Challenges of Modeling Ocean Basin Ecosystems

A three-dimensional mixotrophic model of Karlodinium veneficum blooms for a eutrophic estuary

Blooms of dinoflagellate Karlodinium veneficum are widely distributed in estuarine and coastal waters and have been found to cause fish kills worldwide. K. veneficum has a mixed nutritional mode and relies on both photosynthesis and phagotrophy for growth; it is a mixotroph. Here, a model of mixotrophic growth of K. veneficum (MIXO) was developed, calibrated with previously-reported laboratory physiological data, and subsequently embedded in a 3D-coupled hydrodynamic (ROMS)-biogeochemical (RCA) model of eutrophic Chesapeake Bay, USA. The resulting ROMS-RCA-MIXO model was applied in hindcast mode to investigate seasonal and spatial distributions. Simulations showed that K. veneficum blooms occurred during June-August and were confined to the upper and middle Bay, consistent with long-term field observations. Autotrophic growth dominated in spring but heterotrophic growth dominated during the summer. The number of prey ingested by K. veneficum varied from 0.1 to 0.6 day^-1 and the food vacuole content reached up to 50% of the core mixotroph biomass. The ingestion rate increased with prey density and also when P:N ratio fell below ∼0.03 (N:P ∼ 33), indicating that K. veneficum only switched to mixotrophic feeding in P-deficient waters when sufficient prey were available; this occurred during the summer months. The digestion rate increased with both the food vacuole content and temperature. The modeling analysis affirms K. veneficum as a phagotrophic 'alga' which is primarily photosynthetic but switches to mixotrophic feeding under nutrient deficient conditions.

Zooplankton species composition and diversity in the seagrass habitat of Lawas, Sarawak, Malaysia

Seagrass habitats are considered to be some of the most biodiverse ecosystems on the planet and safeguard some ecologically and economically important fauna, amongst which are some globally threatened species, including dugong. Malaysian seagrass ecosystems are not widespread, but their existence supports some significant marine fauna. A rigorous zooplankton study was conducted from May 2016 to February 2017, in the seagrass habitat of Lawas, Sarawak, Malaysia, to examine their temporal composition and diversity, together with their ecological influences. A total of 45 zooplankton species from 13 significant groups were recorded in the seagrass habitat. The population density of zooplankton ranged between 2,482 ind/m³ and 22,670 ind/m³ over three different seasons. A single zooplankton copepod was found to be dominant (47.40%), while bivalves were the second largest (31.8%) group in terms of total abundance. It was also noticed that the average relative abundance (0.62) and important species index (62.08) of copepods were higher than for other groups that exist in the seagrass meadow, whereas copepod Parvocalanuscrassirostris showed both the highest average relative abundance (0.41) and the highest important species index (41.15). The diversity (H') and richness index of the intermediate season were found to be highest due to favourable physico-chemical conditions. Within the referred seasonal cluster, the wet and dry seasons were almost similar in terms of species abundance, while the intermediate season was distinct, with high species diversity backed by ANOSIM analysis results. Copepod and bivalves formed one group with a common similarity level of 0.80. The CCA (Canonical Correspondence Analysis) model established that abiotic factors, especially turbidity, NO₂, rainfall, dissolved oxygen and pH were significantly correlated with abundance of individual groups of zooplankton. Zooplankton assemblage and abundance in Lawas were found to be very rich in multiple seasons, indicating that the productivity of uninterrupted seagrass habitat might be high and the system rich in biodiversity.

Effects of terrestrial inputs and seawater intrusion on zooplankton community structure in Daya Bay, South China Sea

Daya Bay is a eutrophic coastal region with dynamic physico-chemical conditions influenced by terrestrial inputs and seawater intrusion. Zooplankton is a crucial trophic intermediary for energy transfer and fishery resources. In this study, we assessed the distribution and composition of zooplankton in Daya Bay during summer and winter of 2015. We found that zooplankton diversity was the lowest and dominated by small copepods (Acartia spp. and Paracalanus spp.) and gelatinous Oikopleura spp. under terrestrial inputs in the Dan'ao River estuary and Aotou barbour. The highest zooplankton diversity was observed at the bay mouth that influenced by salty intruded seawater, and the dominant oceanic species (such as Euchaeta concinna and Subeucalanus subcrassus invaded into the top of the bay in winter. The dominant species in the estuary shift from Penilia avirostris to Acartia spp. compared with historical researches, indicating the effect of human activities on the succession of dominant species.

A three-dimensional mechanistic model of Prorocentrum minimum blooms in eutrophic Chesapeake Bay

Planktonic Prorocentrum, common harmful dinoflagellate, are increasing in frequency, duration, and magnitude globally, as exemplified by the number of blooms of P. minimum in Chesapeake Bay that have nearly doubled over the past 3 decades. Although the dynamics of transport and seasonal occurrence of this species have been previously described, it has been challenging to predict the timing and location of P. minimum blooms in Chesapeake Bay. We developed a new three-dimensional mechanistic model of this species that integrates physics, nutrient cycling and plankton physiology and embedded it within a coupled hydrodynamic-biogeochemical model originally developed for simulating water quality in eutrophic estuarine and coastal waters. Hindcast simulations reproduced the observed time series and spatial distribution of cell density, in particular capturing well its peak in May in the mid-to-upper part of the estuary. Timing and duration of the blooms were mostly determined by the temperature-dependent growth function, while mortality due to grazing and respiration played a minor role. The model also reproduced the pattern of overwintering populations, which are located in bottom waters of the lower Bay, and are transported upstream in spring by estuarine flow. Blooms develop in the mid-upper parts of the estuary when these transported cells encounter high nutrient concentrations from the Susquehanna River and favorable light conditions. Diagnostic analysis and model-sensitivity experiments of nutrient conditions showed that high nitrogen:phosphorus conditions favor bloom development. The model also captured the observed interannual variations in the magnitude and spatial distribution of P. minimum blooms.

Deep diving with Clio

An autonomous underwater vehicle, named Clio, can sample ocean basin-scale biogeochemistry at depths up to 6000 meters.

Probabilistic modeling to estimate jellyfish ecophysiological properties and size distributions

While Ocean modeling has made significant advances over the last decade, its complex biological component is still oversimplified. In particular, modeling organisms in the ocean system must integrate parameters to fit both physiological and ecological behaviors that are together very difficult to determine. Such difficulty occurs for modeling Pelagia noctiluca. This jellyfish has a high abundance in the Mediterranean Sea and could contribute to several biogeochemical processes. However, gelatinous zooplanktons remain poorly represented in biogeochemical models because uncertainties about their ecophysiology limit our understanding of their potential role and impact. To overcome this issue, we propose, for the first time, the use of the Statistical Model Checking Engine (SMCE), a probability-based computational framework that considers a set of parameters as a whole. Contrary to standard parameter inference techniques, SMCE identifies sets of parameters that fit both laboratory-culturing observations and in situ patterns while considering uncertainties. Doing so, we estimated the best parameter sets of the ecophysiological model that represents the jellyfish growth and degrowth in laboratory conditions as well as its size. Behind this application, SMCE remains a computational framework that supports the projection of a model with uncertainties in broader contexts such as biogeochemical processes to drive future studies.

Pacific Decadal and El Niño oscillations shape survival of a seabird

Understanding and modeling population change is urgently needed to predict effects of climate change on biodiversity. High trophic-level organisms are influenced by fluctuations of prey quality and abundance, which themselves may depend on climate oscillations. Modeling effects of such fluctuations is challenging because prey populations may vary with multiple climate oscillations occurring at different time scales. The analysis of a 28-yr time series of capture-recapture data of a tropical seabird, the Nazca Booby (Sula granti), in the Galápagos, Ecuador, allowed us to test for demographic effects of two major ocean oscillations occurring at distinct time-scales: the inter-annual El Niño Southern Oscillation (ENSO) and inter-decadal oscillations. As expected for a tropical seabird, survival of fledgling birds was highly affected by extreme ENSO events; by contrast, neither recruitment nor breeding participation were affected by either ENSO or decadal oscillations. More interesting, adult survival, a demographic trait that canalizes response to environmental variations, was unaffected by inter-annual ENSO oscillations yet was shaped by the Pacific Decadal Oscillation and small pelagic fish regime. Adult survival decreased during oceanic conditions associated with higher breeding success, an association probably mediated in this species by costs of reproduction that reduce survival when breeding attempts end later. To our knowledge, this is the first study suggesting that survival of a vertebrate can be vulnerable to a natural multidecadal oscillation.

Vast assembly of vocal marine mammals from diverse species on fish spawning ground

Observing marine mammal (MM) populations continuously in time and space over the immense ocean areas they inhabit is challenging but essential for gathering an unambiguous record of their distribution, as well as understanding their behaviour and interaction with prey species. Here we use passive ocean acoustic waveguide remote sensing (POAWRS) in an important North Atlantic feeding ground to instantaneously detect, localize and classify MM vocalizations from diverse species over an approximately 100,000 km(2) region. More than eight species of vocal MMs are found to spatially converge on fish spawning areas containing massive densely populated herring shoals at night-time and diffuse herring distributions during daytime. We find the vocal MMs divide the enormous fish prey field into species-specific foraging areas with varying degrees of spatial overlap, maintained for at least two weeks of the herring spawning period. The recorded vocalization rates are diel (24 h)-dependent for all MM species, with some significantly more vocal at night and others more vocal during the day. The four key baleen whale species of the region: fin, humpback, blue and minke have vocalization rate trends that are highly correlated to trends in fish shoaling density and to each other over the diel cycle. These results reveal the temporospatial dynamics of combined multi-species MM foraging activities in the vicinity of an extensive fish prey field that forms a massive ecological hotspot, and would be unattainable with conventional methodologies. Understanding MM behaviour and distributions is essential for management of marine ecosystems and for accessing anthropogenic impacts on these protected marine species.

Fractal Hypothesis of the Pelagic Microbial Ecosystem-Can Simple Ecological Principles Lead to Self-Similar Complexity in the Pelagic Microbial Food Web?

Trophic interactions are highly complex and modern sequencing techniques reveal enormous biodiversity across multiple scales in marine microbial communities. Within the chemically and physically relatively homogeneous pelagic environment, this calls for an explanation beyond spatial and temporal heterogeneity. Based on observations of simple parasite-host and predator-prey interactions occurring at different trophic levels and levels of phylogenetic resolution, we present a theoretical perspective on this enormous biodiversity, discussing in particular self-similar aspects of pelagic microbial food web organization. Fractal methods have been used to describe a variety of natural phenomena, with studies of habitat structures being an application in ecology. In contrast to mathematical fractals where pattern generating rules are readily known, however, identifying mechanisms that lead to natural fractals is not straight-forward. Here we put forward the hypothesis that trophic interactions between pelagic microbes may be organized in a fractal-like manner, with the emergent network resembling the structure of the Sierpinski triangle. We discuss a mechanism that could be underlying the formation of repeated patterns at different trophic levels and discuss how this may help understand characteristic biomass size-spectra that hint at scale-invariant properties of the pelagic environment. If the idea of simple underlying principles leading to a fractal-like organization of the pelagic food web could be formalized, this would extend an ecologists mindset on how biological complexity could be accounted for. It may furthermore benefit ecosystem modeling by facilitating adequate model resolution across multiple scales.

Factors driving the seasonal distribution of zooplankton in a eutrophicated Mediterranean Lagoon

The distribution of the zooplankton community was studied along with environmental factors at five sampling stations in Ghar El Melh Lagoon (GML) (Mediterranean Sea, northern Tunisia). GML is characterized by specific following properties: broad and shallow, freshwater supply (Station 1); connection to the sea (S2); stagnation (S3 especially), and eutrophic conditions with enhanced nutrient concentrations (S4 and S5). Samples were taken twice monthly from February 2011 to January 2012. Twenty-three zooplankton groups comprising 10 larval stages were identified. Zooplankton assemblages were largely dominated by copepods (37.25%), followed respectively by ciliates (21.09%), bivalve larvae (14.88%) and gastropod veligers (12.53%). Redundancy analysis indicated that while no significant difference was found in the distribution of zooplankton at any station, a strong difference was observed according to season. Both temporal and physicochemical fluctuations explain more than 50% of changes in zooplankton abundances.

Bivalve and barnacle larvae distribution driven by water temperature in a Mediterranean lagoon

The objective of this study was to explore the relationships between the distribution of some meroplanktonic species and water temperature. Meroplankton larvae abundance of bivalves, and barnacles and water temperature fluctuations were studied from February 2011 to January 2012 at five stations in Ghar El Melh lagoon (GML) Mediterranean Sea, northern Tunisia). According to redundancy analysis (RDA), a significant difference was found in the distribution of larvae among the seasons (F = 10.28, p < 0.001); summer and autumn appear to be the period of bivalve larvae development, whereas the arrival of barnacle larvae coincided with winter and spring. The generalized additive models (GAMs) show strong correlation of bivalve larvae with high temperature (F = 23.2; p < 0.001) and the affinity of barnacle larvae to low temperature values (F = 8.41; p = 0.004). This environmental parameter accounted for 26 % of the deviance in variability in larvae abundance. The development process of many generations of larvae may therefore have been predetermined by temperature.

What factors drive copepod community distribution in the Gulf of Gabes, Eastern Mediterranean Sea?

The spatial and temporal variations in copepod communities were investigated during four oceanographic cruises conducted between July 2005 and March 2007 aboard the R/V Hannibal. A close relationship was observed between the temperature, salinity, hydrographic properties and water masses characterising the Gulf of Gabes. Indeed, water thermal stratification began in May-June, and a thermocline was established at a 20-m depth, but ranged from 25 m in July to more than 30 m in September. The zooplankton community is dominated by copepods representing 69 % to 83 % of total zooplankton. Spatial and temporal variation of copepods in relation to environmental factors shows their close relationship with the hydrodynamic features of the water column. Thermal stratification in the column, established in summer, supports copepod development. In fact, copepod abundance increases gradually with rising water temperature and salinity, starting from the beginning of thermal stratification (May-June 2006) and lasting until its completion (July 2005 and September 2006). When the water column is well mixed (March 2007), copepod abundance decreased. Our finding shows that temperature and salinity seem to be the most important physical factors and thus strongly influence the taxonomic diversity and distribution of the copepod population. They are characterised by the dominance of Oithona nana, representing 75-86 % of total cyclopoid abundance. The most abundant species during the stratification period were O. nana, Acartia clausi and Stephos marsalensis in July 2005 and September 2006. However, during the mixing period, Euterpina acutifrons was more abundant, representing 21 % of the total. Unlike the copepod community, which is more abundant during the period of high stratification, phytoplankton proliferates during semi-mixed conditions.

Predictive systems ecology

Human societies, and their well-being, depend to a significant extent on the state of the ecosystems that surround them. These ecosystems are changing rapidly usually in response to anthropogenic changes in the environment. To determine the likely impact of environmental change on ecosystems and the best ways to manage them, it would be desirable to be able to predict their future states. We present a proposal to develop the paradigm of predictive systems ecology, explicitly to understand and predict the properties and behaviour of ecological systems. We discuss the necessary and desirable features of predictive systems ecology models. There are places where predictive systems ecology is already being practised and we summarize a range of terrestrial and marine examples. Significant challenges remain but we suggest that ecology would benefit both as a scientific discipline and increase its impact in society if it were to embrace the need to become more predictive.

Biodiversity and ecosystem function in the Gulf of Maine: pattern and role of zooplankton and pelagic nekton

This paper forms part of a broader overview of biodiversity of marine life in the Gulf of Maine area (GoMA), facilitated by the GoMA Census of Marine Life program. It synthesizes current data on species diversity of zooplankton and pelagic nekton, including compilation of observed species and descriptions of seasonal, regional and cross-shelf diversity patterns. Zooplankton diversity in the GoMA is characterized by spatial differences in community composition among the neritic environment, the coastal shelf, and deep offshore waters. Copepod diversity increased with depth on the Scotian Shelf. On the coastal shelf of the western Gulf of Maine, the number of higher-level taxonomic groups declined with distance from shore, reflecting more nearshore meroplankton. Copepod diversity increased in late summer, and interdecadal diversity shifts were observed, including a period of higher diversity in the 1990s. Changes in species diversity were greatest on interannual scales, intermediate on seasonal scales, and smallest across regions, in contrast to abundance patterns, suggesting that zooplankton diversity may be a more sensitive indicator of ecosystem response to inter annual climate variation than zoo plankton abundance. Local factors such as bathymetry, proximity of the coast, and advection probably drive zooplankton and pelagic nekton diversity patterns in the GoMA, while ocean-basin scale diversity patterns probably contribute to the increase in diversity at the Scotian Shelf break, a zone of mixing between the cold-temperate community of the shelf and the warm-water community offshore. Pressing research needs include establishment of a comprehensive system for observing change in zooplankton and pelagic nekton diversity, enhanced observations of "underknown" but important functional components of the ecosystem, population and metapopulation studies, and development of analytical modeling tools to enhance understanding of diversity patterns and drivers. Ultimately, sustained observations and modeling analysis of biodiversity must be effectively communicated to managers and incorporated into ecosystem approaches for management of GoMA living marine resources.

Ecological forecasting under climate change: the case of Baltic cod

Good decision making for fisheries and marine ecosystems requires a capacity to anticipate the consequences of management under different scenarios of climate change. The necessary ecological forecasting calls for ecosystem-based models capable of integrating multiple drivers across trophic levels and properly including uncertainty. The methodology presented here assesses the combined impacts of climate and fishing on marine food-web dynamics and provides estimates of the confidence envelope of the forecasts. It is applied to cod (Gadus morhua) in the Baltic Sea, which is vulnerable to climate-related decline in salinity owing to both direct and indirect effects (i.e. through species interactions) on early-life survival. A stochastic food web-model driven by regional climate scenarios is used to produce quantitative forecasts of cod dynamics in the twenty-first century. The forecasts show how exploitation would have to be adjusted in order to achieve sustainable management under different climate scenarios.

Introgressive hybridization in North American hakes after secondary contact

High levels of bidirectional introgressive hybridization were found between the two Atlantic North American hakes Merluccius albidus and M. bilinearis in their overlapping distribution area between the 34 and the 42 degrees N parallels, employing mitochondrial and nuclear DNA markers. Absence of F(1) hybrids, and varied levels of bidirectional introgression, indicate long-time hybridization and backcrossing. Based on the evolutionary history of the genus Merluccius, originated in this area from the ancestor of the present M. bilinearis by the rise of the Panama Isthmus, secondary contact between the two species has probably been promoted by northwards displacement of M. albidus. Higher introgression rates in southern areas of M. albidus could be explained by restricted gene flow in that area which may allow long-term accumulation of introgressed genes.

Preventing the collapse of the Baltic cod stock through an ecosystem-based management approach

Worldwide a number of fish stocks have collapsed because of overfishing and climate-induced ecosystem changes. Developing ecosystem-based fisheries management (EBFM) to prevent these catastrophic events in the future requires ecological models incorporating both internal food-web dynamics and external drivers such as fishing and climate. Using a stochastic food-web model for a large marine ecosystem (i.e., the Baltic Sea) hosting a commercially important cod stock, we were able to reconstruct the history of the stock. Moreover we demonstrate that in hindsight the collapse could only have been avoidable by adapting fishing pressure to environmental conditions and food-web interactions. The modeling approach presented here represents a significant advance for EBFM, the application of which is important for sustainable resource management in the future.

High dispersal potential has maintained long-term population stability in the North Atlantic copepod Calanus finmarchicus

The cool-water copepod Calanus finmarchicus is a key species in North Atlantic marine ecosystems since it represents an important food resource for the developmental stages of several fish of major economic value. Over the last 40 years, however, data from the Continuous Plankton Recorder survey have highlighted a 70 per cent reduction in C. finmarchicus biomass, coupled with a gradual northward shift in the species's distribution, which have both been linked with climate change. To determine the potential for C. finmarchicus to track changes in habitat availability and maintain stable effective population sizes, we have assessed levels of gene flow and dispersal in current populations, as well as using a coalescent approach together with palaeodistribution modelling to elucidate the historical population demography of the species over previous changes in Earth's climate. Our findings indicate high levels of dispersal and a constant effective population size over the period 359,000-566,000 BP and suggest that C. finmarchicus possesses the capacity to track changes in available habitat, a feature that may be of crucial importance to the species's ability to cope with the current period of global climate change.

Regime shifts in marine ecosystems: detection, prediction and management

Regime shifts are abrupt changes between contrasting, persistent states of any complex system. The potential for their prediction in the ocean and possible management depends upon the characteristics of the regime shifts: their drivers (from anthropogenic to natural), scale (from the local to the basin) and potential for management action (from adaptation to mitigation). We present a conceptual framework that will enhance our ability to detect, predict and manage regime shifts in the ocean, illustrating our approach with three well-documented examples: the North Pacific, the North Sea and Caribbean coral reefs. We conclude that the ability to adapt to, or manage, regime shifts depends upon their uniqueness, our understanding of their causes and linkages among ecosystem components and our observational capabilities.

Spatial and temporal operation of the Scotia Sea ecosystem: a review of large-scale links in a krill centred food web

The Scotia Sea ecosystem is a major component of the circumpolar Southern Ocean system, where productivity and predator demand for prey are high. The eastward-flowing Antarctic Circumpolar Current (ACC) and waters from the Weddell-Scotia Confluence dominate the physics of the Scotia Sea, leading to a strong advective flow, intense eddy activity and mixing. There is also strong seasonality, manifest by the changing irradiance and sea ice cover, which leads to shorter summers in the south. Summer phytoplankton blooms, which at times can cover an area of more than 0.5 million km2, probably result from the mixing of micronutrients into surface waters through the flow of the ACC over the Scotia Arc. This production is consumed by a range of species including Antarctic krill, which are the major prey item of large seabird and marine mammal populations. The flow of the ACC is steered north by the Scotia Arc, pushing polar water to lower latitudes, carrying with it krill during spring and summer, which subsidize food webs around South Georgia and the northern Scotia Arc. There is also marked interannual variability in winter sea ice distribution and sea surface temperatures that is linked to southern hemisphere-scale climate processes such as the El Niño-Southern Oscillation. This variation affects regional primary and secondary production and influences biogeochemical cycles. It also affects krill population dynamics and dispersal, which in turn impacts higher trophic level predator foraging, breeding performance and population dynamics. The ecosystem has also been highly perturbed as a result of harvesting over the last two centuries and significant ecological changes have also occurred in response to rapid regional warming during the second half of the twentieth century. This combination of historical perturbation and rapid regional change highlights that the Scotia Sea ecosystem is likely to show significant change over the next two to three decades, which may result in major ecological shifts.

Scaling of Connectivity in Marine Populations

Defining the scale of connectivity, or exchange, among marine populations and determining the factors driving this exchange are pivotal to our understanding of the population dynamics, genetic structure, and biogeography of many coastal species. Using a high-resolution biophysical model for the Caribbean region, we report that typical larval dispersal distances of ecologically relevant magnitudes are on the scale of only 10 to 100 kilometers for a variety of reef fish species. We also show the importance of the early onset of active larval movement mediating the dispersal potential. In addition to self-recruitment, larval import from outside the local area is required to sustain most populations, although these population subsidies are very limited in particular systems. The results reveal distinct regions of population isolation based on larval dispersal that also correspond to genetic and morphological clines observed across a range of marine organisms.