Diversity and function of fluorescent molecules in marine animals

Fluorescence in marine animals has mainly been studied in Cnidaria but is found in many different phyla such as Annelida, Crustacea, Mollusca, and Chordata. While many fluorescent proteins and molecules have been identified, very little information is available about the biological functions of fluorescence. In this review, we focus on describing the occurrence of fluorescence in marine animals and the behavioural and physiological functions of fluorescent molecules based on experimental approaches. These biological functions of fluorescence range from prey and symbiont attraction, photoprotection, photoenhancement, stress mitigation, mimicry, and aposematism to inter- and intraspecific communication. We provide a comprehensive list of marine taxa that utilise fluorescence, including demonstrated effects on behavioural or physiological responses. We describe the numerous known functions of fluorescence in anthozoans and their underlying molecular mechanisms. We also highlight that other marine taxa should be studied regarding the functions of fluorescence. We suggest that an increase in research effort in this field could contribute to understanding the capacity of marine animals to respond to negative effects of climate change, such as rising sea temperatures and increasing intensities of solar irradiation.

The sugar kelp Saccharina latissima I: recent advances in a changing climate

BACKGROUND

The sugar kelp Saccharina latissima is a Laminariales species widely distributed in the Northern Hemisphere. Its physiology and ecology have been studied since the 1960s, given its ecological relevance on western temperate coasts. However, research interest has been rising recently, driven mainly by reports of negative impacts of anthropogenically induced environmental change and by the increased commercial interest in cultivating the species, with several industrial applications for the resulting biomass.

SCOPE

We used a variety of sources published between 2009 to May 2023 (but including some earlier literature where required), to provide a comprehensive review of the ecology, physiology, biochemical and molecular biology of S. latissima. In so doing we aimed to better understand the species' response to stressors in natural communities, but also inform the sustainable cultivation of the species.

CONCLUSION

Due to its wide distribution, S. latissima has developed a variety of physiological and biochemical mechanisms to adjust to environmental changes, including adjustments in photosynthetic parameters, modulation of osmolytes and antioxidants, reprogramming of gene expression and epigenetic modifications, among others summarized in this review. This is particularly important because massive changes in the abundance and distribution of S. latissima have already been observed. Namely, presence and abundance of S. latissima has significantly decreased at the rear edges on both sides of the Atlantic, and increased in abundance at the polar regions. These changes were mainly caused by climate change and will therefore be increasingly evident in the future. Recent developments in genomics, transcriptomics and epigenomics have clarified the existence of genetic differentiation along its distributional range with implications in the fitness at some locations. The complex biotic and abiotic interactions unraveled here demonstrated the cascading effects the disappearance of a kelp forest can have in a marine ecosystem. We show how S. latissima is an excellent model to study acclimation and adaptation to environmental variability and how to predict future distribution and persistence under climate change.

Phytoplankton thermal trait parameterization alters community structure and biogeochemical processes in a modeled ocean

Phytoplankton exhibit diverse physiological responses to temperature which influence their fitness in the environment and consequently alter their community structure. Here, we explored the sensitivity of phytoplankton community structure to thermal response parameterization in a modelled marine phytoplankton community. Using published empirical data, we evaluated the maximum thermal growth rates (μmax ) and temperature coefficients (Q10 ; the rate at which growth scales with temperature) of six key Phytoplankton Functional Types (PFTs): coccolithophores, cyanobacteria, diatoms, diazotrophs, dinoflagellates, and green algae. Following three well-documented methods, PFTs were either assumed to have (1) the same μmax and the same Q10 (as in to Eppley, 1972), (2) a unique μmax but the same Q10 (similar to Kremer et al., 2017), or (3) a unique μmax and a unique Q10 (following Anderson et al., 2021). These trait values were then implemented within the Massachusetts Institute of Technology biogeochemistry and ecosystem model (called Darwin) for each PFT under a control and climate change scenario. Our results suggest that applying a μmax and Q10 universally across PFTs (as in Eppley, 1972) leads to unrealistic phytoplankton communities, which lack diatoms globally. Additionally, we find that accounting for differences in the Q10 between PFTs can significantly impact each PFT's competitive ability, especially at high latitudes, leading to altered modeled phytoplankton community structures in our control and climate change simulations. This then impacts estimates of biogeochemical processes, with, for example, estimates of export production varying by ~10% in the Southern Ocean depending on the parameterization. Our results indicate that the diversity of thermal response traits in phytoplankton not only shape community composition in the historical and future, warmer ocean, but that these traits have significant feedbacks on global biogeochemical cycles.

High amino acid osmotrophic incorporation by marine eukaryotic phytoplankton revealed by click chemistry

The osmotrophic uptake of dissolved organic compounds in the ocean is considered to be dominated by heterotrophic prokaryotes, whereas the role of planktonic eukaryotes is still unclear. We explored the capacity of natural eukaryotic plankton communities to incorporate the synthetic amino acid L-homopropargylglycine (HPG, analogue of methionine) using biorthogonal noncanonical amino acid tagging (BONCAT), and we compared it with prokaryotic HPG use throughout a 9-day survey in the NW Mediterranean. BONCAT allows to fluorescently identify translationally active cells, but it has never been applied to natural eukaryotic communities. We found a large diversity of photosynthetic and heterotrophic eukaryotes incorporating HPG into proteins, with dinoflagellates and diatoms showing the highest percentages of BONCAT-labelled cells (49 ± 25% and 52 ± 15%, respectively). Among them, pennate diatoms exhibited higher HPG incorporation in the afternoon than in the morning, whereas small (≤5 μm) photosynthetic eukaryotes and heterotrophic nanoeukaryotes showed the opposite pattern. Centric diatoms (e.g. Chaetoceros, Thalassiosira, and Lauderia spp.) dominated the eukaryotic HPG incorporation due to their high abundances and large sizes, accounting for up to 86% of the eukaryotic BONCAT signal and strongly correlating with bulk 3H-leucine uptake rates. When including prokaryotes, eukaryotes were estimated to account for 19-31% of the bulk BONCAT signal. Our results evidence a large complexity in the osmotrophic uptake of HPG, which varies over time within and across eukaryotic groups and highlights the potential of BONCAT to quantify osmotrophy and protein synthesis in complex eukaryotic communities.

Grouping groupers in the Mediterranean: Ecological baselines revealed by ancient proteins

Marine historical ecology provides a means to establish baselines to inform current fisheries management. Groupers (Epinephelidae) are key species for fisheries in the Mediterranean, which have been heavily overfished. Species abundance and distribution prior to the 20th century in the Mediterranean remains poorly known. To reconstruct the past biogeography of Mediterranean groupers, we investigated whether Zooarchaeology by Mass Spectrometry (ZooMS) can be used for identifying intra-genus grouper bones to species level. We discovered 22 novel, species-specific ZooMS biomarkers for groupers. Applying these biomarkers to Kinet Höyük, a Mediterranean archaeological site, demonstrated 4000 years of regional Epinephelus aeneus dominance and resiliency through millennia of fishing pressures, habitat degradation and climatic changes. Combining ZooMS identifications with catch size reconstructions revealed the Epinephelus aeneus capacity for growing 30 cm larger than hitherto documented, revising the maximum Total Length from 120 to 150 cm. Our results provide ecological baselines for a key Mediterranean fishery which could be leveraged to define and assess conservation targets.

The Red Squat Lobster Pleuroncodes monodon in the Humboldt Current System: From Their Ecology to Commercial Attributes as Marine Bioresource

This study focused on gathering available information on Pleuroncodes monodon, a widely distributed crustacean in the Humboldt Current System. Off the Chilean coast, this species presents benthic habits and constitutes the main resource of the industrial crustacean fishery; many studies have been carried out on its life cycle during the last century. In contrast, off the coast of Peru, this species exhibits mainly pelagic habits, with latent information gaps on aspects of its life history and no commercial fishery activities, such as catching, taking or harvesting from the marine environment. P. monodon is an ecologically important species, as a source of energy for its predators, which include invertebrates, birds, marine mammals and fish of commercial interest. Thus, P. monodon seems to play a key role in this ecosystem, mainly as an intermediate link between top predators and the first links in the food chain. In addition, this species presents various adaptation strategies to the changing oceanographic parameters of the areas it inhabits, even tolerating hypoxic environments and great depths in order to avoid being predated. Likewise, from an economic viewpoint, it has a high commercial value as a marine bioresource with great potential in the pharmaceutical and food industries. Considering this, more studies must be carried out to corroborate the biological, ecological, and fishing importance of this species in order to generate efficient management measures and ensure a sustainable fishery.

Online Monitoring of Seawater Carbon Dioxide Based on an Infrared Rear Beam Splitter

The ocean is one of the most extensive ecosystems on Earth and can absorb large amounts of carbon dioxide. Changes in seawater carbon dioxide concentrations are one of the most important factors affecting marine ecosystems. Excess carbon dioxide can lead to ocean acidification, threatening the stability of marine ecosystems and species diversity. Dissolved carbon dioxide detection in seawater has great scientific significance. Conducting online monitoring of seawater carbon dioxide can help to understand the health status of marine ecosystems and to protect marine ecosystems. Current seawater detection equipment is large and costly. This study designed a low-cost infrared carbon dioxide detection system based on molecular theory. Using the HITRAN database, the absorption spectra and coefficients of carbon dioxide molecules under different conditions were calculated and derived, and a wavelength of 2361 cm^-1 was selected as the measurement channel for carbon dioxide. In addition, considering the interference effect of direct light, an infrared post-splitting method was proposed to eliminate the interference of light and improve the detection accuracy of the system. The system was designed for the online monitoring of carbon dioxide in seawater, including a peristaltic pump to accelerate gas-liquid separation, an optical path structure, and carbon dioxide concentration inversion. The experimental results showed that the standard deviation of the gas test is 3.05, the standard deviation of the seawater test is 6.04, and the error range is within 20 ppm. The system can be flexibly deployed and has good stability and portability, which can meet the needs of the online monitoring of seawater carbon dioxide concentration.

High-latitude kelps and future oceans: A review of multiple stressor impacts in a changing world

Kelp forests worldwide are threatened by both climate change and localized anthropogenic impacts. Species with cold-temperate, subpolar, or polar distributions are projected to experience range contractions over the coming decades, which may be exacerbated by climatic events such as marine heatwaves and increased freshwater and sediment input from rapidly contracting glaciers. The northeast Pacific has an extensive history of harvesting and cultivating kelps for subsistence, commercial, and other uses, and, therefore, declines in kelp abundance and distributional shifts will have significant impacts on this region. Gaps in our understanding of how cold-temperate kelp species respond to climate stressors have limited our ability to forecast the status of kelp forests in future oceans, which hampers conservation and management efforts. Here, we conducted a structured literature review to provide a synthesis of the impacts of multiple climate-related stressors on kelp forests in the northeast Pacific, assess existing knowledge gaps, and suggest potential research priorities. We chose to focus on temperature, salinity, sediment load, and light as the stressors most likely to vary and impact kelps as climate change progresses. Our results revealed biases in the existing literature toward studies investigating the impacts of temperature, or temperature in combination with light. Other stressors, particularly salinity and sediment load, have received much less focus despite rapidly changing conditions in high-latitude regions. Furthermore, multiple stressor studies appear to focus on kelp sporophytes, and it is necessary that we improve our understanding of how kelp microstages will be affected by stressor combinations. Finally, studies that investigate the potential of experimental transplantation or selective cultivation of genotypes resilient to environmental changes are lacking and would be useful for the conservation of wild populations and the seaweed aquaculture industry.

What does the future look like for kelp when facing multiple stressors?

As primary producers and ecosystem engineers, kelp (generally Order Laminariales) are ecologically important, and their decline could have far-reaching consequences. Kelp are valuable in forming habitats for fish and invertebrates and are crucial for adaptation to climate change by creating coastal defenses and in providing key functions, such as carbon sequestration and food provision. Kelp are threatened by multiple stressors, such as climate change, over-harvesting of predators, and pollution. In this opinion paper, we discuss how these stressors may interact to affect kelp, and how this varies under different contexts. We argue that more research that bridges kelp conservation and multiple stressor theory is needed and outline key questions that should be addressed as a priority. For instance, it is important to understand how previous exposure (either to earlier generations or life stages) determines responses to emerging stressors, and how responses in kelp scale up to alter food webs and ecosystem functioning. By increasing the temporal and biological complexity of kelp research in this way, we will improve our understanding allowing better predictions. This research is essential for the effective conservation and potential restoration of kelp in our rapidly changing world.

Leveraging Public Data to Predict Global Niches and Distributions of Rhizostome Jellyfishes

As climate change progresses rapidly, biodiversity declines, and ecosystems shift, it is becoming increasingly difficult to document dynamic populations, track fluctuations, and predict responses to climate change. Concurrently, publicly available databases and tools are improving scientific accessibility, increasing collaboration, and generating more data than ever before. One of the most successful projects is iNaturalist, an AI-driven social network doubling as a public database designed to allow citizen scientists to report personal biodiversity reports with accuracy. iNaturalist is especially useful for the research of rare, dangerous, and charismatic organisms, but requires better integration into the marine system. Despite their abundance and ecological relevance, there are few long-term, high-sample datasets for jellyfish, which makes management difficult. To provide some high-sample datasets and demonstrate the utility of publicly collected data, we synthesized two global datasets for ten genera of jellyfishes in the order Rhizostomeae containing 8412 curated datapoints from both iNaturalist (n = 7807) and the published literature (n = 605). We then used these reports in conjunction with publicly available environmental data to predict global niche partitioning and distributions. Initial niche models inferred that only two of ten genera have distinct niche spaces; however, the application of machine learning-based random forest models suggests genus-specific variation in the relevance of abiotic environmental variables used to predict jellyfish occurrence. Our approach to incorporating reports from the literature with iNaturalist data helped evaluate the quality of the models and, more importantly, the quality of the underlying data. We find that free, accessible online data is valuable, yet subject to biases through limited taxonomic, geographic, and environmental resolution. To improve data resolution, and in turn its informative power, we recommend increasing global participation through collaboration with experts, public figures, and hobbyists in underrepresented regions capable of implementing regionally coordinated projects.

Implications of plastic pollution on global marine carbon cycling and climate

Plastic pollution can both chemically and physically impede marine biota. But it can also provide novel substrates for colonization, and its leachate might stimulate phytoplankton growth. Plastic contains carbon, which is released into the environment upon breakdown. All of these mechanisms have been proposed to contribute global impacts on open ocean carbon cycling and climate from ubiquitous plastic pollution. Laboratory studies produce compelling data showing both stimulation and inhibition of primary producers and disruption of predatory lifecycles at individual scale, but global carbon cycle impacts remain mostly unquantified. Preliminary modelling estimates ecosystem alterations and direct carbon release due to plastic pollution will remain vastly less disruptive to global carbon cycling than the direct damage wrought by fossil fuel carbon emissions. But when considered by mass, carbon in the form of bulky, persistent plastic particles may be disproportionally more influential on biogeochemical cycling than carbon as a gas in the atmosphere or as a dissolved component of seawater. Thus, future research should pay particular attention to the optical and other physical effects of marine plastic pollution on Earth system and ecological function, and resulting impacts on oxygen and nutrient cycling. Improved understanding of the breakdown of plastics in the marine environment should also be considered high-priority, as any potential perturbation of biological carbon cycling by plastic pollution is climate-relevant on centennial timescales and longer.

The novel mangrove environment and composition of the Amazon Delta

Both freshwater floodplain (várzeas and igapós) forests and brackish-saline mangroves are abundant and well-described ecosystems in Brazil.¹ However, an interesting and unique wetland forest exists in the Amazon Delta where extensive mangroves occur in essentially freshwater tidal environments. Unlike the floodplain forests found upriver, the hydrology of these ecosystems is driven largely by large macro-tides of 4-8 m coupled with the significant freshwater discharge from the Amazon River. We explored these mangroves on the Amazon Delta (00°52' N to 01°41' N) and found surface water salinity to be consistently <5; soil pore water salinity in these mangrove forests ranged from 0 nearest the Amazon mouth to only 5-11 at the coastal margins to the north (01°41' N, 49°55' W). We also recorded a unique mix of mangrove-obligate (Avicennia sp., Rhizophora mangle) and facultative-wetland species (Mauritia flexuosa, Pterocarpus sp.) dominating these forests. This unique mix of plant species and soil porewater chemistry exists even along the coastal strands and active coastlines of the Atlantic Ocean. Part of these unique mangroves have escaped current global satellite mapping efforts, and we estimate that they may add over 180 km² (20% increase in mangrove area) within the Amazon Delta. Despite having a unique structure and function, these freshwater-brackish ecosystems likely provide similar ecosystem services to most mangroves worldwide, such as sequestering large quantities of organic carbon, protection of shoreline ecosystems from erosion, and habitats to many terrestrial and aquatic species (monkeys, birds, crabs, and fish).

Occurrence of Fibropapillomatosis in Green Turtles (Chelonia mydas) in Relation to Environmental Changes in Coastal Ecosystems in Texas and Florida: A Retrospective Study

Fibropapillomatosis is a neoplastic disease of marine turtles, with green turtles (Chelonia mydas) being the most affected species. Fibropapillomatosis causes debilitating tumor growths on soft tissues and internal organs, often with lethal consequences. Disease incidence has been increasing in the last few decades and the reason is still uncertain. The potential viral infectious agent of Fibropapillomatosis, chelonid herpesvirus 5, has been co-evolving with its sea turtle host for millions of years and no major mutation linked with increased disease occurrence has been detected. Hence, frequent outbreaks in recent decades are likely attributable to external drivers such as large-scale anthropogenic changes in the green turtle coastal marine ecosystem. This study found that variations in sea surface temperature, salinity, and nutrient effluent discharge from nearby rivers were correlated with an increased incidence of the disease, substantiating that these may be among the significant environmental drivers impacting Fibropapillomatosis prevalence. This study offers data and insight on the need to establish a baseline of environmental factors which may drive Fibropapillomatosis and its clinical exacerbation. We highlight the multifactorial nature of this disease and support the inclusion of interdisciplinary work in future Fibropapillomatosis research efforts.

Contribution of genome-scale metabolic modelling to niche theory

Standard niche modelling is based on probabilistic inference from organismal occurrence data but does not benefit yet from genome‐scale descriptions of these organisms. This study overcomes this shortcoming by proposing a new conceptual niche that resumes the whole metabolic capabilities of an organism. The so‐called metabolic niche resumes well‐known traits such as nutrient needs and their dependencies for survival. Despite the computational challenge, its implementation allows the detection of traits and the formal comparison of niches of different organisms, emphasising that the presence–absence of functional genes is not enough to approximate the phenotype. Further statistical exploration of an organism's niche sheds light on genes essential for the metabolic niche and their role in understanding various biological experiments, such as transcriptomics, paving the way for incorporating better genome‐scale description in ecological studies.

Host genetics, phenotype and geography structure the microbiome of a foundational seaweed

Interactions between hosts and their microbiota are vital to the functioning and resilience of macro-organisms. Critically, for hosts that play foundational roles in communities, understanding what drives host-microbiota interactions is essential for informing ecosystem restoration and conservation. We investigated the relative influence of host traits and the surrounding environment on microbial communities associated with the foundational seaweed Phyllospora comosa. We quantified 16 morphological and functional phenotypic traits, including host genetics (using 354 single nucleotide polymorphisms) and surface-associated microbial communities (using 16S rRNA gene amplicon sequencing) from 160 individuals sampled from eight sites spanning Phyllospora's entire latitudinal distribution (1,300 km). Combined, these factors explained 54% of the overall variation in Phyllospora's associated microbial community structure, much of which was related to the local environment (~32%). We found that putative "core" microbial taxa (i.e., present on all Phyllospora individuals sampled) exhibited slightly higher associations with host traits when compared to "variable" taxa (not present on all individuals). We identified several key genetic loci and phenotypic traits in Phyllospora that were strongly related to multiple microbial amplicon sequence variants, including taxa with known associations to seaweed defence, disease and tissue degradation. This information on how host-associated microbial communities vary with host traits and the environment enhances our current understanding of how "holobionts" (hosts plus their microbiota) are structured. Such understanding can be used to inform management strategies of these important and vulnerable habitats.

Environmental control of marine phytoplankton stoichiometry in the North Atlantic Ocean

The stoichiometric coupling of carbon to limiting nutrients in marine phytoplankton regulates the magnitude of biological carbon sequestration in the ocean. While clear links between plankton C:N ratios and environmental drivers have been identified, the nature and direction of these links, as well as their underlying physiological and ecological controls, remain uncertain. We show, with a well-constrained mechanistic model of plankton ecophysiology, that while nitrogen availability and temperature emerge as the main drivers of phytoplankton C:N stoichiometry in the North Atlantic, the biological mechanisms involved vary depending on the spatiotemporal scale and region considered. We find that phytoplankton C:N stoichiometry is overall controlled by nitrogen availability below 40° N, predominantly driven by ecoevolutionary shifts in the functional composition of the phytoplankton communities, while phytoplankton stoichiometric plasticity in response to dropping temperatures and increased grazing pressure dominates at higher latitudes. Our findings highlight the potential of "organisms-to-ecosystems" modeling approaches based on mechanistic models of plankton biology accounting for physiology, ecology, and trait evolution to explore and explain complex observational data and ultimately improve the predictions of global ocean models.

Fear dynamically structures the ocean's pelagic zone

Fear of predation can have wide-ranging ecological effects.^1-4 This is especially true in the ocean's pelagic zone, the Earth's largest habitat, where vertical gradients in light and primary productivity force numerous taxa to migrate vertically each night to feed at the surface while minimizing risk from visual predators.^5-7 Despite its importance and the fact that it is driven by spatial differences in perceived risk,⁸ diel vertical migration (DVM) is rarely considered within the "landscape of fear"^3,8,9 framework.¹⁰ It is also far from the only such process in the pelagic zone. We used continuous, year-long records from an upward-looking echosounder and broadband hydrophone at a cabled observatory off Central California, USA, to observe avoidance reactions by several groups of pelagic animals to the presence of their predators. As expected, vertical migration was ubiquitous, but we also observed behaviors at shorter and longer timescales that were best explained by fear of predation. The presence of foraging odontocetes induced immediate diving behavior in mesopelagic sound-scattering layers, and schools of epipelagic fishes induced similar reaction in layers of zooplankton and mesopelagic micronekton. At longer timescales, the presence of fish schools significantly deepened vertical migration, rearranging life throughout the water column. We argue that behavioral reactions to predation risk are common in the pelagic zone at a range of spatiotemporal scales and that our understanding of food webs and biogeochemical cycling in this immense biome will be incomplete unless we account for fear.

Disentangling tropicalization and deborealization in marine ecosystems under climate change

As climate change accelerates, species are shifting poleward and subtropical and tropical species are colonizing temperate environments.^1-3 A popular approach for characterizing such responses is the community temperature index (CTI), which tracks the mean thermal affinity of a community. Studies in marine,⁴ freshwater,⁵ and terrestrial⁶ ecosystems have documented increasing CTI under global warming. However, most studies have only linked increasing CTI to increases in warm-affinity species. Here, using long-term monitoring of marine fishes across the Northern Hemisphere, we decomposed CTI changes into four underlying processes-tropicalization (increasing warm-affinity), deborealization (decreasing cold-affinity), borealization (increasing cold-affinity), and detropicalization (decreasing warm-affinity)-for which we examined spatial variability and drivers. CTI closely tracked changes in sea surface temperature, increasing in 72% of locations. However, 31% of these increases were primarily due to decreases in cold-affinity species, i.e., deborealization. Thus, increases in warm-affinity species were prevalent, but not ubiquitous. Tropicalization was stronger in areas that were initially warmer, experienced greater warming, or were deeper, while deborealization was stronger in areas that were closer to human population centers or that had higher community thermal diversity. When CTI (and temperature) increased, species that decreased were more likely to be living closer to their upper thermal limits or to be commercially fished. Additionally, warm-affinity species that increased had smaller body sizes than those that decreased. Our results show that CTI changes arise from a variety of underlying community responses that are linked to environmental conditions, human impacts, community structure, and species characteristics.

A switch in species dominance of a recovering pelagic ecosystem

Although many marine ecosystems have been adversely impacted by human activities,¹ some are now recovering due to reductions in fishing pressure.^2-4 Here, we document the recovery of an ecosystem subjected to intense anthropogenic activity for over 200 years, the Clyde Sea.⁵ This region once had productive fisheries for herring (Clupea harengus) and other fish, but these disappeared at the turn of the century.^6,7 Using acoustic surveys of the pelagic ecosystem, we found that the Clyde Sea supports 100 times as many forage fish as in the late 1980s. However, herring has now been replaced by sprat (Sprattus sprattus), despite virtually no fishing on herring for 20 years. A combination of a warming sea,⁶ bycatch of herring in the prawn (Nephrops norvegicus) fishery,^8,9 and susceptibility of herring to poor recruitment may have contributed to this unexpected recovery. We compare this to similar unexpected "recoveries" involving unforeseen ecosystem effects, such as the return of hake (Merluccius merluccius) to the North Sea;^10,11 the recent expansion of the pelagic squat lobster, "munida," (Pleuroncodes monodon) off Peru;¹² and the increase in scallop (Placopecten magellanicus) numbers on Georges Bank.¹³ The lack of a current sprat fishery in the Clyde presents a unique opportunity to develop an alternative industry for its seafaring community: ecotourism. Charismatic megafauna (whales, dolphins, and seabirds) that people will pay to see¹⁴ will, in time-if not already^15,16-be drawn in by the abundance of forage fish now present, further restoring the biodiversity of the region after centuries of overexploitation.

An Embeddable Algorithm for Automatic Garbage Detection Based on Complex Marine Environment

With the continuous development of artificial intelligence, embedding object detection algorithms into autonomous underwater detectors for marine garbage cleanup has become an emerging application area. Considering the complexity of the marine environment and the low resolution of the images taken by underwater detectors, this paper proposes an improved algorithm based on Mask R-CNN, with the aim of achieving high accuracy marine garbage detection and instance segmentation. First, the idea of dilated convolution is introduced in the Feature Pyramid Network to enhance feature extraction ability for small objects. Secondly, the spatial-channel attention mechanism is used to make features learn adaptively. It can effectively focus attention on detection objects. Third, the re-scoring branch is added to improve the accuracy of instance segmentation by scoring the predicted masks based on the method of Generalized Intersection over Union. Finally, we train the proposed algorithm in this paper on the Transcan dataset, evaluating its effectiveness by various metrics and comparing it with existing algorithms. The experimental results show that compared to the baseline provided by the Transcan dataset, the algorithm in this paper improves the mAP indexes on the two tasks of garbage detection and instance segmentation by 9.6 and 5.0, respectively, which significantly improves the algorithm performance. Thus, it can be better applied in the marine environment and achieve high precision object detection and instance segmentation.

Genomic vulnerability of a dominant seaweed points to future-proofing pathways for Australia's underwater forests

Globally, critical habitats are in decline, threatening ecological, economic and social values and prompting calls for 'future proofing' efforts that enhance resilience to climate change. Such efforts rely on predicting how neutral and adaptive genomic patterns across a species' distribution will change under future climate scenarios, but data is scant for most species of conservation concern. Here, we use seascape genomics to characterise genetic diversity, structure and gene-environmental associations in a dominant forest-forming seaweed, Phyllospora comosa, along its entire latitudinal (12° latitude), and thermal (~14°C) range. Phyllospora showed high connectivity throughout its central range, with evidence of genetic structure and potential selection associated with sea surface temperatures (SSTs) at its rear and leading edges. Rear and leading-edge populations harboured only half the genetic diversity of central populations. By modelling genetic turnover as a function of SST, we assessed the genomic vulnerability across Phyllospora's distributional range under climate change scenarios. Despite low diversity, range-edge populations were predicted to harbour beneficial adaptations to marginal conditions and overall adaptability of the species may be compromised by their loss. Assisted gene flow from range edge populations may be required to enhance adaptation and increase resilience of central and leading-edge populations under warming oceans. Understanding genomic vulnerability can inform proactive restoration and future-proofing strategies for underwater forests and ensure their persistence in changing oceans.

Sponge-dwelling fauna: a review of known species from the Northwest Tropical Atlantic coral reefs

Background

Within tropical shallow-water coral reefs, marine sponges provide microhabitats for a wide range of fauna. Although there have been numerous studies and reports of symbiotic relationships amongst sponges and their associated fauna, those pieces of information are isolated and disconnected. For this reason, based on the available literature, we compiled a species-interaction dataset of coral reef marine sponge-associated fauna known to date.

New information

We introduce a dataset that includes 67 literature items that report 101 species of sponge hosts clustered in 12 Orders having a host/guest interaction with 284 guest species from six Phyla present in the Northwestern Tropical Atlantic coral reefs. This dataset consists of two types of information: 1. Machine-readable data and 2. Human-readable data. These two types of coding improve the scope of the dataset and facilitate the link between machine platforms and human-friendly displays. We also created an interactive visualisation of the species-interactions dataset and of a dynamic Chord Diagram of the host-guest species connections to generate a user-friendly link between the user and the dataset.

Exploring biogeochemical and ecological redundancy in phytoplankton communities in the global ocean

Climate-change-induced alterations of oceanic conditions will lead to the ecological niches of some marine phytoplankton species disappearing, at least regionally. How will such losses affect the ecosystem and the coupled biogeochemical cycles? Here, we couch this question in terms of ecological redundancy (will other species be able to fill the ecological roles of the extinct species) and biogeochemical redundancy (can other species replace their biogeochemical roles). Prior laboratory and field studies point to a spectrum in the degree of redundancy. We use a global three-dimensional computer model with diverse planktonic communities to explore these questions further. The model includes 35 phytoplankton types that differ in size, biogeochemical function and trophic strategy. We run two series of experiments in which single phytoplankton types are either partially or fully eliminated. The niches of the targeted types were not completely reoccupied, often with a reduction in the transfer of matter from autotrophs to heterotrophs. Primary production was often decreased, but sometimes increased due to reduction in grazing pressure. Complex trophic interactions (such as a decrease in the stocks of a predator's grazer) led to unexpected reshuffling of the community structure. Alterations in resource utilization may cause impacts beyond the regions where the type went extinct. Our results suggest a lack of redundancy, especially in the 'knock on' effects on higher trophic levels. Redundancy appeared lowest for types on the edges of trait space (e.g. smallest) or with unique competitive strategies. Though highly idealized, our modelling findings suggest that the results from laboratory or field studies often do not adequately capture the ramifications of functional redundancy. The modelled, often counterintuitive, responses-via complex food web interactions and bottom-up versus top-down controls-indicate that changes in planktonic community will be key determinants of future ocean global change ecology and biogeochemistry.

The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms

The Ocean Barcode Atlas (OBA) is a user friendly web service designed for biologists who wish to explore the biodiversity and biogeography of marine organisms locked in otherwise difficult to mine planetary scale DNA metabarcode data sets. Using just a web browser, a comprehensive picture of the diversity of a taxon or a barcode sequence is visualized graphically on world maps and interactive charts. Interactive results panels allow dynamic threshold adjustments and the display of diversity results in their environmental context measured at the time of sampling (temperature, oxygen, latitude, etc). Ecological analyses such as alpha and beta-diversity plots are produced via publication quality vector graphics representations. Currently, the Ocean Barcode Altas is deployed online with the (i) Tara Oceans eukaryotic 18S-V9 rDNA metabarcodes; (ii) Tara Oceans 16S/18S rRNA _mi Tags; and (iii) 16S-V4 V5 metabarcodes collected during the Malaspina-2010 expedition. Additional prokaryotic or eukaryotic plankton barcode data sets will be added upon availability, given they provide the required complement of barcodes (including raw reads to compute barcode abundance) associated with their contextual environmental variables. Ocean Barcode Atlas is a freely-available web service at: http://oba.mio.osupytheas.fr/ocean-atlas/.

Intraspecific variation and energy channel coupling within a Chilean kelp forest

The widespread importance of variable types of primary production, or energy channels, to consumer communities has become increasingly apparent. However, the mechanisms underlying this "multichannel" feeding remain poorly understood, especially for aquatic ecosystems that pose unique logistical constraints given the diversity of potential energy channels. Here, we use bulk tissue isotopic analysis along with carbon isotope (δ13 C) analysis of individual amino acids to characterize the relative contribution of pelagic and benthic energy sources to a kelp forest consumer community in northern Chile. We measured bulk tissue δ13 C and δ15 N for >120 samples; of these we analyzed δ13 C values of six essential amino acids (EAA) from nine primary producer groups (n = 41) and 11 representative nearshore consumer taxa (n = 56). Using EAA δ13 C data, we employed linear discriminant analysis (LDA) to assess how distinct EAA δ13 C values were between local pelagic (phytoplankton/particulate organic matter), and benthic (kelps, red algae, and green algae) endmembers. With this model, we were able to correctly classify nearly 90% of producer samples to their original groupings, a significant improvement on traditional bulk isotopic analysis. With this EAA isotopic library, we then generated probability distributions for the most important sources of production for each individual consumer and species using a bootstrap-resampling LDA approach. We found evidence for multichannel feeding within the community at the species level. Invertebrates tended to focus on either pelagic or benthic energy, deriving 13-67% of their EAA from pelagic sources. In contrast, mobile (fish) taxa at higher trophic levels used more equal proportions of each channel, ranging from 19% to 47% pelagically derived energy. Within a taxon, multichannel feeding was a result of specialization among individuals in energy channel usage, with 37 of 56 individual consumers estimated to derive >80% of their EAA from a single channel. Our study reveals how a cutting-edge isotopic technique can characterize the dynamics of energy flow in coastal food webs, a topic that has historically been difficult to address. More broadly, our work provides a mechanism as to how multichannel feeding may occur in nearshore communities, and we suggest this pattern be investigated in additional ecosystems.

In a comfort zone and beyond-Ecological plasticity of key marine mediators

Copepods of the genus Calanus are the key components of zooplankton. Understanding their response to a changing climate is crucial to predict the functioning of future warmer high-latitude ecosystems. Although specific Calanus species are morphologically very similar, they have different life strategies and roles in ecosystems. In this study, C. finmarchicus and C. glacialis were thoroughly studied with regard to their plasticity in morphology and ecology both in their preferred original water mass (Atlantic vs. Arctic side of the Polar Front) and in suboptimal conditions (due to, e.g., temperature, turbidity, and competition in Hornsund fjord). Our observations show that "at the same place and time," both species can reach different sizes, take on different pigmentation, be in different states of population development, utilize different reproductive versus lipid accumulation strategies, and thrive on different foods. Size was proven to be a very mutable morphological trait, especially with regard to reduced length of C. glacialis. Both species exhibited pronounced red pigmentation when inhabiting their preferred water mass. In other domains, C. finmarchicus individuals tended to be paler than C. glacialis individuals. Gonad maturation and population development indicated mixed reproductive strategies, although a surprisingly similar population age structure of the two co-occurring species in the fjord was observed. Lipid accumulation was high and not species-specific, and its variability was due to diet differences of the populations. According to the stable isotope composition, both species had a more herbivorous diatom-based diet in their original water masses. While the diet of C. glacialis was rather consistent among the domains studied, C. finmarchicus exhibited much higher variability in its feeding history (based on lipid composition). Our results show that the plasticity of both Calanus species is indeed impressive and may be regulated differently, depending on whether they live in their "comfort zone" or beyond it.

Shell Growth of Large Benthic Foraminifera under Heavy Metals Pollution: Implications for Geochemical Monitoring of Coastal Environments

This study was promoted by the recent efforts using larger benthic foraminiferal (LBF) shells geochemistry for the monitoring of heavy metals (HMs) pollution in the marine environment. The shell itself acts as a recorder of the ambient water chemistry in low to extreme HMs-polluted environments, allowing the monitoring of recent-past pollution events. This concept, known as sclerochronology, requires the addition of new parts (i.e., new shell) even in extreme pollution events. We evaluated the physiological resilience of three LBF species with different shell types and symbionts to enriched concentrations of Cd, Cu, and Pb at levels several folds higher than the ecological criteria maximum concentration (CMC) (165-166, 33-43, 1001-1206 µg L^-1, respectively), which is derived from aquatic organisms' toxicity tests. The physiological response of the holobiont was expressed by growth rates quantified by the addition of new chambers (new shell parts), and by the chlorophyll a of the algal symbionts. The growth rate decrease varied between 0% and 30% compared to the unamended control for all HMs tested, whereas the algal symbionts exhibited a general non-fatal but significant response to Pb and Cu. Our results highlight that shell growth inhibition of LBF is predicted in extreme concentrations of 57 × CMC of Cu and 523 × CMC of Cd, providing a proof of concept for shell geochemistry monitoring, which is currently not used in the regulatory sectors.

Behavioural inference from signal processing using animal-borne multi-sensor loggers: a novel solution to extend the knowledge of sea turtle ecology

The identification of sea turtle behaviours is a prerequisite to predicting the activities and time-budget of these animals in their natural habitat over the long term. However, this is hampered by a lack of reliable methods that enable the detection and monitoring of certain key behaviours such as feeding. This study proposes a combined approach that automatically identifies the different behaviours of free-ranging sea turtles through the use of animal-borne multi-sensor recorders (accelerometer, gyroscope and time-depth recorder), validated by animal-borne video-recorder data. We show here that the combination of supervised learning algorithms and multi-signal analysis tools can provide accurate inferences of the behaviours expressed, including feeding and scratching behaviours that are of crucial ecological interest for sea turtles. Our procedure uses multi-sensor miniaturized loggers that can be deployed on free-ranging animals with minimal disturbance. It provides an easily adaptable and replicable approach for the long-term automatic identification of the different activities and determination of time-budgets in sea turtles. This approach should also be applicable to a broad range of other species and could significantly contribute to the conservation of endangered species by providing detailed knowledge of key animal activities such as feeding, travelling and resting.

Reductions in the dietary niche of southern sea otters (Enhydra lutris nereis) from the Holocene to the Anthropocene

The sea otter (Enhydra lutris) is a marine mammal hunted to near extinction during the 1800s. Despite their well-known modern importance as a keystone species, we know little about historical sea otter ecology. Here, we characterize the ecological niche of ancient southern sea otters (E. lutris nereis) using δ13C analysis and δ15N analysis of bones recovered from archaeological sites spanning ~7,000 to 350 years before present (N = 112 individuals) at five regions along the coast of California. These data are compared with previously published data on modern animals (N = 165) and potential modern prey items. In addition, we analyze the δ15N of individual amino acids for 23 individuals to test for differences in sea otter trophic ecology through time. After correcting for tissue-specific and temporal isotopic effects, we employ nonparametric statistics and Bayesian niche models to quantify differences among ancient and modern animals. We find ancient otters occupied a larger isotopic niche than nearly all modern localities; likely reflecting broader habitat and prey use in prefur trade populations. In addition, ancient sea otters at the most southerly sites occupied an isotopic niche that was more than twice as large as ancient otters from northerly regions. This likely reflects greater invertebrate prey diversity in southern California relative to northern California. Thus, we suggest the potential dietary niche of sea otters in southern California could be larger than in central and northern California. At two sites, Año Nuevo and Monterey Bay, ancient otters had significantly higher δ15N values than modern populations. Amino acid δ15N data indicated this resulted from shifting baseline isotope values, rather than a change in sea otter trophic ecology. Our results help in better understanding the contemporary ecological role of sea otters and exemplify the strength of combing zooarchaeological and biological information to provide baseline data for conservation efforts.

Viral Attachment to Biotic and Abiotic Surfaces in Seawater

Viruses influence microbial community structure and biogeochemical cycles in marine environments. Viral attachment to nonhost surfaces could influence host viral infection rates; however, the prevalence of such viral attachment is not investigated quantitatively. We used coastal seawater viral assemblages and, as models, marine vibriophage (SIO-2) and enterobacteriophages (T2 and T4) to investigate their attachment to probable nonhost marine bacteria. We also studied viral attachment to colloids and other abiotic surfaces in seawater. Centrifugation experiments with bacterium-virus mixtures showed substantial viral loss in the supernatant presumably due to the viral attachment to bacteria. This attachment (0.04 to 24 viruses μm^-2 [bacterial surface area]) varied with bacterium-virus combinations. Surprisingly, filtering seawater on 0.2-μm Anodisc or polycarbonate filters retained ∼12 to 84% of viruses presumably attached to ≥0.2-μm-sized particles and/or the filter surface. Enzymatic digestion followed by epifluorescence and atomic force microscopy suggested that 7 to 25% of the total viruses were attached via β-glycosidic linkages. Furthermore, a substantial proportion (7 to 48%) of viruses became attached to model abiotic surfaces (polycarbonate, polypropylene, and glass), and this has significance for laboratory protocols as well as studies of virus ecology in particle-rich marine environments. Substantial attachment of viruses to nonhost surfaces could influence virus-driven biogeochemical cycles and microbial community structure.IMPORTANCE Viruses play important roles in altering microbial community structure and biogeochemical cycles in marine environments. Viral attachment to nonhost surfaces can influence host viral infection rates; however, the prevalence of viral attachment to nonhost surfaces and the ratio of attached viruses to total viruses are little known. We used coastal seawater viral assemblages and used marine vibriophage (SIO-2) and enterobacteriophages (T2 and T4) as models to investigate their attachment to abiotic and biotic surfaces in seawater. Viral attachment was observed on several surfaces, such as nonhost bacteria, polymers, filters, cover glasses, and tube surfaces. This study cautions against commonly used protocols that require viral incubation and seawater fractionation. More importantly, these results could influence virus-driven biogeochemical cycles and microbial community structure in the ocean.

Modelling microbial communities using biochemical resource allocation analysis

To understand the functioning and dynamics of microbial communities is a fundamental challenge in current biology. To tackle this challenge, the construction of computational models of interacting microbes is an indispensable tool. There is, however, a large chasm between ecologically motivated descriptions of microbial growth used in many current ecosystems simulations, and detailed metabolic pathway and genome-based descriptions developed in the context of systems and synthetic biology. Here, we seek to demonstrate how resource allocation models of microbial growth offer the potential to advance ecosystem simulations and their parametrization. In particular, recent work on quantitative resource allocation allow us to formulate mechanistic models of microbial growth that are physiologically meaningful while remaining computationally tractable. These models go beyond Michaelis-Menten and Monod-type growth models, and are capable of accounting for emergent properties that underlie the remarkable plasticity of microbial growth. We outline the utility and advantages of using biochemical resource allocation models by considering a coarse-grained model of cyanobacterial growth and demonstrate how the model allows us to address specific questions of relevance for the simulation of marine microbial ecosystems, including the physiological acclimation of protein expression to different environments, the description of co-limitation by several nutrients and the differential use of alternative nutrient sources, as well as the description of metabolic diversity based on our increasing knowledge about quantitative cell physiology.

Understanding interactions between plasticity, adaptation and range shifts in response to marine environmental change

Climate change is leading to shifts in species geographical distributions, but populations are also probably adapting to environmental change at different rates across their range. Owing to a lack of natural and empirical data on the influence of phenotypic adaptation on range shifts of marine species, we provide a general conceptual model for understanding population responses to climate change that incorporates plasticity and adaptation to environmental change in marine ecosystems. We use this conceptual model to help inform where within the geographical range each mechanism will probably operate most strongly and explore the supporting evidence in species. We then expand the discussion from a single-species perspective to community-level responses and use the conceptual model to visualize and guide research into the important yet poorly understood processes of plasticity and adaptation. This article is part of the theme issue 'The role of plasticity in phenotypic adaptation to rapid environmental change'.

Noninvasive Featherlight Wearable Compliant "Marine Skin": Standalone Multisensory System for Deep-Sea Environmental Monitoring

Advances in marine research to understand environmental change and its effect on marine ecosystems rely on gathering data on species physiology, their habitat, and their mobility patterns using heavy and invasive biologgers and sensory telemetric networks. In the past, a lightweight (6 g) compliant environmental monitoring system: Marine Skin was demonstrated. In this paper, an enhanced version of that skin with improved functionalities (500-1500% enhanced sensitivity), packaging, and most importantly its endurance at a depth of 2 km in the highly saline Red Sea water for four consecutive weeks is reported. A unique noninvasive approach for attachment of the sensor by designing a wearable, stretchable jacket (bracelet) that can adhere to any species irrespective of their skin type is also illustrated. The wearable featherlight (<0.5 g in air, 3 g with jacket) gadget is deployed on Barramundi, Seabream, and common goldfish to demonstrate the noninvasive and effective attachment strategy on different species of variable sizes which does not hinder the animals' natural movement or behavior.

Noninvasive Featherlight Wearable Compliant "Marine Skin": Standalone Multisensory System for Deep-Sea Environmental Monitoring

Advances in marine research to understand environmental change and its effect on marine ecosystems rely on gathering data on species physiology, their habitat, and their mobility patterns using heavy and invasive biologgers and sensory telemetric networks. In the past, a lightweight (6 g) compliant environmental monitoring system: Marine Skin was demonstrated. In this paper, an enhanced version of that skin with improved functionalities (500-1500% enhanced sensitivity), packaging, and most importantly its endurance at a depth of 2 km in the highly saline Red Sea water for four consecutive weeks is reported. A unique noninvasive approach for attachment of the sensor by designing a wearable, stretchable jacket (bracelet) that can adhere to any species irrespective of their skin type is also illustrated. The wearable featherlight (<0.5 g in air, 3 g with jacket) gadget is deployed on Barramundi, Seabream, and common goldfish to demonstrate the noninvasive and effective attachment strategy on different species of variable sizes which does not hinder the animals' natural movement or behavior.

Host and parasite thermal ecology jointly determine the effect of climate warming on epidemic dynamics

Host-parasite systems have intricately coupled life cycles, but each interactor can respond differently to changes in environmental variables like temperature. Although vital to predicting how parasitism will respond to climate change, thermal responses of both host and parasite in key traits affecting infection dynamics have rarely been quantified. Through temperature-controlled experiments on an ectothermic host-parasite system, we demonstrate an offset in the thermal optima for survival of infected and uninfected hosts and parasite production. We combine experimentally derived thermal performance curves with field data on seasonal host abundance and parasite prevalence to parameterize an epidemiological model and forecast the dynamical responses to plausible future climate-warming scenarios. In warming scenarios within the coastal southeastern United States, the model predicts sharp declines in parasite prevalence, with local parasite extinction occurring with as little as 2 °C warming. The northern portion of the parasite's current range could experience local increases in transmission, but assuming no thermal adaptation of the parasite, we find no evidence that the parasite will expand its range northward under warming. This work exemplifies that some host populations may experience reduced parasitism in a warming world and highlights the need to measure host and parasite thermal performance to predict infection responses to climate change.

Uncertain recovery of the North Atlantic right whale in a changing ocean

Human activities have placed populations of many endangered species at risk and mitigation efforts typically focus on reducing anthropogenic sources of mortality. However, failing to recognize the additional role of environmental factors in regulating birth and mortality rates can lead to erroneous demographic analyses and conclusions. The North Atlantic right whale population is currently the focus of conservation efforts aimed at reducing mortality rates associated with ship strikes and entanglement in fishing gear. Consistent monitoring of the population since 1980 has revealed evidence that climate-associated changes in prey availability have played an important role in the population's recovery. The considerable interdecadal differences observed in population growth coincide with remote Arctic and North Atlantic oceanographic processes that link to the Gulf of Maine ecosystem. Here, we build capture-recapture models to quantify the role of prey availability on right whale demographic transitional probabilities and use a corresponding demographic model to project population growth rates into the next century. Contrary to previous predictions, the right whale population is projected to recover in the future as long as prey availability and mortality rates remain within the ranges observed during 1980-2012. However, recent events indicate a northward range shift in right whale prey, potentially resulting in decreased prey availability and/or an expansion of right whale habitat into unprotected waters. An annual increase in the number of whale deaths comparable to that observed during the summer 2017 mass mortality event may cause a decline to extinction even under conditions of normal prey availability. This study highlights the importance of understanding the oceanographic context for observed population changes when evaluating the efficacy of conservation management plans for endangered marine species.

Using Click-Chemistry for Visualizing in Situ Changes of Translational Activity in Planktonic Marine Bacteria

A major challenge in microbial ecology is linking diversity and function to determine which microbes are actively contributing to processes occurring in situ. Bioorthogonal non-canonical amino acid tagging (BONCAT) is a promising technique for detecting and quantifying translationally active bacteria in the environment. This technique consists of incubating a bacterial sample with an analog of methionine and using click-chemistry to identify the cells that have incorporated the substrate. Here, we established an optimized protocol for the visualization of protein-synthesizing cells in oligotrophic waters that can be coupled with taxonomic identification using Catalyzed Reporter Deposition Fluorescent in Situ Hybridization. We also evaluated the use of this technique to track shifts in translational activity by comparing it with leucine incorporation, and used it to monitor temporal changes in both cultures and natural samples. Finally, we determined the optimal concentration and incubation time for substrate incorporation during BONCAT incubations at an oligotrophic site. Our results demonstrate that BONCAT is a fast and powerful semi-quantitative approach to explore the physiological status of marine bacteria.

Signatures of the collapse and incipient recovery of an overexploited marine ecosystem

The Northwest Atlantic cod stocks collapsed in the early 1990s and have yet to recover, despite the subsequent establishment of a continuing fishing moratorium. Efforts to understand the collapse and lack of recovery have so far focused mainly on the dynamics of commercially harvested species. Here, we use data from a 33-year scientific trawl survey to determine to which degree the signatures of the collapse and recovery of the cod are apparent in the spatial and temporal dynamics of the broader groundfish community. Over this 33-year period, the groundfish community experienced four phases of change: (i) a period of rapid, synchronous biomass collapse in most species, (ii) followed by a regime shift in community composition with a concomitant loss of functional diversity, (iii) followed in turn by periods of slow compositional recovery, and (iv) slow biomass growth. Our results demonstrate how a community-wide perspective can reveal new aspects of the dynamics of collapse and recovery unavailable from the analysis of individual species or a combination of a small number of species. Overall, we found evidence that such community-level signals should be useful for designing more effective management strategies to ensure the persistence of exploited marine ecosystems.

Behavioral Hypervolumes of Predator Groups and Predator-Predator Interactions Shape Prey Survival Rates and Selection on Prey Behavior

Predator-prey interactions often vary on the basis of the traits of the individual predators and prey involved. Here we examine whether the multidimensional behavioral diversity of predator groups shapes prey mortality rates and selection on prey behavior. We ran individual sea stars (Pisaster ochraceus) through three behavioral assays to characterize individuals' behavioral phenotype along three axes. We then created groups that varied in the volume of behavioral space that they occupied. We further manipulated the ability of predators to interact with one another physically via the addition of barriers. Prey snails (Chlorostome funebralis) were also run through an assay to evaluate their predator avoidance behavior before their use in mesocosm experiments. We then subjected pools of prey to predator groups and recorded the number of prey consumed and their behavioral phenotypes. We found that predator-predator interactions changed survival selection on prey traits: when predators were prevented from interacting, more fearful snails had higher survival rates, whereas prey fearfulness had no effect on survival when predators were free to interact. We also found that groups of predators that occupied a larger volume in behavioral trait space consumed 35% more prey snails than homogeneous predator groups. Finally, we found that behavioral hypervolumes were better predictors of prey survival rates than single behavioral traits or other multivariate statistics (i.e., principal component analysis). Taken together, predator-predator interactions and multidimensional behavioral diversity determine prey survival rates and selection on prey traits in this system.

Low ratios of silica to dissolved nitrogen supplied to rivers arise from agriculture not reservoirs

Coastal marine systems are greatly altered by toxic marine algae, eutrophication and hypoxia. These problems have been linked to decreased ratios of dissolved silica to inorganic nitrogen (Si : DIN) delivered from land. Two mechanisms for this decline under consideration are enhanced nitrogen (N) fertiliser losses from agricultural lands or Si sequestration in reservoirs. Here we examine these mechanisms via nutrient concentrations in impoundments receiving water from 130 watersheds in a landscape representative of the agriculture that often dominates coastal nutrient inputs. Decreased Si : DIN was correlated with agriculture, not impoundment. Watersheds with > 60% agricultural land yielded highest DIN, whereas Si was uncorrelated with agricultural intensity. Furthermore, eutrophic lakes were dominated by Cyanobacteria that use little Si, so reservoirs did not diminish Si : DIN. Instead, Si : DIN increased slightly as reservoir residence time increased. These data suggest that impoundments in agricultural watersheds may enhance the water quality of coastal ecosystems, whereas fertiliser losses are detrimental.

HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts

Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments.

Observations and Experiments on the Biology and Life History of Riseriellus occultus (Heteronemertea: Lineidae)

Studies on the biology and life history of nemerteans are scarce, mostly because these animals are nocturnal. In order to broaden the knowledge base on the life history of nemerteans as a prerequisite for comparative analyses, we studied a population of Riseriellus occultus (Heteronemertea: Lineidae) inhabiting the rocky intertidal in southern Brittany near Concarneau (France) for more than 10 years. Our studies show that R. occultus is an iteroparous, perennial species exclusively inhabiting rocky shore crevices that result from onionskin weathering of the granite. From September through October R. occultus reproduces by external fertilization and develops via a planktonic pilidium larva, which, under laboratory conditions, metamorphoses after about six weeks. Adults of R. occultus are nocturnal macrophagous predators that preferentially feed on the gastropods Gibbula umbilicalis and Patella species, but also consume the bivalve Mytilus edulis. Since R. occultus devours the snail inside the shell, we fixed individuals while feeding, and serially sectioned them. Reconstruction of the sections shows that R. occultus swallows the entire soft body and finally detaches the columellar muscle from the shell. Estimates on the density of R. occultus inside the rock crevices provide evidence for clustered distribution and locally high abundance on the rocky shore. These data strongly suggest that R. occultus affects the structure of the rocky shore gastropod community. Although our data are still fragmentary with respect to the ecology of this species and its role in the local food web, our knowledge has grown to such extent that R. occultus can now be regarded as one of the few well characterized nemertean species.

Nutritional input from dinoflagellate symbionts in reef-building corals is minimal during planula larval life stage

Dispersion of larval offspring is of fundamental ecological importance to sessile marine organisms. Photosymbiotic planulae emitted by many reef-forming corals may travel over large distances before settling to form a new colony. It is not clear whether the metabolic requirements of these planula larvae are met exclusively with lipid and protein reservoirs inherited from the mother colony or when metabolic inputs from their endosymbiotic dinoflagellates become important. Pulse-chase experiments using [(13)C]bicarbonate and [(15)N]nitrate, combined with subcellular structural and isotopic imaging of freshly emitted symbiotic larvae from the coral Pocillopora damicornis, show that metabolic input from the dinoflagellates is minimal in the planulae compared with adult colonies. The larvae are essentially lecithotrophic upon emission, indicating that a marked shift in metabolic interaction between the symbiotic partners takes place later during ontogeny. Understanding the cellular processes that trigger and control this metabolic shift, and how climate change might influence it, is a key challenge in coral biology.

Synchronous marine pelagic regime shifts in the Northern Hemisphere

Regime shifts are characterized by sudden, substantial and temporally persistent changes in the state of an ecosystem. They involve major biological modifications and often have important implications for exploited living resources. In this study, we examine whether regime shifts observed in 11 marine systems from two oceans and three regional seas in the Northern Hemisphere (NH) are synchronous, applying the same methodology to all. We primarily infer marine pelagic regime shifts from abrupt shifts in zooplankton assemblages, with the exception of the East Pacific where ecosystem changes are inferred from fish. Our analyses provide evidence for quasi-synchronicity of marine pelagic regime shifts both within and between ocean basins, although these shifts lie embedded within considerable regional variability at both year-to-year and lower-frequency time scales. In particular, a regime shift was detected in the late 1980s in many studied marine regions, although the exact year of the observed shift varied somewhat from one basin to another. Another regime shift was also identified in the mid- to late 1970s but concerned less marine regions. We subsequently analyse the main biological signals in relation to changes in NH temperature and pressure anomalies. The results suggest that the main factor synchronizing regime shifts on large scales is NH temperature; however, changes in atmospheric circulation also appear important. We propose that this quasi-synchronous shift could represent the variably lagged biological response in each ecosystem to a large-scale, NH change of the climatic system, involving both an increase in NH temperature and a strongly positive phase of the Arctic Oscillation. Further investigation is needed to determine the relative roles of changes in temperature and atmospheric pressure patterns and their resultant teleconnections in synchronizing regime shifts at large scales.

Marine algae and land plants share conserved phytochrome signaling systems

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 light-input 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 photosynthesis-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.

Marine metaproteomics: deciphering the microbial metabolic food web

Metaproteomics can be applied to marine systems to discover metabolic processes in the ocean. This review describes current breakthroughs regarding marine microbes in the areas of microbial procurement of nutrients, important and previously unrecognized metabolic processes, functional roles for proteins with previously unknown functions, and intricate networks of metabolic interactions between symbiotic microbes and their hosts. By recognizing that metaproteomics empowers our understanding of the roles that marine microbes play in global biogeochemical cycles, the achievements to date from this advancing field highlight the enormous potential that the future holds.

Light-driven tipping points in polar ecosystems

Some ecosystems can undergo abrupt transformation in response to relatively small environmental change. Identifying imminent 'tipping points' is crucial for biodiversity conservation, particularly in the face of climate change. Here, we describe a tipping point mechanism likely to induce widespread regime shifts in polar ecosystems. Seasonal snow and ice-cover periodically block sunlight reaching polar ecosystems, but the effect of this on annual light depends critically on the timing of cover within the annual solar cycle. At high latitudes, sunlight is strongly seasonal, and ice-free days around the summer solstice receive orders of magnitude more light than those in winter. Early melt that brings the date of ice-loss closer to midsummer will cause an exponential increase in the amount of sunlight reaching some ecosystems per year. This is likely to drive ecological tipping points in which primary producers (plants and algae) flourish and out-compete dark-adapted communities. We demonstrate this principle on Antarctic shallow seabed ecosystems, which our data suggest are sensitive to small changes in the timing of sea-ice loss. Algae respond to light thresholds that are easily exceeded by a slight reduction in sea-ice duration. Earlier sea-ice loss is likely to cause extensive regime shifts in which endemic shallow-water invertebrate communities are replaced by algae, reducing coastal biodiversity and fundamentally changing ecosystem functioning. Modeling shows that recent changes in ice and snow cover have already transformed annual light budgets in large areas of the Arctic and Antarctic, and both aquatic and terrestrial ecosystems are likely to experience further significant change in light. The interaction between ice-loss and solar irradiance renders polar ecosystems acutely vulnerable to abrupt ecosystem change, as light-driven tipping points are readily breached by relatively slight shifts in the timing of snow and ice-loss.

Fluid dynamical niches of phytoplankton types

The biogeochemical role of phytoplanktonic organisms strongly varies from one plankton type to another, and their relative abundance and distribution have fundamental consequences at the global and climatological scales. In situ observations find dominant types often associated to specific physical and chemical water properties. However, the mechanisms and spatiotemporal scales by which marine ecosystems are organized are largely not known. Here we investigate the spatiotemporal organization of phytoplankton communities by combining multisatellite data, notably high-resolution ocean-color maps of dominant types and altimetry-derived Lagrangian diagnostics of the surface transport. We find that the phytoplanktonic landscape is organized in (sub-)mesoscale patches (10-100 km) of dominant types separated by physical fronts induced by horizontal stirring. These physical fronts delimit niches supported by water masses of similar history and whose lifetimes are comparable with the timescale of the bloom onset (few weeks). The resonance between biological activity and physical processes suggest that the spatiotemporal (sub-)mesoscales associated to stirring are determinant in the observation and modeling of marine ecosystems.