The virtual ecologist approach: simulating data and observers

Ecologists carry a well‐stocked toolbox with a great variety of sampling methods, statistical analyses and modelling tools, and new methods are constantly appearing. Evaluation and optimisation of these methods is crucial to guide methodological choices. Simulating error‐free data or taking high‐quality data to qualify methods is common practice. Here, we emphasise the methodology of the ‘virtual ecologist’ (VE) approach where simulated data and observer models are used to mimic real species and how they are ‘virtually’ observed. This virtual data is then subjected to statistical analyses and modelling, and the results are evaluated against the ‘true’ simulated data. The VE approach is an intuitive and powerful evaluation framework that allows a quality assessment of sampling protocols, analyses and modelling tools. It works under controlled conditions as well as under consideration of confounding factors such as animal movement and biased observer behaviour. In this review, we promote the approach as a rigorous research tool, and demonstrate its capabilities and practical relevance. We explore past uses of VE in different ecological research fields, where it mainly has been used to test and improve sampling regimes as well as for testing and comparing models, for example species distribution models. We discuss its benefits as well as potential limitations, and provide some practical considerations for designing VE studies. Finally, research fields are identified for which the approach could be useful in the future. We conclude that VE could foster the integration of theoretical and empirical work and stimulate work that goes far beyond sampling methods, leading to new questions, theories, and better mechanistic understanding of ecological systems.     

Long- and short-term phosphate deprivation in bean roots: plasma membrane lipid alterations and transient stimulation of phospholipases

In a long-term experiment bean (Phaseolus vulgaris L.) seedlings were grown for 18 days in hydroponics in either phosphate-sufficient (+P) or phosphate-deficient (-P) nutrient solutions. Phosphate deprivation halved the phosphorous content of roots. In plasma membrane (PM) fractions isolated from -P roots the phospholipid (PL) level was reduced from 35 to 21 mol%, while PL composition and degree of unsaturation were hardly altered. Digalactosyldiacylglycerol (DGDG) accumulated up to 26% of total PM lipids, replacing PL to a large extent. Molecular species and fatty acid compositions of DGDG in root PM were different compared to DGDG present in the -P plastids. In a short-term study, bean seedlings were grown for 18 days in hydroponics with a complete nutrient solution containing phosphate and then incubated in a -P medium for increasing time ranging from 1 up to 96 h. At the end of the starvation period phosphorous content of -P roots was reduced by 30% compared to +P ones. An activation of phospholipase D and phospholipase C was observed after 1 and 2h of phosphate deprivation, respectively. Maximal phosphatidic acid accumulation was detected after 4h of phosphate deprivation, when also DGDG started to accumulate in PM of bean roots. The fatty acid composition of PLD-derived phosphatidylbutanol resembled that of phosphatidylcholine.     

Spatial and temporal distribution patterns of the macrozoobenthos assemblage in the salt marshes of Tejo estuary (Portugal)

The present study focuses on the spatial and temporal distribution of the macroinvertebrate community of the salt marsh areas of the Tejo estuary, based on surveys conducted from autumn 1998 to summer 2000. Samples were collected quarterly in five different intertidal areas along an elevation gradient in: mudflats, creek mouths, creeks, pioneer salt marsh areas and middle marsh areas. A total of 36 benthic invertebrate taxa were identified. Insect larvae were the most well represented group, with 10 taxa identified. Oligochaetes and ostracods were the most numerically abundant taxa, whereas bivalves dominated in biomass. Benthic macroinvertebrate assemblages were dominated, both in number and biomass, by deposit feeders. Three distinct macroinvertebrate assemblages were distinguished along the elevation gradient, based on species presence, density and biomass: the unvegetated muddy areas with a macrobenthic assemblage composed mostly by infauna; the salt marsh pioneer areas of Spartina maritima in which several epibenthic taxa were found, as well as endobenthic taxa characteristic of muddy sediment; and the creek margins, with epifauna taxa such as insect larvae and crustaceans and a low abundance of benthic infauna. Total biomass in the unvegetated and Spartina areas was higher during spring and summer mainly due to the increase in biomass of Scrobicularia plana and Hydrobia ulvae. No decreases in the salt marsh macroinvertebrate biomass values were observed during the highest densities of their potential nektonic predators (summer). This fact might indicate that macroinvertebrates are not a limiting resource for the nektonic species, and that the natural biomass increment of these invertebrate species could be masking the predation/disturbance caused by the nektonic species.     

Trophic structure of macrobenthos in the Tagus estuary and adjacent coastal shelf

The trophic structure of benthic communities in the Tagus estuary and adjacent coastal shelf was characterized according to a functional guild approach, based on sampling surveys conducted between 1987 and 2000. Macrobenthic organisms were assigned to seven distinct trophic groups (herbivorous, filter feeders, surface deposit feeders, subsurface deposit feeders, carnivores, filter feeders/detritivores, carnivores/detritivores) and the dominance of these groups was related to environmental variables using multivariate ordination techniques. Surface-deposit feeders were numerically dominant in the Tagus estuary, making up 52% of the benthic communities, while in the adjacent coastal shelf the assemblage was dominated by both surface-deposit feeders and filter feeders (37% and 33%, respectively). When biomass was considered, filter feeders and filter feeders/detritivores were the dominant groups in the estuary, while for the adjacent coastal shelf filter feeders represented 83% of the total biomass. Salinity, depth and sediment composition were the main factors structuring spatial distribution. Surface-deposit feeders were the most abundant macrobenthos of the upper estuary. Surface deposit feeders also dominated the middle and the lower estuary but the proportion of filter feeders as well as other trophic groups increased with salinity. Generally, a more even distribution of trophic structure was found at stations with high salinity. In the adjacent coastal shelf, the trophic diversity decreased with depth. The trophic structure revealed that filter feeders dominated in abundance and biomass in shallow sandy sediments (<25 m), while in deeper sandy mud and muddy habitats (>50 m to 260 m), deposit feeders and carnivores were the most important groups in abundance and biomass, respectively.     

Phytosterols: applications and recovery methods

Phytosterols, or plant sterols, are compounds that occur naturally and bear close structural resemblance to cholesterol, but have different side-chain configurations. Phytosterols are relevant in pharmaceuticals (production of therapeutic steroids), nutrition (anti-cholesterol additives in functional foods, anti-cancer properties), and cosmetics (creams, lipstick). Phytosterols can be obtained from vegetable oils or from industrial wastes, which gives an added value to the latter. Considerable efforts have been recently dedicated to the development of efficient processes for phytosterol isolation from natural sources. The present work aims to summarize information on the applications of phytosterols and to review recent approaches, mainly from the industry, for the large-scale recovery of phytosterols.     

Potential mineralization of nitrogen from organic wastes to ryegrass and wheat crops

Two-pot experiments with ryegrass and wheat plants were conducted in a Cambic Arenosol to test the reliability of N fate predicted by incubation experiments previously performed, with the same soil, to assess potentially mineralizable nitrogen from six organic wastes (municipal solid waste compost, secondary pulp mill sludge, horn meal, poultry manure, solid phase from pig slurry and composted pig manure). Two treatments, corresponding to 80 and 160 kgN/ha were tested, with or without mineral N fertilization. Experimental data obtained in the pot trials was consistent with nitrogen net mineralization trend observed in the aerobic incubations with all the wastes tested. Values of potentially mineralizable nitrogen (N(0)) from the equations obtained by model fitting, to the incubation data, were well correlated to ryegrass and wheat N uptake. Poultry manure was the most efficient N supplier to crops.     

Biological evaluation of glucose and deoxyglucose derivatives radiolabeled with [99mTc(CO)3(H2O)3]+ core as potential melanoma imaging agents

Glucose 9 and 2-deoxyglucose 10 were successfully synthesized and radiolabeled with [(99m)Tc(CO)(3)(H(2)0)(3)](+) intermediate in high yield. The complexes were characterized by HPLC and its stability with histidine over time was challenged. Cell uptake and biodistribution studies in melanoma-bearing C57BL/6 mice were performed. Both compounds showed accumulation in tumor tissue with high tumor-to-muscle ratios. Thus, D-glucose- and D-2-deoxyglucose-(99m)Tc complex could be considered as agents for melanoma diagnosis.     

Kinetics and mechanism of the cutinase-catalyzed transesterification of oils in AOT reversed micellar system

The kinetics of the enzymatic transesterification between a mixture of triglycerides (oils) and methanol for biodiesel production in a bis(2-ethylhexyl) sodium sulfosuccinate (AOT)/isooctane reversed micellar system, using recombinant cutinase from Fusarium solani pisi as a catalyst, was investigated. In order to describe the results that were obtained, a mechanistic scheme was proposed, based on the literature and on the experimental data. This scheme includes the following reaction steps: the formation of the active enzyme–substrate complex, the addition of an alcohol molecule to the complex followed by the separation of a molecule of the fatty acid alkyl ester and a glycerol moiety, and release of the active enzyme. Enzyme inhibition and deactivation effects due to methanol and glycerol were incorporated in the model. This kinetic model was fitted to the concentration profiles of the fatty acid methyl esters (the components of biodiesel), tri-, di- and monoglycerides, obtained for a 24 h transesterification reaction performed in a stirred batch reactor under different reaction conditions of enzyme and initial substrates concentration.