Ecological-network models link diversity, structure and function in the plankton food-web

GIS-based integration of marine data for assessment and management of a highly anthropized coastal area

Monitoring coastal marine environments by evaluating and comparing their chemical, physical, biological, and anthropogenic components is essential for ecological assessment and socio-economic development. In this study, we conducted an integrated multivariate analysis to assess the descriptors of the Marine Strategy Framework Directive at a regional scale in the Tyrrhenian Sea (Italy), with a specific focus on the densely populated coastal zone of the Campania region. Physical, chemical, and biological data were collected and analyzed in 22 sampling sites during three oceanographic surveys in the Gulf of Gaeta (GoG), Naples (GoN), and Salerno (GoS) in autumn 2020. Our results indicated that these three gulfs were distinct overall, with GoN being more divergent and heterogeneous than GoG and GoS. The marine area studied in the GoN had more favorable hydrographic and trophic conditions and food web characteristics, except for the mesozooplankton biomass, and was closer to socio-economic factors compared to the GoS and GoG. Our analysis helped us find the key ecological features that define different sub-regions and connect them to social and economic factors, including human activities. We highlighted the relevance of primary and secondary variables in terms of the comprehensive ecological assessment of a marine area and its impact on specific socio-economic activities. These findings support the need to describe and integrate multiple descriptors at the spatial scale.

Calibration of an ecological model of a eutrophic coastal lagoon and assessment of the effect of management strategies on dissolved oxygen

Eutrophication is one of the biggest ecological concerns for water bodies worldwide. Shallow coastal areas under high anthropogenic pressure are particularly vulnerable to water quality deterioration. This work presents the development of a two-dimensional ecological model of the processes in the Orbetello Lagoon (central Italy), a highly eutrophic coastal basin subject to several human-induced and natural stressors. The ecological model, coupled with a hydrodynamic model, simulates the nutrient cycle in the water column and in the sediment, the growth and decay of rooted vegetation, macroalgae, phytoplankton, and zooplankton, as well as the oxygen cycle. Once calibrated and validated with field measurements, the model has been used as a decision-support tool for lagoon management, providing qualitative insights into the impact of various stress factors and intervention actions. This study allowed the quantification of the effects on dissolved oxygen of different interventions (pumping systems, removal of obstructions at inlets, channels dredging), proving that the minimum dissolved oxygen concentration in the lagoon in the summer months is relevantly affected by the human intervention on the system.

The complex structure of aquatic food webs emerges from a few assembly rules

Food-web theory assumes that larger-bodied predators generally select larger prey. This allometric rule fails to explain a considerable fraction of trophic links in aquatic food webs. Here we show that food-web constraints result in guilds of predators that vary in size but have specialized on prey of the same size, and that the distribution of such specialist guilds explains about one-half of the food-web structure. We classified 517 pelagic species into five predator functional groups. Most of these follow three prey selection strategies: a guild following the allometric rule whereby larger predators eat larger prey and two guilds of specialists that prefer either smaller or larger prey than predicted by the allometric rule. Such coexistence of non-specialist and specialist guilds independent from taxa or body size points towards structural principles behind ecological complexity. We show that the pattern describes >90% of observed linkages in 218 food webs in 18 aquatic ecosystems worldwide. The pattern can be linked to eco-evolutionary constraints to prey exploitation and provides a blueprint for more effective food-web models.

Stay Connected to Be Diverse!

Plankton biodiversity is crucial for the functioning of aquatic ecosystems, influencing nutrient cycling, food web dynamics, and carbon storage. Global change and habitat destruction disrupt these ecosystems, reducing species diversity and ecosystem resilience. Connectivity between aquatic habitats supports biodiversity by enabling species migration, genetic diversity, and recovery from disturbances. However, research on how connectivity loss impacts plankton remains limited. A study by Szabó et al. used controlled experiments to show that habitat fragmentation significantly influences phytoplankton diversity. These findings highlight the need to conserve both biodiversity and habitat connectivity to sustain freshwater ecosystems and combat global environmental challenges.

Microplastics alter the functioning of marine microbial ecosystems

Microplastics pervade ocean ecosystems. Despite their effects on individuals or populations are well documented, the consequences of microplastics on ecosystem functioning are still largely unknown. Here, we show how microplastics alter the structure and functioning of pelagic microbial ecosystems. Using experimental pelagic mesocosms, we found that microplastics indirectly affect marine productivity by changing the bacterial and phytoplankton assemblages. Specifically, the addition of microplastics increased phytoplankton biomass and shifted bacterial assemblages' composition. Such changes altered the interactions between heterotrophic and autotrophic microbes and the cycling of ammonia in the water column, which ultimately benefited photosynthetic efficiency. The effects of microplastics on marine productivity were consistent for different microplastic types. This study demonstrates that microplastics affect bacteria and phytoplankton communities and influence marine productivity, which ultimately alters the functioning of the whole ocean ecosystem.

Spatial food webs in the Barents Sea: atlantification and the reorganization of the trophic structure

Climate change affects ecosystems at several levels: by altering the spatial distribution of individual species, by locally rewiring interspecific interactions, and by reorganizing trophic networks at larger scales. The dynamics of marine food webs are becoming more and more sensitive to spatial processes and connections in the seascape. As a case study, we study the atlantification of the Barents Sea: we compare spatio-temporal subsystems at three levels: the identity of key organisms, critically important interactions and the entire food web. Network analysis offers quantitative measurements, including centrality indices, trophic similarity indices, a topological measure of interaction asymmetry and network-level measures. We found that atlantification alters the identity of key species (boreal demersals becoming hubs), results in strongly asymmetric interactions (dominated by haddock), changes the dominant regulation regime (from bottom-up to wasp-waist control) and makes the food web less modular. Since the results of food web analysis may be quite sensitive to network construction, the aggregation of food web data was explicitly studied to increase the robustness of food web analysis. We found that an alternative, mathematical aggregation algorithm better preserves some network properties (e.g. density) of the original, unaggregated network than the biologically inspired aggregation into functional groups. This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

Importance of integrating mixoplankton into marine ecosystem policy and management-Examples from the Marine Strategy Framework Directive

Marine plankton capable of photosynthesis and predation ("mixoplankton") comprise up to 50% of protist plankton and include many harmful species. However, marine environmental management policies, including the European Union Marine Strategy Framework Directive (MSFD) and the USEPA, assume a strict dichotomy between autotrophic phytoplankton and heterotrophic zooplankton. Mixoplankton often differ significantly from these two categories in their response to environmental pressures and affect the marine environment in ways we are only beginning to understand. While the management policies may conceptually provide scope for incorporating mixoplankton, such action is rarely implemented. We suggest that the effectiveness of monitoring and management programs could benefit from explicit implementations regarding the ecological roles and impact of mixoplankton. Taking the MSFD as an example of marine management guidelines, we propose appropriate methods to explicitly include mixoplankton in monitoring and marine management. Integr Environ Assess Manag 2024;20:1366-1383. © 2024 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Population bottlenecks and sexual recombination shape diatom microevolution

Diatoms are single-celled organisms that contribute approximately 20% of the global primary production and play a crucial role in biogeochemical cycles and trophic chains. Despite their ecological importance, our knowledge of microevolution is limited. We developed a model using the SLiM evolutionary framework to address this knowledge gap. As a reference, we used the diatom Pseudo-nitzschia multistriata, which has been extensively studied in the Gulf of Naples. Our model recapitulates what we observe in natural populations, with microevolutionary processes that occur annually during a three-stage bloom phase. Interestingly, we found that non-bloom phases allow the population to maintain sex-generated diversity produced during blooms. This finding suggests that non-bloom phases are critical to counteract bloom-related pressures and mitigate genetic divergence at the species level. Moreover, our model showed that despite the consistent genetic differentiation during bloom phases, the population tends to return to pre-bloom states. While our model is limited to neutral dynamics, our study provides valuable insights into diatoms' microevolution, paving the way to explore the ecological implications of the life history dynamics of these organisms.

The response of zooplankton network indicators to winter water warming using shallow artificial reservoirs as model case study

To predict the most likely scenarios, the consequences of the rise in water surface temperature have been studied using various methods. We tested the hypothesis that winter water warming significantly alters the importance and nature of the relationships in zooplankton communities in shallow reservoirs. These relationships were investigated using network graph analysis for three thermal variants: warm winters (WW), moderate winters (MW) and cold winters (CW). The CW network was the most cohesive and was controlled by eutrophic Rotifera and Copepoda, with a corresponding number of positive and negative interspecific relationships. An increase in water temperature in winter led to a decrease in the centrality of MW and WW networks, and an increase in the importance of species that communicated with the highest number of species in the subnetworks. The WW network was the least cohesive, controlled by psammophilous and phytophilous rotifers, and littoral cladocerans. Adult copepods were not identified in the network and the importance of antagonistic relationships decreased, indicating that the WW network structure was weak and unstable. This study can serve as a model for generalisations of zooplankton community response to the disappearance of long winter periods of low temperatures, as predicted in global climate change projections.

Planktonic ecological networks support quantification of changes in ecosystem health and functioning

Plankton communities are the foundation of marine food webs and have a large effect on the dynamics of entire ecosystems. Changes in physicochemical factors strongly influence planktonic organisms and their turnover rates, making their communities useful for monitoring ecosystem health. We studied and compared the planktonic food webs of Palude della Rosa (Venice Lagoon, Italy) in 2005 and 2007. The food webs were developed using a novel approach based on the Monte Carlo random sampling of parameters within specific and realistic ranges to derive 1000 food webs for July of each year. The consumption flows involving Strombididae, Evadne spp. and Podon spp. were identified as the most important in splitting food webs of the July of the two years. Although functional nodes (FNs) differed both in presence and abundance in July of the two years, the whole system indicators showed very similar results. Sediment resuspension acted as a source of stress for the Venice Lagoon, being the most used resource by consumers while inhibiting primary producers by increasing water turbidity. Primary production in the water column was mainly generated by benthic FNs. Although the system was near an equilibrium point, it tended to increase its resilience at the expense of efficiency due to stress. This study highlights the role of plankton communities, which can serve to assess ecosystem health.

Development of a Dynamic Network Model to Identify Temporal Patterns of Structural Malformations in Zebrafish Embryos Exposed to a Model Toxicant, Tris(4-chlorophenyl)methanol

Embryogenesis is a well-coordinated process relying on precise cues and environmental signals that direct spatiotemporal embryonic patterning. Quite often, when one error in this process occurs, others tend to co-occur. We posit that investigating the co-occurrence of these abnormalities over time would yield additional information about the mode of toxicity for chemicals. Here, we use the environmental contaminant tris(4-chlorophenyl)methanol (TCPMOH) as a model toxicant to assess the relationship between exposures and co-occurrence of developmental abnormalities in zebrafish embryos. We propose a dynamic network modeling approach to study the co-occurrence of abnormalities, including pericardial edema, yolk sac edema, cranial malformation, spinal deformity, delayed/failed swim bladder inflation, and mortality induced by TCPMOH exposure. TCPMOH-exposed samples revealed increased abnormality co-occurrence when compared to controls. The abnormalities were represented as nodes in the dynamic network model. Abnormalities with high co-occurrence over time were identified using network centrality scores. We found that the temporal patterns of abnormality co-occurrence varied between exposure groups. In particular, the high TCPMOH exposure group experienced abnormality co-occurrence earlier than the low exposure group. The network model also revealed that pericardial and yolk sac edema are the most common critical nodes among all TCPMOH exposure levels, preceding further abnormalities. Overall, this study introduces a dynamic network model as a tool for assessing developmental toxicology, integrating structural and temporal features with a concentration response.

Comparison of three modelling frameworks for aquatic ecosystems: practical aspects and applicability

Freshwater ecosystems are under multiple stressors and it is crucial to find methods to better describe, manage, and sustain aquatic ecosystems. Ecosystem modelling has become an important tool in integrating trophic relationships into food webs, assessing important nodes using network analysis, and making predictions via simulations. Fortunately, several modelling techniques exist, but the question is which approach is relevant and applicable when? In this study, we compare three modelling frameworks (Ecopath, Loop Analysis in R, STELLA software) using a case study of a small aquatic network (8 nodes). The choice of framework depends on the research question and data availability. We approach this topic from a methodological aspect by describing the data requirements and by comparing the applicability and limitations of each modelling approach. Each modelling framework has its specific focus, but some functionalities and outcomes can be compared. The predictions of Loop Analysis as compared to Ecopath’s Mixed Trophic Impact plot are in good agreement at the top and bottom trophic levels, but the middle trophic levels are less similar. This suggests that further comparisons are needed of networks of varying resolution and size. Generally, when data are limiting, Loop Analysis can provide qualitative predictions, while the other two methods provide quantitative results, yet rely on more data.

Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem

Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove.

Plankton under Pressure: How Water Conditions Alter the Phytoplankton–Zooplankton Link in Coastal Lagoons

Transitional waters (TWs), such as coastal lagoons, are bodies of surface water at the transition between saline and freshwater domains. These environments play a vital role in guaranteeing ecosystem services, including provision of food, protection against meteorological events, as anthropogenic carbon sinks, and in filtering of pollutants. Due to the escalating overpopulation characterising coastlines worldwide, transitional systems are over-exploited, degraded, and reduced in their macroscopic features. However, information on the impact of anthropogenic pressures on planktonic organisms in these systems is still scanty and fragmented. Herein, we summarise the literature, with a special focus on coastal lagoons undergoing anthropogenic pressure. Specifically, we report on the implications of human impacts on the ecological state of plankton, i.e., a fundamental ecological component of aquatic ecosystems. Literature information indicates that human forces may alter ecosystem structures and functions in coastal lagoons, as in other TWs such as estuaries, hampering the phytoplankton–zooplankton link, i.e., the main trophic process occurring in those communities, and which sustains aquatic productivity. Changes in the dominance and lifestyle of key planktonic players, plus the invasion of ‘alien’ species, and consequent regime shifts, are among the most common outcomes of human disturbance.

Zooplankton network conditioned by turbidity gradient in small anthropogenic reservoirs

Water turbidity can significantly influence interspecific interactions in aquatic ecosystems. We tested the hypothesis that the turbidity gradient significantly differentiates the dynamics, significance and type of relationships in the structure of zooplankton communities colonizing mine pit reservoirs. The interactions between zooplankton species were evaluated by network graph analysis for three water turbidity classes: high turbidity (HT), moderate turbidity (MT) and low turbidity (LT). The HT network was most cohesive, and it was controlled by taxa grazing on various food sources within one ecological niche (Polyarthra longiremis, Brachionus angularis, Cyclops vicinus, Codonella cratera) and the positive and negative relationships between them were balanced. The MT biocenotic network was composed of three sub-networks connected by nodes with high communication attributes (Polyarthra vulgaris, Bosmina longirostris, C. vicinus), and antagonistic interactions (predation and competition) were less important. The LT network was most heterogeneous, and Daphnia cuculllata exerted the strongest influence on the network's structure by forming numerous positive (coexistence with predators) and negative (interference competition with microphagous rotifers) interspecific relationships. The study provides new information about the ecology of aquatic ecosystems, that are disturbed by changes in water turbidity.

Niche partitioning of two piscivorous fish species in a river in the western Brazilian Amazon

ABSTRACT We analyzed the seasonal variation in the diet, trophic niche breadth (Levins index), the partitioning of food resources (Pianka’s symmetric index) and trophic level (weighed average of trophic level of each prey determined in FishBase and SeaLifeBase platform) of Plagioscion squamosissimus (Heckel, 1840) and Hydrolycus scomberoides (Cuvier, 1819) in the Machado River, Rondônia, Brazil. Fish samplings were conducted bimonthly from June 2013 to May 2015 in five sites, using eight sets of gillnets. The occurrence frequency and volumetric frequency were used to quantify the food items. We analyzed the stomach contents of 283 individuals, 134 of H. scomberoides and 149 of P. squamosissimus. Fish were the most consumed food item by both piscivorous species. However, H. scomberoides mostly ingested pelagic fish (e.g. Characiformes fishes and Prochilodus nigricas Spix & Agassiz, 1829), while P. squamosissimus mostly consumed benthic fish [e.g. Pimelodus blochii Valenciennes, 1840 and Tenellus trimaculatus (Boulenger, 1898)]. Hydrolycus scomberoides presented the trophic level 3.55 for both periods analyzed, while P. squamosissimus 4.01 in the flood period and 3.82 in the drought period. Seasonal variations in the diet of H. scomberoides and P. squamosissimus were observed (PERMANOVA). Specifically, P. squamosissimus consumed mainly “Siluriformes” fishes and P. blochii in the drought period. The trophic niche breadth of P. squamosissimus was greater than that of H. scomberoides in the flood period. The species P. squamosissimus and H. scomberoides had low (0.35) food niche overlap in both seasons analysed. The data indicated that P. squamosissimus has a generalist feeding habit, while H. scomberoides is specialized in prey selection. The overlap of food niche between the species in both periods of the hydrological cycle was low, indicating that niche partitioning was probably the main mechanism of coexistence of these species, with little relationship with variations of the hydrological cycle.

Seawater intrusion: an appraisal of taxa at most risk and safe salinity levels

Seawater intrusion into low-lying coastal ecosystems carries environmental risks. Salinity levels at these coastal ecosystems may vary substantially, causing ecological effects from mortality to several sublethal endpoints, such as depression of rates of feeding, somatic growth, or reproduction. This review attempts to establish safe salinity levels for both terrestrial and freshwater temperate ecosystems by integrating data available in the literature. We have four specific objectives: (i) to identify the most sensitive ecological taxa to seawater intrusion; (ii) to establish maximum acceptable concentrations-environmental quality standards (MAC-EQSs) for sea water (SW) from species sensitivity distributions (SSDs); (iii) to compile from the literature examples of saline intrusion [to be used as predicted environmental concentrations (PECs)] and to compute risk quotients for the temperate zone; and (iv) to assess whether sodium chloride (NaCl) is an appropriate surrogate for SW in ecological risk assessments by comparing SSD-derived values for NaCl and SW and by comparing these with field data. Zooplankton, early life stages of amphibians and freshwater mussels were the most sensitive ecological receptors for the freshwater compartment, while soil invertebrates were the most sensitive ecological receptors for the terrestrial compartment. Hazard concentration 5% (HC₅ ) values, defined as the concentration (herein measured as conductivity) that affects (causes lethal or sublethal effects) 5% of the species in a distribution, computed for SW were over 22 and 40 times lower than the conductivity of natural SW (≈ 52 mS/cm) for the freshwater and soil compartment, respectively. This sensitivity of both compartments means that small increments in salinity levels or small SW intrusions might represent severe risks for low-lying coastal ecosystems. Furthermore, the proximity between HC₅ values for the soil and freshwater compartments suggests that salinized soils might represent an additional risk for nearby freshwater systems. This sensitivity was corroborated by the derivation of risk quotients using real saline intrusion examples (PECs) collected from the literature: risk was >1 in 34 out of 37 examples. By contrast, comparisons of HC₅ values obtained from SSDs in field surveys or mesocosm studies suggest that natural communities are more resilient to salinization than expected. Finally, NaCl was found to be slightly more toxic than SW, at both lethal and sublethal levels, and, thus, is suggested to be an acceptable surrogate for use in risk assessment.

Linking Microbial Functioning and Trophic Pathways to Ecological Status in a Coastal Mediterranean Ecosystem

Coastal marine ecosystems host complex microbial communities whose composition and metabolism are influenced by continental inputs and mesoscale properties of seawater masses. The identifying traits of the phytoplankton and bacteria such as biomass, size, shape and their metabolism related to organic matter production and degradation, recognized as indicators of the functioning of an ecosystem, were observed in the Gulf of Manfredonia (South Adriatic Sea, Italy) in late spring. This Gulf area is characterized by terrestrial inputs and mesoscale circulation influence such as coastal waters flowing southward from the North Adriatic and offshore waters interested by the Ionian Sea. Water samples were grouped in clusters (Coastal, Intermediate, Offshore and Deep Systems) according to the water column properties. Phytoplankton community biomass and composition, autotrophic and total prokaryotic abundances and microbial metabolism such as enzyme activity rates and prokaryotic heterotrophic production were analyzed to elucidate the trophic pathways with the objective to infer on the ecosystem status. As expected, size-fractionated phytoplankton biomass and production showed greater concentration in coastal waters with prevalence of the largest fractions (micro- and nano-) supported by the diatoms. Conversely, lower biomass and production were measured in all off-shore waters, mainly sustained by smallest fractions (nano-sized phytoflagellates and picophytoplankton). Total and autotrophic prokaryotic abundance decreased from coastal to offshore stations, inversely with respect to cell volume. Prokaryotic heterotrophic production was just below 50% compared to that of phytoplankton in all waters, evidencing an active biomass synthesis. High alkaline phosphatase and leucine aminopeptidase in coastal and offshore waters suggested the quick regeneration of Phosphorus and protein decomposition, respectively. Different levels of phytoplankton-bacteria association might provide a tool to define the ecological status of the studied system in the observed period; an approach to ecosystem assessment exportable to other coastal systems is proposed.

Marine Microbial Food Web Networks During Phytoplankton Bloom and Non-bloom Periods: Warming Favors Smaller Organism Interactions and Intensifies Trophic Cascade

Microbial food web organisms are at the base of the functioning of pelagic ecosystems and support the whole marine food web. They are very reactive to environmental changes and their interactions are modified in response to different productive periods such as phytoplankton bloom and non-bloom as well as contrasted climatic years. To study ecological associations, identify potential interactions between microorganisms and study the structure of the microbial food web in coastal waters, a weekly monitoring was carried out in the Thau Lagoon on the French Mediterranean coast. The monitoring lasted from winter to late spring during two contrasting climatic years, a typical Mediterranean (2015) and a year with an extreme warm winter (2016). Correlation networks comprising 110 groups/taxa/species were constructed to characterize potential possible interactions between the microorganisms during bloom and non-bloom periods. Complex correlation networks during the bloom and dominated by negative intraguild correlations and positive correlations of phytoplankton with bacteria. Such pattern can be interpreted as a dominance of competition and mutualism. In contrast, correlation networks during the non-bloom period were less complex and mostly dominated by tintinnids associations with bacteria mostly referring to potential feeding on bacteria, which suggests a shift of biomass transfer from phytoplankton-dominated food webs during bloom to more bacterioplankton-based food webs during non-bloom. Inter-annual climatic conditions significantly modified the structure of microbial food webs. The warmer year favored relationships among smaller group/taxa/species at the expense of large phytoplankton and ciliates, possibly due to an intensification of the trophic cascade with a potential shift in energy circulation through microbial food web. Our study compares a typical Mediterranean spring with another mimicking the prospected intensification of global warming; if such consideration holds true, the dominance of future coastal marine ecosystems will be shifted from the highly productive herbivorous food web to the less productive microbial food web.

The emergent interactions that govern biodiversity change

Observational studies have not yet shown that environmental variables can explain pervasive nonlinear patterns of species abundance, because those patterns could result from (indirect) interactions with other species (e.g., competition), and models only estimate direct responses. The experiments that could extract these indirect effects at regional to continental scales are not feasible. Here, a biophysical approach quantifies environment- species interactions (ESI) that govern community change from field data. Just as species interactions depend on population abundances, so too do the effects of environment, as when drought is amplified by competition. By embedding dynamic ESI within framework that admits data gathered on different scales, we quantify responses that are induced indirectly through other species, including probabilistic uncertainty in parameters, model specification, and data. Simulation demonstrates that ESI are needed for accurate interpretation. Analysis demonstrates how nonlinear responses arise even when their direct responses to environment are linear. Applications to experimental lakes and the Breeding Bird Survey (BBS) yield contrasting estimates of ESI. In closed lakes, interactions involving phytoplankton and their zooplankton grazers play a large role. By contrast, ESI are weak in BBS, as expected where year-to-year movement degrades the link between local population growth and species interactions. In both cases, nonlinear responses to environmental gradients are induced by interactions between species. Stability analysis indicates stability in the closed-system lakes and instability in BBS. The probabilistic framework has direct application to conservation planning that must weigh risk assessments for entire habitats and communities against competing interests.

Complex food webs coincide with high genetic potential for chemolithoautotrophy in fractured bedrock groundwater

Groundwater ecosystems face the challenge of energy limitation due to the absence of light-driven primary production. Lack of space and low oxygen availability might further contribute to generally assumed low food web complexity. Chemolithoautotrophy provides additional input of carbon within the subsurface, however, we still do not understand how abundances of chemolithoautotrophs, differences in surface carbon input, and oxygen availability control subsurface food web complexity. Using a molecular approach, we aimed to disentangle the different levels of potential trophic interactions in oligotrophic groundwater along a hillslope setting of alternating mixed carbonate-/siliciclastic bedrock with contrasting hydrochemical conditions and hotspots of chemolithoautotrophy. Across all sites, groundwater harbored diverse protist communities including Ciliophora, Cercozoa, Centroheliozoa, and Amoebozoa but correlations with hydrochemical parameters were less pronounced for eukaryotes compared to bacteria. Ciliophora-affiliated reads dominated the eukaryotic data sets across all sites. DNA-based evidence for the presence of metazoan top predators such as Cyclopoida (Arthropoda) and Stenostomidae (Platyhelminthes) was only found at wells where abundances of functional genes associated with chemolithoautotrophy were 10-100 times higher compared to wells without indications of these top predators. At wells closer to recharge areas with presumably increased inputs of soil-derived substances and biota, fungi accounted for up to 85% of the metazoan-curated eukaryotic sequence data, together with a low potential for chemolithoautotrophy. Although we did not directly observe higher organisms, our results point to the existence of complex food webs with several trophic levels in oligotrophic groundwater. Chemolithoautotrophy appears to provide strong support to more complex trophic interactions, feeding in additional biomass produced by light-independent CO₂-fixation.

Machine learning identifies a strong association between warming and reduced primary productivity in an oligotrophic ocean gyre

Phytoplankton play key roles in the oceans by regulating global biogeochemical cycles and production in marine food webs. Global warming is thought to affect phytoplankton production both directly, by impacting their photosynthetic metabolism, and indirectly by modifying the physical environment in which they grow. In this respect, the Bermuda Atlantic Time-series Study (BATS) in the Sargasso Sea (North Atlantic gyre) provides a unique opportunity to explore effects of warming on phytoplankton production across the vast oligotrophic ocean regions because it is one of the few multidecadal records of measured net primary productivity (NPP). We analysed the time series of phytoplankton primary productivity at BATS site using machine learning techniques (ML) to show that increased water temperature over a 27-year period (1990–2016), and the consequent weakening of vertical mixing in the upper ocean, induced a negative feedback on phytoplankton productivity by reducing the availability of essential resources, nitrogen and light. The unbalanced availability of these resources with warming, coupled with ecological changes at the community level, is expected to intensify the oligotrophic state of open-ocean regions that are far from land-based nutrient sources.

Soil Microbial Networks Shift Across a High-Elevation Successional Gradient

While it is well established that microbial composition and diversity shift along environmental gradients, how interactions among microbes change is poorly understood. Here, we tested how community structure and species interactions among diverse groups of soil microbes (bacteria, fungi, non-fungal eukaryotes) change across a fundamental ecological gradient, succession. Our study system is a high-elevation alpine ecosystem that exhibits variability in successional stage due to topography and harsh environmental conditions. We used hierarchical Bayesian joint distribution modeling to remove the influence of environmental covariates on species distributions and generated interaction networks using the residual species-to-species variance-covariance matrix. We hypothesized that as ecological succession proceeds, diversity will increase, species composition will change, and soil microbial networks will become more complex. As expected, we found that diversity of most taxonomic groups increased over succession, and species composition changed considerably. Interestingly, and contrary to our hypothesis, interaction networks became less complex over succession (fewer interactions per taxon). Interactions between photosynthetic microbes and any other organism became less frequent over the gradient, whereas interactions between plants or soil microfauna and any other organism were more abundant in late succession. Results demonstrate that patterns in diversity and composition do not necessarily relate to patterns in network complexity and suggest that network analyses provide new insight into the ecology of highly diverse, microscopic communities.

Vascular Expression of Hemoglobin Alpha in Antarctic Icefish Supports Iron Limitation as Novel Evolutionary Driver

Frigid temperatures of the Southern Ocean are known to be an evolutionary driver in Antarctic fish. For example, many fish have reduced red blood cell (RBC) concentration to minimize vascular resistance. Via the oxygen-carrying protein hemoglobin, RBCs contain the vast majority of the body's iron, which is known to be a limiting nutrient in marine ecosystems. Since lower RBC levels also lead to reduced iron requirements, we hypothesize that low iron availability was an additional evolutionary driver of Antarctic fish speciation. Antarctic Icefish of the family Channichthyidae are known to have an extreme alteration of iron metabolism due to loss of RBCs and two iron-binding proteins, hemoglobin and myoglobin. Loss of hemoglobin is considered a maladaptive trait allowed by relaxation of predator selection since extreme adaptations are required to compensate for the loss of oxygen-carrying capacity. However, iron dependency minimization may have driven hemoglobin loss instead of a random evolutionary event. Given the variety of functions that hemoglobin serves in the endothelium, we suspected the protein corresponding to the 3' truncated Hbα fragment (Hbα-3'f) that was not genetically excluded by icefish may still be expressed as a protein. Using whole mount confocal microscopy, we show that Hbα-3'f is expressed in the vascular endothelium of icefish retina, suggesting this Hbα fragment may still serve an important role in the endothelium. These observations support a novel hypothesis that iron minimization could have influenced icefish speciation with the loss of the iron-binding portion of Hbα in Hbα-3'f, as well as hemoglobin β and myoglobin.

Rewiring and indirect effects underpin modularity reshuffling in a marine food web under environmental shifts

Species are characterized by physiological and behavioral plasticity, which is part of their response to environmental shifts. Nonetheless, the collective response of ecological communities to environmental shifts cannot be predicted from the simple sum of individual species responses, since co-existing species are deeply entangled in interaction networks, such as food webs. For these reasons, the relation between environmental forcing and the structure of food webs is an open problem in ecology. To this respect, one of the main problems in community ecology is defining the role each species plays in shaping community structure, such as by promoting the subdivision of food webs in modules-that is, aggregates composed of species that more frequently interact-which are reported as community stabilizers. In this study, we investigated the relationship between species roles and network modularity under environmental shifts in a highly resolved food web, that is, a "weighted" ecological network reproducing carbon flows among marine planktonic species. Measuring network properties and estimating weighted modularity, we show that species have distinct roles, which differentially affect modularity and mediate structural modifications, such as modules reconfiguration, induced by environmental shifts. Specifically, short-term environmental changes impact the abundance of planktonic primary producers; this affects their consumers' behavior and cascades into the overall rearrangement of trophic links. Food web re-adjustments are both direct, through the rewiring of trophic-interaction networks, and indirect, with the reconfiguration of trophic cascades. Through such "systemic behavior," that is, the way the food web acts as a whole, defined by the interactions among its parts, the planktonic food web undergoes a substantial rewiring while keeping almost the same global flow to upper trophic levels, and energetic hierarchy is maintained despite environmental shifts. This behavior suggests the potentially high resilience of plankton networks, such as food webs, to dramatic environmental changes, such as those provoked by global change.

Creating a surrogate commuter network from Australian Bureau of Statistics census data

Between the 2011 and 2016 national censuses, the Australian Bureau of Statistics changed its anonymity policy compliance system for the distribution of census data. The new method has resulted in dramatic inconsistencies when comparing low-resolution data to aggregated high-resolution data. Hence, aggregated totals do not match true totals, and the mismatch gets worse as the data resolution gets finer. Here, we address several aspects of this inconsistency with respect to the 2016 usual-residence to place-of-work travel data. We introduce a re-sampling system that rectifies many of the artifacts introduced by the new ABS protocol, ensuring a higher level of consistency across partition sizes. We offer a surrogate high-resolution 2016 commuter dataset that reduces the difference between the aggregated and true commuter totals from ~34% to only ~7%, which is on the order of the discrepancy across partition resolutions in data from earlier years.

Combining Marine Ecology and Economy to Roadmap the Integrated Coastal Management: A Systematic Literature Review

Integrated coastal management (ICM) relies on the inclusion of economic issues within marine ecology. To assess the progress of this integration, we applied topic modelling and network analysis to explore the pertinent literature (583 Isi-WoS, and 5459 Scopus papers). We classified the topics of interest (i.e., concepts, approaches, and sectors) that combined ecological and economic issues within marine science, we aggregated these topics in fields pertinent to ICM, and tracked the knowledge-exchange between these fields by using an information-flow network. Main findings were: (i) the high trans-disciplinary fashion of studies about marine protection and of those about commercial fisheries, (ii) the weak interaction between studies focusing on potential biohazards and those about environmental management, (iii) the isolation, in the overall information-flow, of studies about ecotourism and aquaculture. We included in a roadmap all the integration routes we detected within ICM, based on the combination of ecological and economic issues. We conclude that, to improve integration, ICM should: (i) Exploit marine protection as a bridge between ecological and economic concepts and approaches, and between maritime economy sectors, (ii) employ systems ecology to pursue trans-disciplinary investigations, (iii) complement systems ecology with citizen science by means of inclusive economic initiatives, such as ecotourism.

Time series and beyond: multifaceted plankton research at a marine Mediterranean LTER site

Plankton are a pivotal component of the diversity and functioning of coastal marine ecosystems. A long time-series of observations is the best tool to trace their patterns and variability over multiple scales, ultimately providing a sound foundation for assessing, modelling and predicting the effects of anthropogenic and natural environmental changes on pelagic communities. At the same time, a long time-series constitutes a formidable asset for different kinds of research on specific questions that emerge from the observations, whereby the results of these complementary studies provide precious interpretative tools that augment the informative value of the data collected. In this paper, we review more than 140 studies that have been developed around a Mediterranean plankton time series gathered in the Gulf of Naples at the station LTER-MC since 1984. These studies have addressed different topics concerning marine plankton, which have included: i) seasonal patterns and trends; ii) taxonomic diversity, with a focus on key or harmful algal species and the discovery of many new taxa; iii) molecular diversity of selected species, groups of species or the whole planktonic community; iv) life cycles of several phyto- and zooplankton species; and v) interactions among species through trophic relationships, parasites and viruses. Overall, the products of this research demonstrate the great value of time series besides the record of fluctuations and trends, and highlight their primary role in the development of the scientific knowledge of plankton much beyond the local scale.

Similarities, differences and mechanisms of climate impact on terrestrial vs. marine ecosystems

Comparisons between terrestrial and marine ecosystems are generally not in the main stream of scientific literature even though Webb (2012) listed several points for which the transfer of knowledge and concepts related to one or to the other system would benefit our understanding of both. Even sharing this view, the leading hypothesis behind this contribution is that the pelagic system, where the dominant biotic component by number and biomass is microscopic, has specific features which strongly differentiate it from the above-the-surface terrestrial systems. Due to this, climate change, i.e. changes in temperature, precipitation and most importantly in the dynamics of the two fluid media, atmosphere and ocean, act with different mechanisms which prevents proceeding with analogies in many cases. In addition, the non-linearity of most of the processes and responses to perturbations requires, in order to obtain reliable forecasts or hindcasts, a detailed analysis of the path followed by the system which is normally overlooked in the step-change simulations or projections.

Aggregating a Plankton Food Web: Mathematical versus Biological Approaches

Species are embedded in a web of intricate trophic interactions. Understanding the functional role of species in food webs is of fundamental interests. This is related to food web position, so positional similarity may provide information about functional overlap. Defining and quantifying similar trophic functioning can be addressed in different ways. We consider two approaches. One is of mathematical nature involving network analysis where unique species can be defined as those whose topological position is very different to others in the same food web. A species is unique if it has very different connection pattern compared to others. The second approach is of biological nature, based on trait-based aggregations. Unique species are not easy to aggregate with others because their traits are not in common with the ones of most others. Our goal here is to illustrate how mathematics can provide an alternative perspective on species aggregation, and how this is related to its biological counterpart. We illustrate these approaches using a toy food web and a real food web and demonstrate the sensitive relationships between those approaches. The trait-based aggregation focusing on the trait values of size (sv) can be best predicted by the mathematical aggregation algorithms.

Life-history strategies in zooplankton promote coexistence of competitors in extreme environments with high metal content

The toxicity of pollutants on aquatic communities is determined by the specific sensitivities and by the ecological relationships between species, although the role of ecological interactions on the specific sensitivity to pollutants is complex. We tested the effect of exposure to copper on the life-history strategies of two coexisting rotifer species of the genus Brachionus from Inca-Coya lagoon, an isolated water body located in Atacama Desert. The experiments looked at differences in the response to the stress by chemical pollution mimicking field conditions of copper exposure, levels of food, and salinity, between single-species cultures and coexisting species. Under single species cultures, B. ‘Nevada’ had lower densities, growth rates, and resting eggs production than B. quadridentatus; when in competition, B. ‘Nevada’ performed better than B. quadridentatus in most life-history traits. B. ‘Nevada’ was a copper-tolerant species, which outcompeted B. quadridentatus, more copper-sensitive, with higher levels of copper. Species-specific responses to environmental conditions and pollution, plus differential relationships between population density and production of resting eggs, resulted in reduced niche overlap between species, allowing stabilized coexistence. The extreme environmental conditions and the isolation of the Inca-Coya lagoon, make it an excellent model to understand the adaption of aquatic organisms to stressed environments.

Architecture of marine food webs: To be or not be a 'small-world'

The search for general properties in network structure has been a central issue for food web studies in recent years. One such property is the small-world topology that combines a high clustering and a small distance between nodes of the network. This property may increase food web resilience but make them more sensitive to the extinction of connected species. Food web theory has been developed principally from freshwater and terrestrial ecosystems, largely omitting marine habitats. If theory needs to be modified to accommodate observations from marine ecosystems, based on major differences in several topological characteristics is still on debate. Here we investigated if the small-world topology is a common structural pattern in marine food webs. We developed a novel, simple and statistically rigorous method to examine the largest set of complex marine food webs to date. More than half of the analyzed marine networks exhibited a similar or lower characteristic path length than the random expectation, whereas 39% of the webs presented a significantly higher clustering than its random counterpart. Our method proved that 5 out of 28 networks fulfilled both features of the small-world topology: short path length and high clustering. This work represents the first rigorous analysis of the small-world topology and its associated features in high-quality marine networks. We conclude that such topology is a structural pattern that is not maximized in marine food webs; thus it is probably not an effective model to study robustness, stability and feasibility of marine ecosystems.

Mammoth grazers on the ocean's minuteness: a review of selective feeding using mucous meshes

Mucous-mesh grazers (pelagic tunicates and thecosome pteropods) are common in oceanic waters and efficiently capture, consume and repackage particles many orders of magnitude smaller than themselves. They feed using an adhesive mucous mesh to capture prey particles from ambient seawater. Historically, their grazing process has been characterized as non-selective, depending only on the size of the prey particle and the pore dimensions of the mesh. The purpose of this review is to reverse this assumption by reviewing recent evidence that shows mucous-mesh feeding can be selective. We focus on large planktonic microphages as a model of selective mucus feeding because of their important roles in the ocean food web: as bacterivores, prey for higher trophic levels, and exporters of carbon via mucous aggregates, faecal pellets and jelly-falls. We identify important functional variations in the filter mechanics and hydrodynamics of different taxa. We review evidence that shows this feeding strategy depends not only on the particle size and dimensions of the mesh pores, but also on particle shape and surface properties, filter mechanics, hydrodynamics and grazer behaviour. As many of these organisms remain critically understudied, we conclude by suggesting priorities for future research.

How are species interactions structured in species-rich communities? A new method for analysing time-series data

Estimation of intra- and interspecific interactions from time-series on species-rich communities is challenging due to the high number of potentially interacting species pairs. The previously proposed sparse interactions model overcomes this challenge by assuming that most species pairs do not interact. We propose an alternative model that does not assume that any of the interactions are necessarily zero, but summarizes the influences of individual species by a small number of community-level drivers. The community-level drivers are defined as linear combinations of species abundances, and they may thus represent e.g. the total abundance of all species or the relative proportions of different functional groups. We show with simulated and real data how our approach can be used to compare different hypotheses on community structure. In an empirical example using aquatic microorganisms, the community-level drivers model clearly outperformed the sparse interactions model in predicting independent validation data.

Temporal variations in a phytoplankton community in a subtropical reservoir: An interplay of extrinsic and intrinsic community effects

The phytoplankton community structure is potentially influenced by both extrinsic effects originating from the surrounding environment and intrinsic effects relying on interspecific interactions between two species. However, few studies have simultaneously considered both types of effects and assessed the relative importance of these factors. In this study, we used data collected over nine months (August 2012-May 2013) from a typical subtropical reservoir in southeast China to analyze the temporal variation of its phytoplankton community structure and develop a quantitative understanding of the extrinsic and intrinsic effects on phytoplankton community dynamics. Significant temporal variations were observed in environmental variables as well as the phytoplankton and zooplankton communities, whereas their variational trajectories and directions were entirely different. Variance partitioning analysis showed that extrinsic factors significantly explained only 31% of the variation in the phytoplankton community, thus suggesting that these factors were incomplete predictors of the community structure. Random forest-based models showed that 48% of qualified responsible phytoplankton species were more accurately predicted by phytoplankton-only models, which revealed clear effects of interspecific species-to-species interactions. Furthermore, we used association networks to model the interactions among phytoplankton, zooplankton and the environment. Network comparisons indicated that interspecific interactions were widely present in the phytoplankton community and dominated the network rather than those between phytoplankton and extrinsic factors. These findings expand the current understanding of the underlying mechanisms that govern phytoplankton community dynamics.

Clonal expansion behind a marine diatom bloom

Genetic diversity is what selection acts on, thus shaping the adaptive potential of populations. We studied micro-evolutionary patterns of the key planktonic diatom Pseudo-nitzschia multistriata at a long-term sampling site over 2 consecutive years by genotyping isolates with 22 microsatellite markers. We show that both sex and vegetative growth interplay in shaping intraspecific diversity. We document a brief but massive demographic and clonal expansion driven by strains of the same mating type. The analysis of an extended data set (6 years) indicates that the genetic fingerprint of P. multistriata changed over time with a nonlinear pattern, with intermittent periods of weak and strong diversification related to the temporary predominance of clonal expansions over sexual recombination. These dynamics, rarely documented for phytoplankton, contribute to the understanding of bloom formation and of the mechanisms that drive microevolution in diatoms.

Disentangling physical and biological drivers of phytoplankton dynamics in a coastal system

This proof-of-concept study integrates the surface currents measured by high-frequency coastal radars with plankton time-series data collected at a fixed sampling point from the Mediterranean Sea (MareChiara Long Term Ecological Research site in the Gulf of Naples) to characterize the spatial origin of phytoplankton assemblages and to scrutinize the processes ruling their dynamics. The phytoplankton community generally originated from the coastal waters whereby species succession was mainly regulated by biological factors (life-cycle processes, species-specific physiological performances and inter-specific interactions). Physical factors, e.g. the alternation between coastal and offshore waters and the horizontal mixing, were also important drivers of phytoplankton dynamics promoting diversity maintenance by i) advecting species from offshore and ii) diluting the resident coastal community so as to dampen resource stripping by dominant species and thereby increase the numerical importance of rarer species. Our observations highlight the resilience of coastal communities, which may favour their persistence over time and the prevalence of successional events over small time and space scales. Although coastal systems may act differently from one another, our findings provide a conceptual framework to address physical-biological interactions occurring in coastal basins, which can be generalised to other areas.

Surface properties of SAR11 bacteria facilitate grazing avoidance

Oceanic ecosystems are dominated by minute microorganisms that play a major role in food webs and biogeochemical cycles ¹ . Many microorganisms thrive in the dilute environment due to their capacity to locate, attach to, and use patches of nutrients and organic matter ^2,3 . We propose that some free-living planktonic bacteria have traded their ability to stick to nutrient-rich organic particles for a non-stick cell surface that helps them evade predation by mucous filter feeders. We used a combination of in situ sampling techniques and next-generation sequencing to study the biological filtration of microorganisms at the phylotype level. Our data indicate that some marine bacteria, most notably the highly abundant Pelagibacter ubique and most other members of the SAR 11 clade of the Alphaproteobacteria, can evade filtration by slipping through the mucous nets of both pelagic and benthic tunicates. While 0.3 µm polystyrene beads and other similarly-sized bacteria were efficiently filtered, SAR11 members were not captured. Reversed-phase chromatography revealed that most SAR11 bacteria have a much less hydrophobic cell surface than that of other planktonic bacteria. Our data call for a reconsideration of the role of surface properties in biological filtration and predator-prey interactions in aquatic systems.