-specific characters? Our research on five commonly occurring coccolithophores supports the hypothesis that such variation represents pseudocryptic speciation events, occurring between 0.3 and 12.9 million years ago from a molecular clock estimation. This finding suggests strong stabilizing selection acting on coccolithophorid phenotypes. Our results also provide strong support for the use of fine scale morphological characters of coccoliths in the fossil record to improve biostratigraphic resolution and paleoceanographic data retrieval.

Description: Cephalopods are a diverse group of highly derived molluscs, including nautiluses, squids, octopuses and cuttlefish. Evolution of the cephalopod body plan from a monoplacophoran-like ancestor1 entailed the origin of several key morphological innovations contributing to their impressive evolutionary success2. Recruitment of regulatory genes3, or even pre-existing regulatory networks4, may be a common genetic mechanism for generating new structures. Hox genes encode a family of transcriptional regulatory proteins with a highly conserved role in axial patterning in bilaterians5; however, examples highlighting the importance of Hox gene recruitment for new developmental functions are also known6,7. Here we examined developmental expression patterns for eight out of nine Hox genes8 in the Hawaiian bobtail squid Euprymna scolopes, by whole-mount in situ hybridization. Our data show that Hox orthologues have been recruited multiple times and in many ways in the origin of new cephalopod structures. The manner in which these genes have been co-opted during cephalopod evolution provides insight to the nature of the molecular mechanisms driving morphological change in the Lophotrochozoa, a clade exhibiting the greatest diversity of body plans in the Metazoa.

Description: The climate of the Atlantic sector exhibits considerable variability on a wide range of time scales. A substantial portion is associated with the North Atlantic Oscillation (NAO), a hemispheric meridional oscillation in atmospheric mass with centers of action near Iceland and over the subtropical Atlantic. NAO-related impacts on winter climate extend from Florida to Greenland and from northwestern Africa over Europe far into northern Asia. Over the last 3 decades, the phase of the NAO has been shifting from mostly negative to mostly positive index values. Much remains to be learned about the mechanisms that produce such low frequency changes in the North Atlantic climate, but it seems increasingly likely that human activities are playing a significant role. When the North Atlantic Oscillation (NAO) is in its positive phase, low-pressure anomalies over the Icelandic region and throughout the Arctic combine with high-pressure anomalies across the subtropical Atlantic to produce stronger-than-average westerlies across the midlatitudes. During a positive NAO, conditions are colder and drier than average over the northwestern Atlantic and Mediterranean regions, whereas conditions are warmer and wetter than average in northern Europe, the eastern United States, and parts of Scandinavia (Fig. 1 top). Walker and Bliss (1) were among the first to recognize and study this pattern of climate anomalies, which is most pronounced during boreal winter (December through March).

Description: In vivo expression technology (IVET) has been used to identify 〉100 Salmonella typhimurium genes that are specifically expressed during infection of BALB/c mice and/or murine cultured macrophages. Induction of these genes is shown to be required for survival in the animal under conditions of the IVET selection. One class of in vivo induced (ivi) genes, iviVI-A and iviVI-B, constitute an operon that resides in a region of the Salmonella genome with low G+C content and presumably has been acquired by horizontal transfer, These ipi genes encode predicted proteins that are similar to adhesins and invasins from prokaryotic and eukaryotic pathogens (Escherichia coli [tia], Plasmodium falciparum [PfEMP1]) and have coopted the PhoPQ regulatory circuitry of Salmonella virulence genes. Examination of the in vivo induction profile indicates (i) many ivi genes encode regulatory functions (e.g., phoPQ and pmrAB) that serve to enhance the sensitivity and amplitude of virulence gene expression (e.g., spvB); (ii) the biochemical function of many metabolic genes may not represent their sole contribution to virulence; (iii) the host ecology can be inferred from the biochemical functions of ipi genes; and (iv) nutrient limitation plays a dual signaling role in pathogenesis: to induce metabolic functions that complement host nutritional deficiencies and to induce virulence functions required for immediate survival and spread to subsequent host sites

Description: The eukaryotic green alga Dunaliella tertiolecta acclimates to decreased growth irradiance by increasing cellular levels of light-harvesting chlorophyll protein complex apoproteins associated with photosystem II (LHCIIs), whereas increased growth irradiance elicits the opposite response. Nuclear run-on transcription assays and measurements of cab mRNA stability established that light intensity-dependent changes in LHCII are controlled at the level of transcription. cab gene transcription in high-intensity light was partially enhanced by reducing plastoquinone with 3-(3,4-dichlorophenyl)-1,1-dimethyl urea (DCMU), whereas it was repressed in low-intensity light by partially inhibiting the oxidation of plastoquinol with 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB). Uncouplers of photosynthetic electron transport and inhibition of water splitting had no effect on LHCII levels. These results strongly implicate the redox state of the plastoquinone pool in the chloroplast as a photon-sensing system that is coupled to the light-intensity regulation of nuclear-encoded cab gene transcription. The accumulation of cellular chlorophyll at low-intensity light can be blocked with cytoplasmically directed phosphatase inhibitors, such as okadaic acid, microcystin L-R, and tautomycin. Gel mobility-shift assays revealed that cells grown in high-intensity light contained proteins that bind to the promoter region of a cab gene carrying sequences homologous to higher plant light-responsive elements. On the basis of these experimental results, we propose a model for a light intensity signaling system where cab gene expression is reversibly repressed by a phosphorylated factor coupled to the redox status of plastoquinone through a chloroplast protein kinase.

Description: The emperor penguin (Aptenodytes forsteri), which feeds only at sea, is restricted to the higher latitudes of the antarctic sea-ice habitat1–3. It breeds on the winter fast ice when temperatures are−30 °C and high winds are frequent3. Assuming entirely the task of incubating the single egg, the male fasts for about 120 days in the most severe conditions. When it is relieved by the female around hatching time, the distance between the colony and the open sea may be 100km or more4,5, but where emperors go to forage at that time or during the summer is unknown. The polynias are areas of open water in sea-ice and during winter, with the under-ice habitats at any time of the year, they are among the most difficult of all Antarctic areas to sample. Here we monitor by satellite the routes taken by emperor penguins for foraging and compare them with satellite images of sea-ice. Winter birds walking over fast ice travelled up to 296 km to feed in polynias, whereas those swimming in light pack-ice travelled as far as 895km from the breeding colony. One record of diving showed that although most dives are to mid-water depths, some are near the bottom. Obtaining such detailed information on foraging in emperor penguins means that this bird now offers a unique opportunity to investigate the Antarctic sea-ice habitat.