Biosphere Structure, Carbon Sequestering Potential and the Atmospheric 14C Carbon Record

The behaviour of a numerical model for the global carbon cycleis eluidated by a simple analytical model for the biosphere.In the period 1980—1990 the ocean is estimated to haveabsorbed 33% of the total CO₂ emission to the atmosphere inthat same period. Net deforestation was responsible for 12—17%of this total emission rate, whereas the CO₂-fertilization effectcaused a re-absorption of 20—25%. Aggregation of the above-ground biosphere into a single poolin the model caused an oversitmation of the CO₂-fertilizationeffect. Also, the estimate of this rate increased when the fractionof carbon assumed to remain after the transformation of litterinto humus was increased, but the rate was little influencedby the model structure for soil organic carbon. A larger estimate for carbon uptake in the biosphere (Tans,Fung, and Takahashi, 1990) must be compensated by a reduceduptake in the ocean to arrive at a carbon balance. To do this,either the exchange rate between the upper mixed ocean layerand deep sea, or between ocean surface and atmosphere, shouldbe reduced. In addition, a good match to the observed time-courseof ¹⁴C carbon in the atmosphere must be preserved by the model.The ¹⁴C time-course did not remain well-matched if the atmosphere—oceansurface exchange was reduced, but it was hardly distrubed atall if the exchange rate with the deep sea was reduced. Key words: CO₂-fertilization, global carbon cycle.     

Jelly-falls historic and recent observations: a review to drive future research directions

The biological pump describes the transport of particulate matter from the sea surface to the ocean’s interior including the seabed. The contribution by gelatinous zooplankton bodies as particulate organic matter (POM) vectors (“jelly-falls”) has been neglected owing to technical and spatiotemporal sampling limitations. Here, we assess the existing evidence on jelly-falls from early ocean observations to present times. The seasonality of jelly-falls indicates that they mostly occur after periods of strong upwelling and/or spring blooms in temperate/subpolar zones and during late spring/early summer. A conceptual model helps to define a jelly-fall based on empirical and field observations of biogeochemical and ecological processes. We then compile and discuss existing strategic and observational oceanographic techniques that could be implemented to further jelly-falls research. Seabed video- and photography-based studies deliver the best results, and the correct use of fishing techniques, such as trawling, could provide comprehensive regional datasets. We conclude by considering the possibility of increased gelatinous biomasses in the future ocean induced by upper ocean processes favouring their populations, thus increasing jelly-POM downward transport. We suggest that this could provide a “natural compensation” for predicted losses in pelagic POM with respect to fuelling benthic ecosystems.     

Adaptable mesocosm facility to study oil spill impacts on corals

Although numerous studies have been carried out on the impacts of oil spills on coral physiology, most have relied on laboratory assays. This scarcity is partly explained by the difficulty of reproducing realistic conditions in a laboratory setting or of performing experiments with toxic compounds in the field. Mesocosm systems provide the opportunity to carry out such studies with safe handling of contaminants while reproducing natural conditions required by living organisms. The mesocosm design is crucial and can lead to the development of innovative technologies to mitigate environmental impacts. Therefore, this study aimed to develop a mesocosm system for studies simulating oil spills with several key advantages, including true replication and the use of gravity to control flow‐through that reduces reliance on pumps that can clog thereby decreasing errors and costs. This adaptable system can be configured to (a) have continuous flow‐through; (b) operate as an open or closed system; (c) be fed by gravity; (d) have separate mesocosm sections that can be used for individual and simultaneous experiments; and (e) simulate the migration of oil from ocean oil spills to the nearby reefs. The mesocosm performance was assessed with two experiments using the hydrocoral Millepora alcicornis and different configurations to simulate two magnitudes of oil spills. With few exceptions, physical and chemical parameters remained stable within replicates and within treatments throughout the experiments. Physical and chemical parameters that expressed change during the experiment were still within the range of natural conditions observed in Brazilian marine environments. The photosynthetic potential (F_v/F_m) of the algae associated with M. alcicornis decreased in response to an 1% crude‐oil contamination, suggesting a successful delivery of the toxic contaminant to the targeted replicates. This mesocosm is customizable and adjustable for several types of experiments and proved to be effective for studies of oil spills.     

A designed glycopeptide array for characterization of sugar-binding proteins toward a glycopeptide chip technology

For the realization of a practical high-throughput protein detection and analysis system, a novel peptide array has been constructed using a designed glycopeptide model library with an α-helical secondary structure. This study will contribute the increment of the diversity of such an array system and the application to focused proteomics and ligand screening by effective detection of sugar-binding proteins. Fluorescent glycopeptides with an α-helix, a β-strand, or a loop structure were designed initially to select a suitable scaffold for the detection of a model protein. After selection of the α-helical structure as the best scaffold, a small model library with various saccharides was constructed to have charge and hydrophobicity variations in the peptide sequences. When various sugar-binding proteins were added to the peptide library array, the fluorescent peptides showed different responses in fluorescence intensities depending on their sequences as well as saccharides. The patterns of these responses could be regarded as “protein fingerprints” (PFPs), which are able to establish the identities of the target proteins. The resulting PFPs reflected the recognition properties of the proteins. Furthermore, statistical data analysis from obtained PFPs was performed using a cluster analysis. The PFPs of sugar-binding proteins were clustered successfully depending on their families and binding properties. These studies demonstrate that arrays with glycopeptide libraries based on designed structures can be promising tools to detect and analyze the target proteins. Designed peptides with functional groups such as sugars will play roles as the capturing agents of high-throughput protein nano/micro arrays for focused proteomics and ligand screening studies.     

Tracking and forecasting ecosystem interactions in real time

Evidence shows that species interactions are not constant but change as the ecosystem shifts to new states. Although controlled experiments and model investigations demonstrate how nonlinear interactions can arise in principle, empirical tools to track and predict them in nature are lacking. Here we present a practical method, using available time-series data, to measure and forecast changing interactions in real systems, and identify the underlying mechanisms. The method is illustrated with model data from a marine mesocosm experiment and limnologic field data from Sparkling Lake, WI, USA. From simple to complex, these examples demonstrate the feasibility of quantifying, predicting and understanding state-dependent, nonlinear interactions as they occur in situ and in real time—a requirement for managing resources in a nonlinear, non-equilibrium world.     

Venue and outcome in ecological experiments: manipulations of larval anurans

The choice of venue is believed to be a critical decision for ecologists conducting experiments, yet the existence of tradeoffs in design and the impact of venue on outcome have not been quantitatively evaluated. To these ends we reviewed a set of 227 comparisons from 52 studies designed to quantify the effect of density on the growth performance of larval anurans. We predicted that both design and outcome would be related to experimental venue (laboratory, mesocosm, and field). We found that, in contrast to our predictions, laboratory experiments did not include more factors or yield more precise estimates of responses compared with mesocosm and field manipulations. In partial support of our prediction, we found that laboratory experiments did utilize somewhat larger numbers of replicates and included more levels per factor compared to the alternative venues. In addition we found that, as predicted, raising tadpoles at higher densities of conspecifics, or in the presence of heterospecifics tended to decrease growth. This effect, consistent with competition, was strongly dependent on experimental venue. In particular, we found that interspecific effects were much stronger in mesocosm versus field manipulations. This result is particularly relevant because conceptions of amphibian assemblages have included interspecific competition as integral to natural patterns of amphibian distribution. We conclude that hypothesized tradeoffs among experimental venues have not acted in a particularly strong way in shaping the design of tadpole density manipulations. However, venue may mediate strong effects on the outcome of such experiments. Quantification of such methodology based biases will help ecologists more effectively match the goals of their experiments with decisions regarding venue.     

Evaluating a predator–prey interaction in the field: the interaction between beetle larvae (predator) and tadpoles (prey)

The larval amphibian community of temporary pond ecosystems has served as a model for studies in community ecology, with a majority of this work being conducted in mesocosms. Recent research has suggested that mesocosms may overestimate ecological effects; therefore, experimental studies conducted under field conditions are required to gauge the results of mesocosm studies. To assess a species interaction under more natural conditions, we conducted a series of field experiments examining the predator–prey interaction between beetle larvae ( Dytiscus sp.; predator) and larval wood frogs Rana sylvatica (prey) in central Pennsylvania, USA. Quantitative sampling of woodland ponds indicated that beetle larvae of the genus Dytiscus were the most common predator of tadpoles. In a field enclosure experiment, dytiscids were effective predators of tadpoles in the pond environment. Moreover, tadpoles avoided areas in a pond containing caged dytiscids, demonstrating that tadpoles recognize the chemical stimuli of predators in complex environments. The results of this study are consistent with data from prior laboratory and mesocosm studies and suggest that these venues can produce reliable interpretations of predator–prey dynamics in this community.     

High acclimation potential in floating Macrocystis pyrifera to abiotic conditions even under grazing pressure – a field study

The persistence of floating seaweeds, which depends on abiotic conditions but also herbivory, had previously been mostly tested in outdoor mesocosm experiments. In order to investigate if the obtained mesocosm results of high seaweed persistence under natural environmental conditions and under grazing pressure can be extrapolated to field situations, we conducted in situ experiments. During two summers (2007 and 2008), Macrocystis pyrifera was tethered (for 14 d) to lines in the presence and absence of the amphipod Peramphithoe femorata at three sites (Iquique, Coquimbo, Calfuco). We hypothesized that grazing damage and seaweed persistence vary among sites due to different abiotic factors. By incubating the sporophytes in mesh bags, we were either able to isolate (grazing) or exclude (control) amphipods. To test for a mesh bag artifact, a set of sporophytes was incubated without mesh bags (natural). Mesh bags used to exclude herbivores influenced sporophyte growth and physiological performance. The chlorophyll a (Chl a) content depended largely on grazers and grazed sporophytes grew less than natural and control sporophytes within the two summers. A decrease in Chl a content was found for the sites with the highest prevailing irradiances and temperatures, suggesting an efficient acclimation to these sea surface conditions. Our field‐based results of sporophyte acclimation ability even under grazing pressure widely align with previous mesocosm results. We conclude that M. pyrifera and other temperate floating seaweeds can function as long‐distance dispersal vectors even with hitchhiking mesoherbivores.     

Modular estuarine mesocosm validation: ecotoxicological assessment of direct effects with the model compound endosulfan

This study represents the first in a series of validation experiments for the modular estuarine mesocosm testing direct pesticide effects. Endosulfan, an agricultural insecticide, was selected as a model contaminant for studying direct toxic effects as well as uptake of this model contaminant by estuarine biota. The grass shrimp, Palaemonetes pugio, and the mummichog, Fundulus heteroclitus, showed significant mortality (96 h LC₅₀: 0.12 and 2.2 μg/l, respectively) to endosulfan as predicted by laboratory bioassays. There was no effect on fiddler crabs and eastern oysters. The mesocosm was also useful in demonstrating the bioconcentration of endosulfan by eastern oysters (bioconcentration factor [BCF]=375) similar to results reported in field studies. This study illustrates the modular estuarine mesocosms' ability to detect direct effects of pesticide exposure and the uptake of a pesticide by estuarine fauna.     

Whole-Ecosystem Experiments: Replication Versus Realism: The Need for Ecosystem-Scale Experiments

The results of bottle and mesocosm experiments were compared with those obtained in whole-ecosystem experiments at the Experimental Lakes Area. Unless they can be cleverly designed to mimic major ecosystem processes and community compositions, smaller-scale experiments often give highly replicable, but spurious, answers. Problems with appropriate scaling are difficult to deduce without direct comparisons with whole-ecosystem experiments. Reasons are many, but include inappropriate spatial scales to include whole communities, in particular predators and nocturnally active animals; temporal scales that are too short to assess accurately the response of slow-responding organisms and biogeochemical processes; and elimination of key littoral–pelagic and catchment–lake interactions. Identical studies of limnological processes in lakes of a large range of sizes reveals that scaling correction is also necessary when extrapolating from small lakes to large ones. Accurate management decisions cannot be made with confidence unless ecosystem scales are studied. Received 26 March 1998; accepted 14 May 1998.     

Food-signal theory: population regulation and the functional response

A fully stochastic food-signal model, a function of a patchy-preyencounter sequence, and a prey-processing function is described.The model shows how prey density and its second-order statisticalproperties can sequester prey from predators, questioning theuse of only numerical abundance of predator and prey organismsas a measure of preya — predator interactions. The modelhighlights the notion that patch structure can be generatedby relative velocity of predator and prey as well as by theirspatial distribution. The model extends ideas that include the‘biological pump’ and the downwelling of carbonfrom the upper ocean, the functional response, optimal-foragingtheory, and the connections between population dynamics andvariability in the physical environment.     

Plants Replacing Plants: The Future of Community Modeling and Research

Over the past few decades, several conceptual and mathematical models of plant community organization and dynamics have been put forward. While each of these models has attempted to explain important plant community patterns by attributing them to some aspect of plant niches, or to a higher-level process, their predictive success has been very limited. Here I explore why this has happened by reviewing and summarizing each model individually by highlighting the plant community pattern each is trying to explain and predict, by identifying the mechanisms, tolerances, and/or processes authors propose are producing those patterns and describing how they work within the model, and by examining the assumptions of each model. I then discuss common misconceptions and shortcomings among the models, and finally propose a unifying synthesis and comprehensive framework that can serve as a basis for future plant community modeling and research. This synthesis is composed of three key ideas (1) that plant-plant replacements are the “fundamental process” of plant communities which produce every community-level terrestrial plant pattern, (2) that plants respond to mechanisms and tolerances which work both in spaces inside plants and in those spaces outside plants that influence them and/or they may be able to influence, and (3) that those responses make up plant niches which may be able to predict how plants replace themselves over time and space. Consequently I suggest to future field researchers that the best way to understand plant community patterns is to study plant-plant replacements, first by sampling long-term vegetation plots in order to map them, and then by manipulating mechanisms and tolerances in field experiments in order to understand what causes them.     

Development of an epiphyte indicator of nutrient enrichment: A critical evaluation of observational and experimental studies

An extensive review of the literature describing epiphytes on submerged aquatic vegetation (SAV), especially seagrasses, was conducted in order to evaluate the evidence for response of epiphyte metrics to increased nutrients. Evidence from field observational studies, together with laboratory and field mesocosm experiments, was assembled from the literature and evaluated for a hypothesized positive response to nutrient addition. There was general consistency in the results to confirm that elevated nutrients tended to increase the load of epiphytes on the surface of SAV, in the absence of other limiting factors. In spite of multiple sources of uncontrolled variation, positive relationships of epiphyte load to nutrient concentration or load (either nitrogen or phosphorus) often were observed along strong anthropogenic or natural nutrient gradients in coastal regions. Such response patterns may only be evident for parts of the year. Results from both mesocosm and field experiments also generally support the increase of epiphytes with increased nutrients, although outcomes from field experiments tended to be more variable. Relatively few studies with nutrient addition in mesocosms have been done with tropical or subtropical species, and more such controlled experiments would be helpful. Experimental duration influenced results, with more positive responses of epiphytes to nutrients at shorter durations in mesocosm experiments versus more positive responses at longer durations in field experiments. In the field, response of epiphyte biomass to nutrient additions was independent of climate zone. Mesograzer activity was a critical covariate for epiphyte response under experimental nutrient elevation, but the epiphyte response was highly dependent on factors such as grazer identity and density, as well as nutrient and ambient light levels. The balance of evidence suggests that epiphytes on SAV will be a useful indicator of persistent nutrient enhancement in many situations. Careful selection of appropriate temporal and spatial constraints for data collection, and concurrent evaluation of confounding factors will help increase the signal to noise ratio for this indicator.     

Using Environmental DNA to Census Marine Fishes in a Large Mesocosm

The ocean is a soup of its resident species'' genetic material, cast off in the forms of metabolic waste, shed skin cells, or damaged tissue. Sampling this environmental DNA (eDNA) is a potentially powerful means of assessing whole biological communities, a significant advance over the manual methods of environmental sampling that have historically dominated marine ecology and related fields. Here, we estimate the vertebrate fauna in a 4.5-million-liter mesocosm aquarium tank at the Monterey Bay Aquarium of known species composition by sequencing the eDNA from its constituent seawater. We find that it is generally possible to detect mitochondrial DNA of bony fishes sufficient to identify organisms to taxonomic family- or genus-level using a 106 bp fragment of the 12S ribosomal gene. Within bony fishes, we observe a low false-negative detection rate, although we did not detect the cartilaginous fishes or sea turtles present with this fragment. We find that the rank abundance of recovered eDNA sequences correlates with the abundance of corresponding species'' biomass in the mesocosm, but the data in hand do not allow us to develop a quantitative relationship between biomass and eDNA abundance. Finally, we find a low false-positive rate for detection of exogenous eDNA, and we were able to diagnose non-native species'' tissue in the food used to maintain the mesocosm, underscoring the sensitivity of eDNA as a technique for community-level ecological surveys. We conclude that eDNA has substantial potential to become a core tool for environmental monitoring, but that a variety of challenges remain before reliable quantitative assessments of ecological communities in the field become possible.     

Enhanced ecological indication based on combined planktic and benthic functional approaches in large river phytoplankton ecology

Environmental DNA (eDNA) is a powerful method for assessing the presence and distribution of invasive aquatic species. We used this tool to detect and monitor several invasive crayfishes Procambarus clarkii, Orconectes limosus and Pacifastacus leniusculus present in, or likely to invade, the ponds of the Brenne Regional Natural Park. A previous study showed that the eDNA method was not very efficient in detecting P. clarkii. In the present study, we explored new improvements in the detection of invasive crayfish. We designed specific primers for each crayfish species, and set up an experimental mesocosm approach to confirm the specificity of the primers and the sampling protocol. We analysed samples taken from ponds in 2014 and 2015. We compared two qPCR protocols involving either SybrGreen or TaqMan assays. Using these same primers, we were able to detect crayfish eDNA with both assays during the mesocosm experiment. However, crayfish from field samples could only be detected by performing qPCR with a SybrGreen assay. We successfully monitored the presence of three invasive species of crayfish using eDNA. This method is a powerful tool for establishing the presence or absence of invasive species in various freshwater environments.     

Effects of temperature, salinity, and fish size on growth and consumption of juvenile bluefish

Consumption and growth rates of juvenile bluefish Pomatomus saltatrix increased with increasing temperature and decreased with increasing fish size in short-term (7 days) experiments. Salinity had no effect on growth or consumption rate in a short-term experiment. In a long-term (90 days) mesocosm experiment, consumption and growth rates declined with increasing body size. Predictive equations developed from short-term experiments did not adequately predict observed consumption rates in the mesocosm experiment. However, growth in the mesocosm experiment was similar to field growth. Also, mesocosm consumption rates and consumption rates calculated using field growth and mesocosm growth efficiencies were similar to published independent field estimates of consumption rate. Our results indicate that experiments to determine the effects of temperature and the allometry of body size on growth and consumption rates should be conducted over long time periods simulating field conditions. Juvenile bluefish have rapid growth and their individual cumulative consumption is large. This result suggests that bluefish may have a large effect on their prey populations. This effect has yet to be quantified.     

Effects of sea surface warming on marine plankton

Ocean warming has been implicated in the observed decline of oceanic phytoplankton biomass. Some studies suggest a physical pathway of warming via stratification and nutrient flux, and others a biological effect on plankton metabolic rates; yet the relative strength and possible interaction of these mechanisms remains unknown. Here, we implement projections from a global circulation model in a mesocosm experiment to examine both mechanisms in a multi‐trophic plankton community. Warming treatments had positive direct effects on phytoplankton biomass, but these were overcompensated by the negative effects of decreased nutrient flux. Zooplankton switched from phytoplankton to grazing on ciliates. These results contrast with previous experiments under nutrient‐replete conditions, where warming indirectly reduced phytoplankton biomass via increased zooplankton grazing. We conclude that the effect of ocean warming on marine plankton depends on the nutrient regime, and provide a mechanistic basis for understanding global change in marine ecosystems.     

Prediction of maize single-cross hybrid performance: support vector machine regression versus best linear prediction

Accurate prediction of the phenotypic performance of a hybrid plant based on the molecular fingerprints of its parents should lead to a more cost-effective breeding programme as it allows to reduce the number of expensive field evaluations. The construction of a reliable prediction model requires a representative sample of hybrids for which both molecular and phenotypic information are accessible. This phenotypic information is usually readily available as typical breeding programmes test numerous new hybrids in multi-location field trials on a yearly basis. Earlier studies indicated that a linear mixed model analysis of this typically unbalanced phenotypic data allows to construct ɛ-insensitive support vector machine regression and best linear prediction models for predicting the performance of single-cross maize hybrids. We compare these prediction methods using different subsets of the phenotypic and marker data of a commercial maize breeding programme and evaluate the resulting prediction accuracies by means of a specifically designed field experiment. This balanced field trial allows to assess the reliability of the cross-validation prediction accuracies reported here and in earlier studies. The limits of the predictive capabilities of both prediction methods are further examined by reducing the number of training hybrids and the size of the molecular fingerprints. The results indicate a considerable discrepancy between prediction accuracies obtained by cross-validation procedures and those obtained by correlating the predictions with the results of a validation field trial. The prediction accuracy of best linear prediction was less sensitive to a reduction of the number of training examples compared with that of support vector machine regression. The latter was, however, better at predicting hybrid performance when the size of the molecular fingerprints was reduced, especially if the initial set of markers had a low information content.     

Predictive Value of Species Sensitivity Distributions for Effects of Herbicides in Freshwater Ecosystems

In this article we present a review of the laboratory and field toxicity of herbicides to aquatic ecosystems. Single-species acute toxicity data and (micro)mesocosm data were collated for nine herbicides. These data were used to investigate the importance of test species selection in constructing species sensitivity distributions (SSDs), and in estimating hazardous concentrations (i.e., HC5) protective for freshwater aquatic ecosystems. A lognormal model was fitted to toxicity data (acute EC50s and chronic NOECs) and the resulting distribution used to estimate lower (95% confidence), median (50% confidence), and upper (5% confidence), HC5 values. The taxonomic composition of the species assemblage used to construct the SSD does have a significant influence on the assessment of hazard and only sensitive primary producers should be included for the risk assessment of herbicides. No systematic difference in sensitivity between standard and non-standard test species was observed. Hazardous concentrations estimated using laboratory-derived acute and chronic toxicity data for sensitive freshwater primary producers were compared to the response of herbicide-stressed freshwater ecosystems using a similar exposure regime. The lower limit of the acute HC5 and the median value of the chronic HC5 were protective of adverse effects in aquatic micro/mesocosms even under a long-term exposure regime. The median HC5 estimate based on acute data was protective of adverse ecological effects in freshwater ecosystems when a pulsed or short-term exposure regime was used in the microcosm and mesocosm experiments. There was also concordance between the predictions from the effect model PERPEST and the concentrations at which clear effects started to emerge in laboratory and field studies. However, compared to the SSD concept, the PERPEST model is able to provide more information on ecological risks when a common toxicological mode of action is evaluated as it considers both recovery and indirect effects.     

Effect of simulated herbivory on growth of the invasive weed Hygrophila polysperma: Experimental and predictive approaches

Herbivory simulation studies, through mechanical removal of leaf tissue, provide valuable insight about plant compensation and tolerance to defoliation. A mesocosm experiment was conducted to examine the effects of defoliation on growth and biomass accumulation of Hygrophila polysperma and thereby determine the critical level of herbivory necessary to achieve significant reduction in growth of this invasive plant. The data collected during the experiment were used to develop an empirical plant growth model to examine the usefulness of a model-based approach for a priori understanding of plant response to defoliation. The results of the mesocosm experiment showed that defoliation significantly influenced growth and biomass accumulation of hygrophila. The empirical plant growth model accurately simulated plant growth response to herbivory across treatments. Based on the results of the mesocosm experiment, an insect defoliator that causes complete defoliation of hygrophila at least at monthly intervals may be able to reduce biomass and growth of hygrophila. The ability of the mathematical model to predict the effects of defoliation on hygrophila suggest that it could be a useful tool for the selection of effective biological control agents.