Observation and inverse problems in coupled cell networks

Rapid, global, anthropogenic alteration of food webs in ecosystems necessitates a better understanding of how consumers regulate natural communities. We provide a global synthesis of consumer control of vegetation in coastal wetlands, where the domineering role of physical factors such as nutrient and salinity, rather than consumers, has been emphasized for decades. Using a data set of 1748 measures of consumer effects reported in 443 experiments/observations on all continents except Antarctica, we examine the generality of consumer control in salt marshes and mangroves globally. Our analyses show that salt marsh herbivores, including insects, snails, crabs, waterfowl, small mammals, and livestock, generally and often strongly suppress plant survival, aboveground biomass, and height, while their effects on plant density, belowground biomass, reproduction, and cover are more variable. These effects occur in forbs, grasses, and shrubs, and in both seedlings and adult plants. Herbivores additionally affect plant nutrient stoichiometry, and mediate plant interactions, though their effects on plant diversity are less consistent. Higher trophic levels also affect plants, as predators facilitate plant growth through trophic cascades that suppress grazer abundance and grazing rate. In mangroves, there are also signs of consumer control, though the relatively few studies available have often focused on mangrove propagules and seedlings rather than adults. Our analyses further reveal that the strength of consumer control is regulated by many physical factors. Nutrient, disturbance, and flooding, for example, amplify the negative effects of herbivores. Along latitudinal gradients, increased temperature enhances the negative effects of ectothermic herbivores, but has no effect on those of endothermic herbivores. Consumer control of coastal plants is also apparent across study methodologies: in field and laboratory settings, in observational studies, in consumer exclusion and addition experiments, in natural and transplanted plants, and in experiments of various durations. The role of consumer control in coastal vegetation worldwide highlights the need to better recognize and theoretically conceptualize both top‐down and bottom‐up forcing and their interactions in coastal wetlands. Improved understanding and conservation of coastal wetlands will only occur if we incorporate what the science has revealed: trophic feedbacks are an important and pervasive determinant of coastal plant communities.

Arctic ecosystems are undergoing major changes as a result of climate change that in many cases results in habitat loss for many species. However, glacial retreat also creates new habitats, such as lakes and ponds, providing an opportunity to test how communities and food webs assemble. Here, we studied the topology of the food webs and analyzed potential drivers such as environmental variables in 16 fishless ponds of contrasting age (8 young < 50 years, 8 old > 150 years) located in an area of rapid glacial retreat on the west coast of Greenland. We tested for differences in beta diversity and nestedness of prey and consumers related to the age class of the ponds. Based on gut content analysis of zooplankton and benthic macroinvertebrates we constructed food webs and investigated the extent to which food web metrics related to pond age and environmental variables. The food items of zooplankton and benthic macroinvertebrates in the young ponds represented a subset of those present in the old ponds' food webs. Food webs of old ponds had higher taxonomic richness, higher linkage density and lower connectance, indicating higher stability. Pond age class was the main explanatory factor for most food web metrics followed by productivity, here assessed by proxies, total nitrogen (TN) and phytoplankton chlorophyll‐a (Chl‐ a ). Food webs in old ponds did not show any significant association with environmental factors. In contrast, in young ponds, connectance and trophic niche overlap were significantly related to TN and Chl‐ a . The different complexity patterns indicate that food web topology in newly created ponds becomes more complex and independent of environmental conditions as ponds age. These differences likely make food webs of young ecosystems more unstable and vulnerable to external disturbances than those of older ecosystems.

This study used sociocultural learning theory to better understand how middle and high school environmental science and biology students and pre- and in-service science teachers connect the daily life activity of eating to the food web model learned in school. We sought to understand how student and teacher perceptions of the environment and their experiences influenced their responses to interview questions regarding this topic. Findings, based on transcribed interviews with 54 study participants, indicate that three quarters of teachers and students were unable to connect the food they eat with ecosystem food webs. Even so, many respondents particularly those from elite public schools, did not demonstrate common food web misconceptions identified by other researchers, instead showing a sophisticated understanding of food web interactions. These findings indicate that even though participants were proficient in their school science understanding of food web interactions, they did not readily think about how their everyday out of school activities, like eating, relate to those interactions. This may be representative of a more general disconnect between formal ecology instruction and daily life activities. We provide several recommendations for how this disconnect can be remedied in our classrooms.

From species distributions to ecosystem structure and function: A methodological perspective

Although invasive plants are a major source of terrestrial ecosystem degradation worldwide, it remains unclear which trophic levels above the base of the food web are most vulnerable to plant invasions. We performed a meta-analysis of 38 independent studies from 32 papers to examine how invasive plants alter major groupings of primary and secondary consumers in three globally distributed ecosystems: wetlands, woodlands and grasslands. Within each ecosystem we examined if green (grazing) food webs are more sensitive to plant invasions compared to brown (detrital) food webs. Invasive plants have strong negative effects on primary consumers (detritivores, bacterivores, fungivores, and/or herbivores) in woodlands and wetlands, which become less abundant in both green and brown food webs in woodlands and green webs in wetlands. Plant invasions increased abundances of secondary consumers (predators and/or parasitoids) only in woodland brown food webs and green webs in wetlands. Effects of invasive plants on grazing and detrital food webs clearly differed between ecosystems. Overall, invasive plants had the most pronounced effects on the trophic structure of wetlands and woodlands, but caused no detectable changes to grassland trophic structure.

Capturing ecological data variability in food web models is an important step for improving model representation of empirical systems. One approach is to use linear inverse modelling and Markov Chain Monte Carlo (LIM-MCMC) techniques to set up an inverse LIM problem using empirical data constraints, and then sample multiple plausible food webs from the inverse problem using an MCMC algorithm. We describe the set of plausible food webs as an ‘ensemble’ of solutions to the inverse problem sampled with the LIM-MCMC algorithm. The extent of data variability eventually integrated into an ensemble depends on how well the LIM-MCMC algorithm samples the solution space. Algorithm quality can be adjusted via user-defined parameters describing starting points, jump sizes, and number of iterations or food webs produced. However, little information exists on how each LIM-MCMC algorithm parameter affects the degree of empirical data variability introduced into the ensemble. Further, post hoc algorithm quality diagnostics with commonly used trace plots and the coefficient of variation (CoV) rarely address critical aspects of algorithm quality, such as (1) if the returned ensemble successfully targeted the solution space distribution (stationarity), (2) correlation between ensemble solutions (mixing), and (3) if the ensemble contains enough solutions to adequately capture input data variability (sampling efficiency). Therefore, we used several established MCMC convergence diagnostics to (1) quantify how algorithm parameters affect ensemble flow values and if these differences propagate to ecological indicators and (2) evaluate algorithm quality and compare to current evaluation and ecosystem modelling methods. We applied 30 LIM-MCMC algorithm combinations of varying starting points, jump sizes, and number of iterations to solve food web ensembles from a single food web model. We analysed ensembles with Ecological Network Analysis (ENA) to calculate indicators describing system function. Results show that LIM-MCMC algorithm parameters, in particular the jump size, affect ensemble flow values, which propagate to ecological indicators describing different ecosystem function of the same model. Thereafter, comparisons of post hoc diagnostics show that MCMC convergence diagnostics provided more robust estimates of algorithm quality than trace plots and CoV. Together, these findings underpin several novel recommendations to enhance LIM-MCMC algorithm parameter selection and quality assessments applicable to any ecological ensemble network study.

Detritus, that is, dead organic matter of any size and origin, forms an important energetic and nutritional basis for food webs in terrestrial, aquatic, and marine ecosystems. Across all ecosystems, crustaceans are strongly involved in the turnover of detritus, thus being important mediators of this fundamental ecosystem process. Crustaceans have evolved physiological, behavioral, and morphological adaptations toward a specialized detritivorous or scavenging lifestyle, yet omnivory is a unifying feature of their feeding ecology. Their diversity, nutritional flexibility, and individual motility assign detritivorous crustaceans a central position in many food webs, connecting them to particularly high numbers of other food web components, in some cases even across habitat boundaries. Large detritivorous crustaceans, in particular, act as shortcuts in detrital food web pathways by directly linking detritus-derived energy to the highest trophic levels. In some ecosystems, crustaceans dominate detritivore communities. In freshwater streams and on vegetated coasts, crabs, isopods, and amphipods shred and consume up to 100% of the plant litter input. In the pelagic zones of lakes and oceans, copepods, mysids, and euphausiids mediate the flux of particulate organic matter through the water column. In the deep sea, scavenging amphipods are the primary consumers of food falls, from jellyfish to whale carcasses, acting as spatial and temporal vectors of detritus-derived energy. Anthropogenic impacts, such as pollution, fisheries, species introductions, or climate change, already affect detritivorous crustacean communities and their contributions to detritus processing in various ways, but their long-term effects are still poorly understood.

Incorporation of diet information derived from Bayesian stable isotope mixing models into mass-balanced marine ecosystem models: A case study from the Marennes-Oléron Estuary, France

Recent applications of molecular genetics to edaphic microbial communities of the McMurdo Dry Valleys and elsewhere have rejected a long-held belief that Antarctic soils contain extremely limited microbial diversity. The Inter-Valley Soil Comparative Survey aims to elucidate the factors shaping these unique microbial communities and their biogeography by integrating molecular genetic approaches with biogeochemical analyses. Although the microbial communities of Dry Valley soils may be complex, there is little doubt that the ecosystem's food web is relatively simple, and evidence suggests that physicochemical conditions may have the dominant role in shaping microbial communities. To examine this hypothesis, bacterial communities from representative soil samples collected in four geographically disparate Dry Valleys were analyzed using molecular genetic tools, including pyrosequencing of 16S rRNA gene PCR amplicons. Results show that the four communities are structurally and phylogenetically distinct, and possess significantly different levels of diversity. Strikingly, only 2 of 214 phylotypes were found in all four valleys, challenging a widespread assumption that the microbiota of the Dry Valleys is composed of a few cosmopolitan species. Analysis of soil geochemical properties indicated that salt content, alongside altitude and Cu(2+), was significantly correlated with differences in microbial communities. Our results indicate that the microbial ecology of Dry Valley soils is highly localized and that physicochemical factors potentially have major roles in shaping the microbiology of ice-free areas of Antarctica. These findings hint at links between Dry Valley glacial geomorphology and microbial ecology, and raise previously unrecognized issues related to environmental management of this unique ecosystem.

The rapid incorporation of biodegradable polymers into daily-use and biomedical products has largely outpaced a comprehensive understanding of their biological effects and metabolic implications. Among the various, polylactic acid (PLA) represents one of the most extensively used, particularly in food-contact applications, and its fragmentation into micro- and nano-plastics (MPs/NPs) is raising increasing concerns for its potential implications for human health. Here, we present an integrated metabolomics and fluxomics investigation of the effects of PLA nanoparticles (PLA-NPs) combining in vitro models with an in vivo experimental model. PLA-NPs were synthesized in-house using a microfluidic-assisted nanoprecipitation approach and fluorescently labeled with rhodamine to enable intracellular localization. Human intestinal-derived HT-29 and Caco-2 cells were exposed to PLA-NPs (100 μg/mL) for 24, 48, and 72 hours, followed by untargeted metabolomics profiling by gas chromatography–mass spectrometry and high-resolution liquid chromatography-mass spectrometry. Metabolic analyses revealed non-overlapping, cell-specific responses to PLA-NPs exposure, involving coordinated perturbations in amino acid utilization, carbohydrate and lipid metabolism, and redox-related pathways. To disambiguate the intracellular fate of PLA-NPs, a fluxomic investigation was implemented by culturing cells in a fully 13C-labeled media. This approach enabled the discrimination of carbon fluxes derived from the polymeric material from those sustained by endogenous cellular metabolism. To extend these observations beyond in vitro systems, a parallel in vivo study was conducted in Wistar rats (n = 20), including 10 animals receiving PLA-NPs via drinking water and 10 matched controls over a 21-day exposure period. Untargeted and targeted metabolomics analyses of intestinal tissues and fecal samples are currently underway to evaluate metabolic adaptations associated with sustained PLA-NPs intake. Overall, these findings demonstrate that PLA-NPs is not metabolically inert, but can be actively integrated into cellular metabolic networks, where they elicit extensive metabolic rewiring. By demonstrating that PLA-derived nanoparticles are capable of actively modulating cellular metabolism, these findings provide a rationale for future investigations aimed at evaluating their effects on systemic metabolic regulation.This work is under the support of the National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, Investment 1.1, “Fund for the National Research Program and for Projects of National Interest (NRP)” by the Italian Ministry of University and Research (MUR), funded by the European Union – NextGenerationEU. Project title: “Plastic Contamination by Poly(Lactic Acid) (PLASTAMINATION): organ injuries and underlying molecular mechanisms”, MUR, PRIN-PNRR2022 CODE NUMBER: P2022AA47Y- CUP D53D23021910001

The chapter summarizes the history of recent scientific understanding of food webs, particularly shallow water food webs. The chapter outlines a history of key papers ranging from Elton to the most recent synthetic studies of meta-analysis of multiple food webs in many ecosystems. Changes in general organizing principles over time and conflicts with recent understanding are emphasized including an outline of the considerable progress over time and hope for an emerging discipline that takes advantage of emerging multidisciplinary tools and collaborations.

Network theory is rapidly changing our understanding of complex systems, but the relevance of topological features for the dynamic behavior of metabolic networks, food webs, production systems, information networks, or cascade failures of power grids remains to be explored. Based on a simple model of networks, we offer an interpretation of instabilities and oscillations observed in biological, ecological, economic, and engineering systems. We find that most networks display damped oscillations, even when their units - and linear chains of these units - behave in a non-oscillatory way. Moreover, networks of damped oscillators tend to produce growing oscillations. This surprising behavior offers, for example, a new interpretation of business cycles and of oscillating or pulsating processes. The network structure of material flows itself turns out to be a source of instability, and cyclical variations are an inherent feature of decentralized adjustments. In particular, we show how to treat production and networks as transport problems governed by balance equations and equations for the adaptation of production speeds. The stability and dynamic behavior of networks is investigated for different topologies, including sequential chains, supply circles, supply ladders, and supply hierarchies. Moreover, analytical conditions for absolute and convective instabilities are derived. The empirically observed bullwhip effect in chains is explained as a form of convective instability based on resonance effects. An application of this theory to the optimization of production networks has large optimization potentials.

Simple SummaryLysosomes are a critical component of the inner membrane system and are involved in various cellular biological processes, including macromolecular degradation, antigen presentation, intracellular pathogen destruction, plasma membrane repair, exosome release, cell adhesion/migration, and apoptosis. Lysosomes are a critical regulator of cellular metabolism, cancer, metastasis, and resistance to anticancer therapy. Additionally, lysosomal activities play a crucial role in acute myeloid leukemia (AML) development and progression, as well as maintaining the hematopoietic stem cells (HSCs) pool. It has been shown that AML cells undergo metabolic alterations due to chemotherapy or targeted treatment. Thus, depending on the molecular subtypes of AML or the treatments involved, lysosomes could have a therapeutic potential.Lysosomes are cellular organelles that regulate essential biological processes such as cellular homeostasis, development, and aging. They are primarily connected to the degradation/recycling of cellular macromolecules and participate in cellular trafficking, nutritional signaling, energy metabolism, and immune regulation. Therefore, lysosomes connect cellular metabolism and signaling pathways. Lysosome’s involvement in the critical biological processes has rekindled clinical interest towards this organelle for treating various diseases, including cancer. Recent research advancements have demonstrated that lysosomes also regulate the maintenance and hemostasis of hematopoietic stem cells (HSCs), which play a critical role in the progression of acute myeloid leukemia (AML) and other types of cancer. Lysosomes regulate both HSCs’ metabolic networks and identity transition. AML is a lethal type of blood cancer with a poor prognosis that is particularly associated with aging. Although the genetic landscape of AML has been extensively described, only a few targeted therapies have been produced, warranting the need for further research. This review summarizes the functions and importance of targeting lysosomes in AML, while highlighting the significance of lysosomes in HSCs maintenance.

Modeling ore generation in a magmatic context

This work is devoted to the development and implementation of a two-step method for solving the vector three-dimensional inverse diffraction problem on an inhomogeneous dielectric scatterer having the form of a hemisphere characterized by piecewise constant permittivity. The original boundary value problem for Maxwell’s equations is reduced to a system of integro-differential equations. An integral formulation of the vector inverse diffraction problem is proposed and the uniqueness of the solution of the first-kind integro-differential equation in special function classes is established. A two-step method for solving the vector inverse diffraction problem on the hemisphere is developed. Unlike traditional approaches, the two-step method for solving the inverse problem is non-iterative and does not require knowledge of the exact initial approximation. Consequently, there are no issues related to the convergence of the numerical method. The results of calculations of approximate solutions to the inverse problem are presented. It is shown that the two-step method is an efficient approach to solving vector problems in near-field tomography.