The building blocks of a virus derived from de novo biosynthesis during infection and/or catabolism of preexisting host cell biomass, and the relative contribution of these 2 sources has important consequences for understanding viral biogeochemistry. We determined the uptake of extracellular nitrogen (N) and its biosynthetic incorporation into both virus and host proteins using an isotope-labeling proteomics approach in a model marine cyanobacterium Synechococcus WH8102 infected by a lytic cyanophage S-SM1. By supplying dissolved N as 15N postinfection, we found that proteins in progeny phage particles were composed of up to 41% extracellularly derived N, while proteins of the infected host cell showed almost no isotope incorporation, demonstrating that de novo amino acid synthesis continues during infection and contributes specifically and substantially to phage replication. The source of N for phage protein synthesis shifted over the course of infection from mostly host derived in the early stages to more medium derived later on. We show that the photosystem II reaction center proteins D1 and D2, which are auxiliary metabolic genes (AMGs) in the S-SM1 genome, are made de novo during infection in an apparently light-dependent manner. We also identified a small set of host proteins that continue to be produced during infection; the majority are homologs of AMGs in S-SM1 or other viruses, suggesting selective continuation of host protein production during infection. The continued acquisition of nutrients by the infected cell and their utilization for phage replication are significant for both evolution and biogeochemical impact of viruses.
Bluehead wrasses undergo dramatic, socially cued female-to-male sex change. We apply transcriptomic and methylome approaches in this wild coral reef fish to identify the primary trigger and subsequent molecular cascade of gonadal metamorphosis. Our data suggest that the environmental stimulus is exerted via the stress axis and that repression of the aromatase gene (encoding the enzyme converting androgens to estrogens) triggers a cascaded collapse of feminizing gene expression and identifies notable sex-specific gene neofunctionalization. Furthermore, sex change involves distinct epigenetic reprogramming and an intermediate state with altered epigenetic machinery expression akin to the early developmental cells of mammals. These findings reveal at a molecular level how a normally committed developmental process remains plastic and is reversed to completely alter organ structures.
Spatial fragmentation is a near-ubiquitous characteristic of marine canopies. Biophysical interactions with fragmented canopies are multi-faceted and have many significant implications at multiple scales. The aims of this paper are to review research on biophysical interactions in fragmented marine canopies, identify current gaps in knowledge and understanding, and propose ways forward. The review starts at the patch/gap scale and focuses initially on hydrodynamic interactions. It then considers the consequences of these interactions for particulate and dissolved material, and distributions of canopy-associated organisms. Finally, it addresses issues of upscaling to landscape-scale and ways in which this research can be applied to marine landscape management. Work on a broad range of canopy types is considered, including micro-algal biofilms and turf algae; macro-algae, seagrasses and coral reefs; saltmarsh vegetation and mangroves. Although the focus is on marine canopies, insights from studies of fragmented canopies in other contexts are drawn on where relevant. These include freshwater environments and terrestrial forests, grasslands, crop canopies, and urban areas. Specific areas requiring greater attention are highlighted. As a result of this meta-analysis, the following recommendations are made for further research. A lack of basic data is identified across all canopy types regarding the formation, fate and spatial and temporal characteristics of canopy patches, gaps, and spatial structure. Studies of hydrodynamics with fragmented canopies would benefit from shifting focus toward more non-uniform, realistic configurations, while ecological research in this area would benefit from a move toward configurations that are more controlled and tractable for quantitative modeling. More comparative studies across canopy types would enable understanding of their biophysical interactions and their consequences to be more fully tested and developed. A greater incorporation of chemical aspects of canopy systems into work that has hitherto focused on biophysical interactions would also be pertinent. Upscaling of patch and gap-scale phenomena to landscape-scale is identified as a crucial topic, since it is at the latter scale that management efforts are most readily carried out. Overall, an approach that balances hydrodynamics, marine canopy ecology, spatial analysis of landscapes, biogeochemistry, and socio-environmental interactions is recommended.
Animals that select the best available habitats are most likely to succeed in degraded environments, but ecological change can create evolutionarily unfamiliar habitats that may be under‐ or over‐utilized by native fauna. In temperate coastal waters, eutrophication and grazing have driven a global decline in native seaweeds and facilitated the establishment of non‐native seaweeds that provide novel macrophyte habitat. We tested whether a non‐native kelp canopy (wakame Undaria pinnatifida) functions as a viable habitat or ecological trap for several endemic reef fishes on urchin‐grazed reefs in southern Australia. We assessed the willingness of fish to utilize native vs. wakame kelp canopy via a laboratory habitat choice experiment and by recording natural recruitment to specially constructed boulder reefs with manipulated kelp canopy. We also compared fish communities on natural reefs using a before‐after‐control‐impact survey of wakame patches, and to assess the quality of wakame habitat for resident fish, compared fitness metrics for fish collected from habitats with native vs. wakame kelp canopy. Endemic fishes did not distinguish between the native or wakame canopy but preferred both to barren reef habitats. On urchin‐grazed natural reefs, fish occurred in higher abundance and diversity where seasonal wakame canopy was present. Fitness metrics in fish collected from wakame patches were comparable to those in fish from adjacent native kelp patches. These findings indicate that the non‐native canopy provides a viable habitat for endemic fish and may play a role in sustaining native fauna populations in this degraded ecosystem. More broadly, we recommend that managers consider the role of non‐native habitats within the context of environmental change, as endemic fauna may benefit from non‐native habitat‐formers in areas where their native counterparts cannot persist.
Knowledge about extreme ocean currents and their vertical structure is important when designing offshore structures. We propose a method for statistical modelling of extreme vertical current velocity profiles, accounting for factors such as directionality, spatial and temporal dependence, and non-stationarity due to the tide. We first pre-process the data by resolving the observed (vector) currents at each of several water depths into orthogonal major and minor axis components by principal component analysis, and use harmonic analysis to decompose the total (observed) current into the sum of (deterministic) tidal and (stochastic) residual currents. A complete marginal model is then constructed for all residual current components, and the dependence structure between the components is characterized using the conditional extremes model by Heffernan and Tawn (2004). By simulating under this model, estimates of various extremal statistics can be acquired. A simple approach for deriving design current velocity profiles is also proposed. The method is tested using measured current profiles at two coastal locations in Norway, covering a period of 2.5 and 1.5 years. It is demonstrated that the method provides good extrapolations at both locations, and the estimated 10-year design current velocity profiles appear realistic compared to the most extreme velocity profiles observed in the measurements.
In the present study, we surveyed the distribution and diversity of fungal assemblages associated with 10 species of marine animals from Antarctica. The collections yielded 83 taxa from 27 distinct genera, which were identified using molecular biology methods. The most abundant taxa were Cladosporium sp. 1, Debaryomyces hansenii, Glaciozyma martinii, Metschnikowia australis, Pseudogymnoascus destructans, Thelebolus cf. globosus, Pseudogymnoascus pannorum, Tolypocladium tundrense, Metschnikowia australis, and different Penicillium species. The diversity, richness, and dominance of fungal assemblages ranged among the host; however, in general, the fungal community, which was composed of endemic and cold-adapted cosmopolitan taxa distributed across the different sites of Antarctic Peninsula, displayed high diversity, richness, and dominance indices. Our results contribute to knowledge about fungal diversity in the marine environment across the Antarctic Peninsula and their phylogenetic relationships with species that occur in other cold, temperate, and tropical regions of the World. Additionally, despite their extreme habitats, marine Antarctic animals shelter cryptic and complex fungal assemblages represented by endemic and cosmopolitan cold-adapted taxa, which may represent interesting models to study different symbiotic associations between fungi and their animal hosts in the extreme conditions of Antarctica.
Purpose of Review
We summarize recent progress on autonomous observations of ocean carbonate chemistry and the development of a network of sensors capable of observing carbonate processes at multiple temporal and spatial scales.
The development of versatile pH sensors suitable for both deployment on autonomous vehicles and in compact, fixed ecosystem observatories has been a major development in the field. The initial large-scale deployment of profiling floats equipped with these new pH sensors in the Southern Ocean has demonstrated the feasibility of a global autonomous open-ocean carbonate observing system.
Our developing network of autonomous carbonate observations is currently targeted at surface ocean CO2 fluxes and compact ecosystem observatories. New integration of developed sensors on gliders and surface vehicles will increase our coastal and regional observational capability. Most autonomous platforms observe a single carbonate parameter, which leaves us reliant on the use of empirical relationships to constrain the rest of the carbonate system. Sensors now in development promise the ability to observe multiple carbonate system parameters from a range of vehicles in the near future.
Model transferability is an emerging and important branch of predictive science that has grown primarily from a need to produce ecological forecasts in the face of widespread data deficiency and escalating environmental novelty. In our recent article in Trends in Ecology and Evolution , we outlined some of the major roadblocks that currently undermine the practice of model transfers in ecology. The response of Radchuk et al.  to our work stresses the value of considering ‘first principles’ in projections of ecosystem change  and offers insights into outstanding challenges specific to mechanistic (synonym: process-based) models .
Sea state information is needed for many applications, ranging from safety at sea and on the coast, for which real time data are essential, to planning and design needs for infrastructure that require long time series. The definition of the wave climate and its possible evolution requires high resolution data, and knowledge on possible drift in the observing system. Sea state is also an important climate variable that enters in air-sea fluxes parameterizations. Finally, sea state patterns can reveal the intensity of storms and associated climate patterns at large scales, and the intensity of currents at small scales. A synthesis of user requirements leads to requests for spatial resolution at kilometer scales, and estimations of trends of a few centimeters per decade. Such requirements cannot be met by observations alone in the foreseeable future, and numerical wave models can be combined with in situ and remote sensing data to achieve the required resolution. As today's models are far from perfect, observations are critical in providing forcing data, namely winds, currents and ice, and validation data, in particular for frequency and direction information, and extreme wave heights. In situ and satellite observations are particularly critical for the correction and calibration of significant wave heights to ensure the stability of model time series. A number of developments are underway for extending the capabilities of satellites and in situ observing systems. These include the generalization of directional measurements, an easier exchange of moored buoy data, the measurement of waves on drifting buoys, the evolution of satellite altimeter technology, and the measurement of directional wave spectra from satellite radar instruments. For each of these observing systems, the stability of the data is a very important issue. The combination of the different data sources, including numerical models, can help better fulfill the needs of users.
Multi-species conservation strategies can be useful to maximize allocation of resources. To effectively plan for multi-species management practices, it is important to have a robust understanding of the variability in the spatial and behavioral ecology of sympatric species. To address this in the context of marine turtles, this study explored fine-scale habitat use by three sympatric species [juvenile green turtles (Chelonia mydas), Kemp’s ridley turtles (Lepidochelys kempii) and loggerhead turtles (Caretta caretta)] in a foraging area near Crystal River, Florida, United States. By combining sighting surveys and satellite tracking methods, we found that the distribution of the three species of marine turtles in this region overlapped both in space and time. We also observed differences in the fine-scale location of hotspots and in-water behavior among species, with some degree of apparent habitat partitioning. Habitat partitioning was particularly evident when assessing the diving and surfacing behavior of tracked turtles, with some degree of differentiation in diel diving patterns, particularly depths utilized during daytime/nighttime and the dive/surface duration. Our study provides ecological baseline data on the spatial overlap, habitat use and behavior of three sympatric marine turtle species, which can inform future management strategies at nearshore marine habitats in the Northeastern Gulf of Mexico.