Competition Drives Clumpy Species Coexistence in Estuarine Phytoplankton

Understanding the mechanisms that maintain biodiversity is a fundamental problem in ecology. Competition is thought to reduce diversity, but hundreds of microbial aquatic primary producers species coexist and compete for a few essential resources (e.g., nutrients and light). Here, we show that resource competition is a plausible mechanism for explaining clumpy distribution on individual species volume (a proxy for the niche) of estuarine phytoplankton communities ranging from North America to South America and Europe, supporting the Emergent Neutrality hypothesis. Furthermore, such a clumpy distribution was also observed throughout the Holocene in diatoms from a sediment core. A Lotka-Volterra competition model predicted position in the niche axis and functional affiliation of dominant species within and among clumps. Results support the coexistence of functionally equivalent species in ecosystems and indicate that resource competition may be a key process to shape the size structure of estuarine phytoplankton, which in turn drives ecosystem functioning.

Phenological trends and trophic mismatch across multiple levels of a North Sea pelagic food web

Differential phenological responses to climate among species are predicted to disrupt trophic interactions, but datasets to evaluate this are scarce. We compared phenological trends for species from 4 levels of a North Sea food web over 24 yr when sea surface temperature (SST) increased significantly. We found little consistency in phenological trends between adjacent trophic levels, no significant relationships with SST, and no significant pairwise correlations between predator and prey phenologies, suggesting that trophic mismatching is occurring. Finer resolution data on timing of peak energy demand (mid-chick-rearing) for 5 seabird species at a major North Sea colony were compared to modelled daily changes in length of 0-group (young of the year) lesser sandeels Ammodytes marinus. The date at which sandeels reached a given threshold length became significantly later during the study. Although the phenology of all the species except shags also became later, these changes were insufficient to keep pace with sandeel length, and thus mean length (and energy value) of 0-group sandeels at mid-chick-rearing showed net declines. The magnitude of declines in energy value varied among the seabirds, being more marked in species showing no phenological response (shag, 4.80 kJ) and in later breeding species feeding on larger sandeels (kittiwake, 2.46 kJ) where, due to the relationship between sandeel length and energy value being non-linear, small reductions in length result in relatively large reductions in energy. However, despite the decline in energy value of 0-group sandeels during chick-rearing, there was no evidence of any adverse effect on breeding success for any of the seabird species. Trophic mismatch appears to be prevalent within the North Sea pelagic food web, suggesting that ecosystem functioning may be disrupted.

Transregional linkages in the North-Eastern Atlantic - An ‘end-to-end ’ analysis of pelagic ecosystems

This review examines interregional linkages and gives an overview perspective on marine ecosystem functioning in the north-eastern Atlantic. It is based on three of the 'systems' considered by the European Network of Excellence for Ocean Ecosystems Analysis (EUR-OC EANS was established in 2004 under the European Framework VI funding programme to promote integration of marine ecological research within Europe), the Arctic and Nordic Seas, North Atlantic shelf seas and North Atlantic. The three systems share common open boundaries and the transport of water, heat, nutrients and particulates across these boundaries modifies local processes. Consistent with the EUR-OC EANS concept of 'end-to-end' analyses of marine food webs, the review takes an integrated approach linking ocean physics, lower trophic levels and working up the food web to top predators such as marine mammals. We begin with an overview of the regions focusing on the major physical patterns and their implications for the microbial community, phytoplankton, zooplankton, fish and top predators. Human-induced links between the regional systems are then considered and finally possible changes in the regional linkages over the next century are discussed. Because of the scale of potential impacts of climate change, this issue is considered in a separate section. The review demonstrates that the functioning of the ecosystems in each of the regions cannot be considered in isolation and the role of the atmosphere and ocean currents in linking the North Atlantic Ocean, North Atlantic shelf seas and the Arctic and Nordic Seas must be taken into account. Studying the North Atlantic and associated shelf seas as an integrated 'basin-scale' system will be a key challenge for the early twenty-first century. This requires a multinational approach that should lead to improved ecosystem-based approaches to conservation of natural resources, the maintenance of biodiversity, and a better understanding of the key role of the north-eastern Atlantic in the global carbon cycle.

Mesoscale fronts as foraging habitats: composite front mapping reveals oceanographic drivers of habitat use for a pelagic seabird

The oceanographic drivers of marine vertebrate habitat use are poorly understood yet fundamental to our knowledge of marine ecosystem functioning. Here, we use composite front mapping and high-resolution GPS tracking to determine the significance of mesoscale oceanographic fronts as physical drivers of foraging habitat selection in northern gannets Morus bassanus. We tracked 66 breeding gannets from a Celtic Sea colony over 2 years and used residence time to identify area-restricted search (ARS) behaviour. Composite front maps identified thermal and chlorophyll-a mesoscale fronts at two different temporal scales—(i) contemporaneous fronts and (ii) seasonally persistent frontal zones. Using generalized additive models (GAMs), with generalized estimating equations (GEE-GAMs) to account for serial autocorrelation in tracking data, we found that gannets do not adjust their behaviour in response to contemporaneous fronts. However, ARS was more likely to occur within spatially predictable, seasonally persistent frontal zones (GAMs). Our results provide proof of concept that composite front mapping is a useful tool for studying the influence of oceanographic features on animal movements. Moreover, we highlight that frontal persistence is a crucial element of the formation of pelagic foraging hotspots for mobile marine vertebrates.

Assimilation of remotely-sensed optical properties to improve marine biogeochemistry modelling

In this paper we evaluate whether the assimilation of remotely-sensed optical data into a marine ecosystem model improves the simulation of biogeochemistry in a shelf sea. A localized Ensemble Kalman filter was used to assimilate weekly diffuse light attenuation coefficient data, Kd(443) from SeaWiFs, into an ecosystem model of the western English Channel. The spatial distributions of (unassimilated) surface chlorophyll from satellite, and a multivariate time series of eighteen biogeochemical and optical variables measured in situ at one long-term monitoring site were used to evaluate the system performance for the year 2006. Assimilation reduced the root mean square error and improved the correlation with the assimilated Kd(443) observations, for both the analysis and, to a lesser extent, the forecast estimates, when compared to the reference model simulation. Improvements in the simulation of (unassimilated) ocean colour chlorophyll were less evident, and in some parts of the Channel the simulation of this data deteriorated. The estimation errors for the (unassimilated) in situ data were reduced for most variables with some exceptions, e.g. dissolved nitrogen. Importantly, the assimilation adjusted the balance of ecosystem processes by shifting the simulated food web towards the microbial loop, thus improving the estimation of some properties, e.g. total particulate carbon. Assimilation of Kd(443) outperformed a comparative chlorophyll assimilation experiment, in both the estimation of ocean colour data and in the simulation of independent in situ data. These results are related to relatively low error in Kd(443) data, and because it is a bulk optical property of marine ecosystems. Assimilation of remotely-sensed optical properties is a promising approach to improve the simulation of biogeochemical and optical variables that are relevant for ecosystem functioning and climate change studies.

Can benthic community structure be used to predict the process of bioturbation in real ecosystems

Disentangling the roles of environmental change and natural environmental variability on biologically mediated ecosystem processes is paramount to predict future marine ecosystem functioning. Bioturbation, the biogenic mixing of sediments, has a regulating role in marine biogeochemical processes. However, our understanding of bioturbation as a community level process and of its environmental drivers is still limited by loose use of terminology, and a lack of consensus about what bioturbation is. To help resolve these challenges, this empirical study investigated the links between four different attributes of bioturbation (bioturbation depth, activity and distance, and biodiffusive transport); the ability of an index of bioturbation (BPc) to predict each of them; and their relation to seasonality, in a shallow coastal system – the Western Channel Observatory, UK. Bioturbation distance depended on changes in benthic community structure, while the other three attributes were more directly influenced by seasonality in food availability. In parallel, BPc successfully predicted bioturbation distance but not the other attributes of bioturbation. This study therefore highlights that community bioturbation results from this combination of processes responding to environmental variability at different time-scales. However, community level measurements of bioturbation across environmental variability are still scarce, and BPc is calculated using commonly available data on benthic community structure and the functional classification of invertebrates. Therefore, BPc could be used to support the growth of landscape scale bioturbation research, but future uses of the index need to consider which bioturbation attributes the index actually predicts. As BPc predicts bioturbation distance, estimated here using a random-walk model applicable to community settings, studies using either of the metrics should be directly comparable and contribute to a more integrated future for bioturbation research.

Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages

Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. Methodology/Principle Findings Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups. Conclusions Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly attractive in future if sequence reference libraries of accurately identified individuals are better populated.

Impacts of ocean acidification in a warming Mediterranean Sea: An overview

Mediterranean Sea fisheries supply significant local and international markets, based largely on small pelagic fish, artisanal fisheries and aquaculture of finfish (mainly seabass and seabream) and shellfish (mussels and oysters). Fisheries and aquaculture contribute to the economy of countries bordering this sea and provide food and employment to coastal communities employing ca 600,000 people. Increasing temperatures and heat wave frequency are causing stress and mortality in marine organisms and ocean acidification is expected to worsen these effects, especially for bivalves and coralligenous systems. Recruitment and seed production present possible bottlenecks for shellfish aquaculture in the future since early life stages are vulnerable to acidification and warming. Although adult finfish seem able to withstand the projected increases in seawater CO2, degradation of seabed habitats and increases in harmful blooms of algae and jellyfish might adversely affect fish stocks. Ocean acidification should therefore be factored into fisheries and aquaculture management plans. Rising CO2 levels are expected to reduce coastal biodiversity, altering ecosystem functioning and possibly impacting tourism being the Mediterranean the world’s most visited region. We recommend that ocean acidification is monitored in key areas of the Mediterranean Sea, with regular assessments of the likely socio-economic impacts to build adaptive strategies for the Mediterranean countries concerned.

Invasion by the amphipod Gammarus pulex alters community composition of native freshwater macroinvertebrates

Assessing the effects of invading species on native community structure is often confounded by environmental factors and weakened by lack of replicated, long-term pre- and post-invasion monitoring. Here, we uncouple the community effects of a freshwater amphipod invader from environmental differences. In Irish rivers, the introduced Gammarus pulex replaces the native Gammarus duebeni celticus. However, the River Lissan in Northern Ireland is dissected by a weir that has slowed the upstream invasion by G. pulex. This allowed us in 2000 to sample three contiguous 150-m reaches that were (1) G. pulex dominated; (2) mixed Gammarus spp.; and (3) G. duebeni celticus only. In 2003, we resampled these reaches and one additional of mixed Gammarus species and one with only G. duebeni celticus further upstream. In temperature, conductivity, and pH, there were statistically significant but no biologically relevant differences among the five reaches of 2003, and between the three reaches surveyed in both years. Although there was evidence of recovery in macroinvertebrate diversity and richness in invaded reaches between years, continued upstream invasion was associated with sustained reductions in these community metrics as compared to un-invaded sites. Community ordination indicated (1) different associations of community composition attributed to the distribution, abundance, and biomass of the invader; and (2) increasing similarity of invaded communities over time. The impact mechanisms of G. pulex on macroinvertebrate community composition may include predation and competition. The consequences of the observed community changes for ecosystem functioning require further investigation.

Simulated predator extinctions: Predator identity affects survival and recruitment of oysters

The rate of species loss is increasing at a global scale, and human-induced extinctions are biased toward predator species. We examined the effects of predator extinctions on a foundation species, the eastern oyster (Crassostrea virginica). We performed a factorial experiment manipulating the presence and abundance of three of the most common predatory crabs, the blue crab (Callinectes sapidus), stone crab (Menippe mercenaria), and mud crab (Panopeus herbstii) in estuaries in the eastern United States. We tested the effects of species richness and identity of predators on juvenile oyster survival, oyster recruitment, and organic matter content of sediment. We also manipulated the density of each of the predators and controlled for the loss of biomass of species by maintaining a constant mass of predators in one set of treatments and simultaneously using an additive design. This design allowed us to test the density dependence of our results and test for functional compensation by other species. The identity of predator species, but not richness, affected oyster populations. The loss of blue crabs, alone or in combination with either of the other species, affected the survival rate of juvenile oysters. Blue crabs and stone crabs both affected oyster recruitment and sediment organic matter negatively. Mud crabs at higher than ambient densities, however, could fulfill some of the functions of blue and stone crabs, suggesting a level of ecological redundancy. Importantly, the strong effects of blue crabs in all processes measured no longer occurred when individuals were present at higher-than-ambient densities. Their role as dominant predator is, therefore, dependent on their density within the system and the density of other species within their guild (e.g., mud crabs). Our findings support the hypothesis that the effects of species loss at higher trophic levels are determined by predator identity and are subject to complex intraguild interactions that are largely density dependent. Understanding the role of biodiversity in ecosystem functioning or addressing practical concerns, such as loss of predators owing to overharvesting, remains complicated because accurate predictions require detailed knowledge of the system and should be drawn from sound experimental evidence, not based on observations or generalized models.

Soil resource supply influences faunal size-specific distributions in natural food webs

The large range of body-mass values of soil organisms provides a tool to assess the ecological organization of soil communities. The goal of this paper is to identify graphical and quantitative indicators of soil community composition and ecosystem functioning, and to illustrate their application to real soil food webs. The relationships between log-transformed mass and abundance of soil organisms in 20 Dutch meadows and heathlands were investigated. Using principles of allometry, maximal use can be made of ecological theory to build and explain food webs. The aggregate contribution of small invertebrates such as nematodes to the entire community is high under low soil phosphorus content and causes shifts in the mass-abundance relationships and in the trophic structures. We show for the first time that the average of the trophic link lengths is a reliable predictor for assessing soil fertility responses. Ordered trophic link pairs suggest a self-organizing structure of food webs according to resource availability and can predict environmental shifts in ecologically meaningful ways.

Loss of functionally unique species may gradually undermine ecosystems

Functionally unique species contribute to the functional diversity of natural systems, often enhancing ecosystem functioning. An abundance of weakly interacting species increases stability in natural systems, suggesting that loss of weakly linked species may reduce stability. Any link between the functional uniqueness of a species and the strength of its interactions in a food web could therefore have simultaneous effects on ecosystem functioning and stability. Here, we analyse patterns in 213 real food webs and show that highly unique species consistently tend to have the weakest mean interaction strength per unit biomass in the system. This relationship is not a simple consequence of the interdependence of both measures on body size and appears to be driven by the empirical pattern of size structuring in aquatic systems and the trophic position of each species in the web. Food web resolution also has an important effect, with aggregation of species into higher taxonomic groups producing a much weaker relationship. Food webs with fewer unique and less weakly interacting species also show significantly greater variability in their levels of primary production. Thus, the loss of highly unique, weakly interacting species may eventually lead to dramatic state changes and unpredictable levels of ecosystem functioning.

Body mass-abundance relationships are robust to cascading effects in marine food webs

Body mass has been shown to scale negatively with abundance in a wide range of habitats and ecosystems. It is believed that this relationship has important consequences for the distribution and maintenance of energy in natural communities. Some studies have shown that the relationship between body mass and abundance may be robust to major food web perturbations, fuelling the belief that natural processes may preserve the slope of this relationship and the associated cycling of energy and nutrients. Here, we use data from a long-term experimental food web manipulation to examine this issue in a semi-natural environment. Similar communities were developed in large experimental mesocosms over a six month period. Some of the mesocosms were then subjected to species removals, based on the mean strength of their trophic interactions in the communities. In treatments where the strongest interactors were removed, a community-level trophic cascade occurred. The biomass density of invertebrates increased dramatically in these communities, which led to a suppression of primary production. In spite of these widespread changes in ecosystem functioning, the slope of the relationship between body mass and abundance remained unchanged. This was the case whether average species body mass and abundance or individual organism size spectra were considered. An examination of changes in species composition before and after the experimental manipulations revealed an important mechanism for maintaining the body mass-abundance relationship. The manipulated communities all had a higher species turnover than the intact communities, with the highest turnover in communities that experienced cascading effects. As some species increased in body mass and abundance, new species filled the available size-abundance niches that were created. This maintained the overall body mass-abundance relationship and provided a stabilising structure to these experimental communities.

Global change alters the stability of food webs

Recent research has generally shown that a small change in the number of species in a food web can have consequences both for community structure and ecosystem processes. However 'change' is not limited to just the number of species in a community, but might include an alteration to such properties as precipitation, nutrient cycling and temperature. How such changes might affect species interactions is important, not just through the presence or absence of interactions, but also because the patterning of interaction strengths among species is intimately associated with community stability. Interaction strengths encompass such properties as feeding rates and assimilation efficiencies, and encapsulate functionally important information with regard to ecosystem processes. Interaction strengths represent the pathways and transfer of energy through an ecosystem. We review the best empirical data available detailing the frequency distribution of interaction strengths in communities. We present the underlying (but consistent) pattern of species interactions and discuss the implications of this patterning. We then examine how such a basic pattern might be affected given various scenarios of 'change' and discuss the consequences for community stability and ecosystem functioning.