Non-lethal sampling of DNA from bumble bees for conservation genetics

Summary Non-lethal sampling of DNA from individuals in wild populations will often be required for studies of the conservation genetics of social insects, since it avoids destroying members of scarce or declining species. We investigated the effectiveness and consequences of methods of non-lethal sampling of DNA from bumble bee workers. In an experiment with two captive and confined Bombus terrestris colonies, we found that, unlike sampling haemolymph, sampling the terminal portion of the tarsus of a mid-leg of a worker reliably yielded amplifiable microsatellite DNA and did not significantly reduce worker survivorship. In a further experiment with four B. terrestris colonies whose workers were allowed to forage freely at flowers in the external environment, tarsal sampling of either a mid-leg or a hind-leg had no significant effects on worker survivorship, the mean body mass of foraging workers, the frequency or duration of foraging trips, mass of pollen loads or mass of nectar loads. We therefore suggest that tarsal sampling of either a mid-leg or a hind-leg is an effective and acceptable means of non-lethally sampling DNA from workers in wild populations of bumble bees, because effects on individual and colony performance are likely to be absent or minimal.Received 2 December 2002; revised 10 April 2003; accepted 25 April 2003.     

The use of stable carbon isotope analysis in rooting studies

Summary Stable carbon isotope analysis was evaluated as a means of predicting the relative proportions of C₃ and C₄ root phytomass in species mixtures. The following mixtures of C₃ and C₄ species were used: 1) big bluestem (Andropogon gerardii)/cheatgrass (Bromus tectorum), 2) little bluestem (Schizachyrium scoparium)/cheatgrass, and 3) sorghum (Sorghum bicolor)/sunflower (Helianthus annuus). There was a significant correlation (P<0.01) between % C₄ phytomass and stable carbon isotope values for each of the three combinations (r²>0.98). Root length per mass varied among the five species studied (10.1–94.3 m/g), which resulted in different conclusions depending on whether root values are expressed as length or mass. For example, field samples from a tallgrass prairie site were estimated to contain about 20% cheatgrass on a mass basis, whereas the figure was 68% when expressed in terms of length. The combination of stable carbon isotope analysis with length-for-mass measurements promises to be a useful means of studying root competition between C₃ and C₄ plants.     

UNiquant, a program for quantitative proteomics analysis using stable isotope labeling

Stable isotope labeling (SIL) methods coupled with nanoscale liquid chromatography and high resolution tandem mass spectrometry are increasingly useful for elucidation of the proteome-wide differences between multiple biological samples. Development of more effective programs for the sensitive identification of peptide pairs and accurate measurement of the relative peptide/protein abundance are essential for quantitative proteomic analysis. We developed and evaluated the performance of a new program, termed UNiquant, for analyzing quantitative proteomics data using stable isotope labeling. UNiquant was compared with two other programs, MaxQuant and Mascot Distiller, using SILAC-labeled complex proteome mixtures having either known or unknown heavy/light ratios. For the SILAC-labeled Jeko-1 cell proteome digests with known heavy/light ratios (H/L = 1:1, 1:5, and 1:10), UNiquant quantified a similar number of peptide pairs as MaxQuant for the H/L = 1:1 and 1:5 mixtures. In addition, UNiquant quantified significantly more peptides than MaxQuant and Mascot Distiller in the H/L = 1:10 mixtures. UNiquant accurately measured relative peptide/protein abundance without the need for postmeasurement normalization of peptide ratios, which is required by the other programs.     

Plastic changes in tadpole trophic ecology revealed by stable isotope analysis

Amphibian larvae constitute a large fraction of the biomass of wetlands and play important roles in their energy flux and nutrient cycling. Interactions with predators and competitors affect their abundance but also their foraging behaviour, potentially leading to non-consumptive cascading effects on the whole trophic web. We experimentally tested for plastic changes in larval trophic ecology of two anuran species in response to competitors and the non-lethal presence of native and non-native predators, using stable isotope analysis. We hypothesized that tadpoles would alter their diet in the presence of competitors and native predators, and to a lesser extent or not at all in the presence of non-native predators. First, we conducted a controlled diet experiment to estimate tadpole turnover rates and discrimination factors using Pelobates cultripes and Bufo calamita. Turnover rates yielded a half-life of 15–20 days (attaining a quasi-isotopic equilibrium after 2 months), whereas discrimination factors for natural controlled diets resulted in different isotopic values essential for calibration. Second, we did an experiment with P. cultripes and Rana perezi (=Pelophylax perezi) where we manipulated the presence/absence of predators and heterospecific tadpoles using microcosms in the laboratory. We detected a significant shift in trophic status of both amphibian species in the presence of non-native crayfish: the δ¹⁵N values and macrophyte consumption of tadpoles increased, whereas their detritus consumption decreased. This suggests that tadpoles could have perceived crayfish as a predatory risk or that crayfish acted as competitors for algae and zooplankton. No dietary changes were observed in the presence of native dragonflies or when both tadpole species co-occurred. Stable isotopic analysis is an efficient way to assess variation in tadpoles’ tropic status and hence understand their role in freshwater ecosystems. Here we provide baseline isotopic information for future trophic studies and show evidence for plastic changes in tadpoles’ use of food resources under different ecological scenarios.     

Analytical error in stable isotope ecology

The increasing popularity of stable isotope analysis (SIA) as an ecological research tool and the ease of automated analysis have created a knowledge gap between ecologists using SIA and the operators of isotope ratio mass spectrometry (IRMS) equipment. This has led to deterioration in the understanding of IRMS methodology and its proper dissemination in the ecological literature. Of 330 ecological research papers surveyed, 63 (19%) failed to report any form of analytical error associated with IRMS. Of the 267 papers that reported analytical error, there was considerable variation both in the terminology and approach used to quantify and describe error. Internal laboratory standards were often used to determine the analytical error associated with IRMS, so chosen because they are homogenous and have isotopic signatures that do not vary over time. We argue that true ecological samples collected in the field are complex bulk mixtures and often fail to adhere to these two criteria. Hence the analytical error associated with samples is potentially greater than that of standards. A set of standard data run over time with a precision typically reported in the ecological literature (1 standard deviation: 1SD=0.26‰) was simulated to determine the likelihood of spurious treatment effects depending on timing of analysis. There was a 90% likelihood of detecting a significant difference in the stable nitrogen ratio of a single sample (homogenized bovine liver) run in two time periods when n>30. Minor protocol adjustments, including the submission of blind replicates by researchers, random assignment of sample repeats within a run by analytical labs, and reporting 1SD of a single sample analyzed both within and between runs, will only serve to strengthen the interpretation of true ecological processes by both researchers and reviewers.     

Methods to collect, preserve, and prepare elasmobranch tissues for stable isotope analysis

Stable isotope analysis has the potential to expand our understanding of elasmobranch ecology. However, elasmobranchs share unique traits (i.e., retention of urea, lack of adipose tissue, cartilaginous skeletons) that require modified preparation techniques. Alternative tissue collection and preservation methods would allow sampling from ichthyology collections and at remote locations. We compared different collection, preservation, and preparation techniques to identify treatments that yielded robust isotopic data. Blood components collected in tubes coated with lithium heparin (an anti-coagulant) were not isotopically distinct from blood collected in no-additive tubes. Compared to frozen muscle, ethanol-treated muscle had altered ??¹³C values, but similar ??¹⁵N values. Finally, we removed lipids and urea with petroleum ether and deionized water, respectively. Although untreated and treated muscle had similar amino acid compositions, treated muscle preferentially lost ¹⁴N and had greater C:N ratios. These results indicate that urea affects isotope ratios and that water treatment removes urea without altering muscle protein composition. Although not exhaustive, our study begins to address the need for elasmobranch-specific methods.     

Isolation and derivatization of plasma taurine for stable isotope analysis by gas chromatography-mass spectrometry

A method for the isolation and derivatization of plasma taurine is described that allows stable isotope determinations of taurine to be made by gas chromatography-mass spectrometry (gc-ms). The isolation procedure can be applied to 0.1 ml of plasma: the recovery of plasma taurine was 70–80%. For gc separation, taurine was converted to its dimethylaminomethylene methyl ester derivative which could not be detected by hydrogen flame ionization, but could be monitored readily by NH₃ chemical ionization mass spectrometry. The derivatization reaction occurred partially on-column and required optimization of injection conditions. Using stable isotope ratiometry multiple ion detection, $\text{[M + 2 + H]}{}^{\mathrm{+}}\text{[M + H]}{}^{\mathrm{+}}$ ion ratio of natural abundance taurine was determined with a standard deviation of less than ±0.07% of the ratio. The [1,2-¹³C]taurine/taurine mole ratios of standard mixtures could be accurately determined to 0.001. This stable isotope gc-ms method is suitable for studying the plasma kinetics of [1,2-¹³C]taurine in infants who are at risk with respect to taurine depletion.     

Spatial analysis of stable isotope data to determine primary sources of nutrition for fish

Carbon and nitrogen stable isotopes were used to determine the ultimate autotrophic sources supporting production of three commercially important fish species over unvegetated mudflats in a subtropical estuary. Mean isotope values over the whole estuary for fish and autotroph sources were modeled to indicate feasible combinations of sources. Variability in isotope values among nine locations (separated by 3-10 km) was then used as a further test of the likelihood that sources were involved in fish nutrition. A positive spatial correlation between isotope values of a fish species and an autotroph indicates a substantial contribution from the autotroph. Spatial correlations were tested with a newly developed randomization procedure using differences between fish and autotroph values at each location, based on carbon and nitrogen isotopes combined in two-dimensional space. Both whole estuary modeling and spatial analysis showed that seagrass, epiphytic algae and particulate organic matter in the water column, including phytoplankton, are likely contributors to bream (Acanthopagrus australis) nutrition. However, spatial analysis also showed that mangroves were involved (up to 33% contribution), despite a very low contribution from whole estuary modeling. Spatial analysis on sand whiting (Sillago ciliata) demonstrated the importance of two sources, mangroves (up to 25%) and microalgae on the mudflats, considered unimportant based on whole estuary modeling. No spatial correlations were found between winter whiting (Sillago maculata) and autotrophs, either because fish moved among locations or relied on different autotrophs at different locations. Spatial correlations between consumer and source isotope values provide a useful analytical tool for identifying the role of autotrophs in foodwebs, and demonstrated here that both in situ production of microalgae and organic matter from adjacent habitats were important to fish over mudflats.     

Feeding ecology of granivorous carabid larvae: a stable isotope analysis

Although most carabids are primarily carnivorous, some carabid species are omnivorous, with mainly granivorous feeding habits during the larval and/or adult stages (granivorous carabids). This feeding habit has been established based on laboratory and field experiments; however, our knowledge of the feeding ecology of these beetles in the field is limited owing to the lack of an appropriate methodology. In this study, we tested the utility of stable isotope analysis in investigations of the feeding ecology of granivorous carabids in the field, using two closely related syntopic species, Amara chalcites and Amara congrua. We addressed two issues concerning the feeding ecology of granivorous carabids: food niche differentiation between related syntopic species during the larval stage and the effect on adult body size of supplementing seeds with an animal diet during the larval stage. To investigate larval feeding habits, we analysed newly emerged adults, most somatic tissues of which are considered of larval origin. In the two populations examined, both δ¹⁵N and δ¹³C were significantly higher in A. chalcites than A. congrua, suggesting that the two species differentiate food niches, with A. chalcites larvae being more carnivorous than A. congrua larvae. The two isotope ratios of A. chalcites samples from one locality were positively correlated with body size, suggesting that more carnivorous larvae become larger adults. However, this relationship was not detected in other species/locality groups. Thus, our results were inconclusive on the issue of diet supplementation. Nevertheless, overall, these results are comparable with those of previous laboratory‐rearing experiments and demonstrate the potential utility of stable isotope analysis in field studies on the feeding ecology of granivorous carabids.     

Insights into fish host-parasite trophic relationships revealed by stable isotope analysis

Trophic relationships between 10 species of fish host and their associated nematode, cestode, and copepod parasites were investigated using stable isotopes of carbon and nitrogen. Nematodes and cestodes were consistently depleted in 15N with respect to their host, and such fractionation patterns are unlike those conventionally observed between consumers and their diets. Species of copepod parasite were sometimes depleted and sometimes enriched in 15N with respect to fish hosts, and this confirms earlier reports that the nature and magnitude of ectoparasite-host fractionations can vary. Significant differences in delta15N and delta13C were observed among fish tissues, and the isotopic signature of parasites did not always closely correspond to that of the tissue with which the parasite was found most closely associated, or on which the parasite was thought to be feeding. Several possible explanations are considered for such discrepancies, including selective feeding on specific amino acids or lipids, migration of the parasite among different fish tissues, changes in the metabolism of the parasite associated with life history and migration between different host animals.     

A stable isotope technique for investigating lactate metabolism in humans

A stable isotope tracer method has been developed for studying lactate metabolism in humans. The method uses lactic acid triple labeled with 13C as the tracer. The stable isotope is infused to attain a level of approximately 1.5% of that of the circulating unlabeled lactate. Following the isolation of lactic acid from the blood, the percentage of triple labeled (13C)lactate is measured using gas chromatography mas spectrometry. We compared this method with tracer methodology using [14C]lactate and found comparable results.     

Trophic relationships in a tropical stream food web assessed by stable isotope analysis

1. Stable isotope analysis, coupled with dietary data from the literature, was used to investigate trophic patterns of freshwater fauna in a tropical stream food web (Guadeloupe, French West Indies).
2. Primary producers (biofilm, algae and plant detritus of terrestrial origin) showed distinct δ¹³C signatures, which allowed for a powerful discrimination of carbon sources. Both autochthonous (¹³C-enriched signatures) and allochthonous (¹³C-depleted signatures) resources enter the food web. The migrating behaviour of fishes and shrimps between marine and freshwater during their life cycles can be followed by carbon isotopes. Here, shrimp δ¹³C signatures were shown to shift from −16‰ (for juveniles under marine influence) to −24.7‰ (for adults in freshwater habitats). For resident species, δ¹³C values partly reflected the species' habitat preferences along the river continuum : species living in river mouths were ¹³C-enriched in comparison with those collected upstream.
3. Nitrogen isotopic ratios were also discriminating and defined three main trophic guilds among consumers. The δ¹⁵N values of herbivores/detritivores were 5.0–8.4‰, omnivores 8.8–10.2‰ and carnivores 11–12.7‰.
4. Mixing model equations were employed to calculate the possible range of contribution made by respective food sources to the diet of each species. The results revealed the importance of omnivorous species and the dependence of riverine biota on terrestrial subsidies, such as leaf detritus and fruits. Finally, the abundance of shrimps and their feeding habits placed in relief their key role in tropical freshwater food webs. Isotopic analysis provides a useful tool for assessing animal feeding patterns.     

Trophic partitioning in tropical rain forest birds: insights from stable isotope analysis

Bird communities reach their highest taxonomic and trophic diversity in tropical rain forest, but the use of different foraging strategies to meet food requirements in such competitive environments is poorly understood. Conventional dietary analyses are poorly suited to investigate dietary patterns in complex systems. We used stable carbon (¹³C/¹²C) and nitrogen (¹⁵N/¹⁴N) isotope analysis of whole blood to examine avian trophic patterns and sources of diet in the tropical rain forest of Los Tuxtlas, Veracruz, Mexico. We used stable nitrogen isotope analysis to delineate trophic levels, and stable carbon isotope analysis to distinguish the relative contribution of C-3 and CAM/C-4 ultimate sources of proteins to diets. There was large inter- and intraspecific variation in whole blood ¹³C and ¹⁵N values in 23 species of birds. Stable nitrogen isotope analysis separated birds into several trophic levels, including species that obtained their dietary protein mostly from plants, insects or a combination of both food sources. Stable carbon isotope analysis showed that most birds fed on C3-based foods but Stub-tailed Spadebills (Platyrinchus cancrominus) included C-3- and C-4/CAM-specialist individuals. Our analyses provided insights into the nutritional contribution of plant and animal sources of protein and distinguish their photosynthetic origin over relatively long average time periods.     

Documenting the diet in ancient human populations through stable isotope analysis of hair

Fundamental to the understanding of human history is the ability to make interpretations based on artefacts and other remains which are used to gather information about an ancient population. Sequestered in the organic matrices of these remains can be information, for example, concerning incidence of disease, genetic defects and diet. Stable isotopic compositions, especially those made on isolates of collagen from bones, have been used to help suggest principal dietary components. A significant problem in the use of collagen is its long-term stability, and the possibility of isotopic alteration during early diagenesis, or through contaminating condensation reactions. In this study, we suggest that a commonly overlooked material, human hair, may represent an ideal material to be used in addressing human diets of ancient civilizations. Through the analysis of the amino-acid composition of modern hair, as well as samples that were subjected to radiation (thus simulating ageing of the hair) and hair from humans that is up to 5200 years old, we have observed little in the way of chemical change. The principal amino acids observed in all of these samples are essentially identical in relative abundances and content. Dominating the compositions are serine, glutamic acid, threonine, glycine and leucine, respectively accounting for approximately 15%, 17%, 10%, 8% and 8% of the total hydrolysable amino acids. Even minor components (for example, alanine, valine, isoleucine) show similar constancy between the samples of different ages. This constancy clearly indicates minimal alteration of the amino-acid composition of the hair. Further, it would indicate that hair is well preserved and is amenable to isotopic analysis as a tool for distinguishing sources of nutrition. Based on this observation, we have isotopically characterized modern individuals for whom the diet has been documented. Both stable nitrogen and carbon isotope compositions were assessed, and together provide an indication of trophic status, and principal type (C3 or C4) of vegetation consumed. True vegans have nitrogen isotope compositions of about 7/1000 whereas humans consuming larger amounts of meat, eggs, or milk are more enriched in the heavy nitrogen isotope. We have also analysed large cross-sections of modern humans from North America and Europe to provide an indication of the variability seen in a population (the supermarket diet). There is a wide diversity in both carbon and nitrogen isotope values based at least partially on the levels of seafood, corn-fed beef and grains in the diets. Following analysis of the ancient hair, we have observed similar trends in certain ancient populations. For example, the Coptics of Egypt (1000 BP) and Chinchorro of Chile (5000-800 BP) have diets of similar diversity to those observed in the modern group but were isotopically influenced by local nutritional sources. In other ancient hair (Egyptian Late Middle Kingdom mummies, ca. 4000 BP), we have observed a much more uniform isotopic signature, indicating a more constant diet. We have also recognized a primary vegetarian component in the diet of the Neolithic Ice Man of the Oetztaler Alps (5200 BP). In certain cases, it appears that sulphur isotopes may help to further constrain dietary interpretations, owing to the good preservation and sulphur content of hair. It appears that analysis of the often-overlooked hair in archaeological sites may represent a significant new approach for understanding ancient human communities.     

Revolution in food web analysis and trophic ecology: diet analysis by DNA and stable isotope analysis

Characterization of energy flow in ecosystems is one of the primary goals of ecology, and the analysis of trophic interactions and food web dynamics is key to quantifying energy flow. Predator‐prey interactions define the majority of trophic interactions and food web dynamics, and visual analysis of stomach, gut or fecal content composition is the technique traditionally used to quantify predator‐prey interactions. Unfortunately such techniques may be biased and inaccurate due to variation in digestion rates ( Sheppard & Hardwood 2005 ); however, those limitations can be largely overcome with new technology. In the last 20 years, the use of molecular genetic techniques in ecology has exploded ( King et al. 2008 ). The growing availability of molecular genetic methods and data has fostered the use of PCR‐based techniques to accurately distinguish and identify prey items in stomach, gut and fecal samples. In this month’s issue of Molecular Ecology Resources, Corse et al. (2010) describe and apply a new approach to quantifying predator‐prey relationships using an ecosystem‐level genetic characterization of available and consumed prey in European freshwater habitats ( Fig. 1a ). In this issue of Molecular Ecology, Hardy et al. (2010) marry the molecular genetic analysis of prey with a stable isotope (SI) analysis of trophic interactions in an Australian reservoir community ( Fig. 1b ). Both papers demonstrate novel and innovative approaches to an old problem – how do we effectively explore food webs and energy movement in ecosystems?

Figure 1 Open in figure viewer PowerPoint The aquatic habitats used for two studies of diet and trophic interactions that employed molecular genetic and stable isotope analyses. Panel a: Example of Rhone basin habitat (France) where fish diet was determined using PCR to classify prey to a series of ecological clades (photo by Emmanuel Corse). Panel b: A weir pool on the lower Murray River (Australia) where food web and prey use was evaluated using a combination of advanced molecular genetic and stable isotope analyses (photo credit: CSIRO).     

A stable isotope assay for phenprocoumon and its metabolites

A gas chromatographic/mass spectrometric assay for quantifying phenprocoumon and its 4'-, 6-, 7- and 8-hydroxy metabolites in microsomal preparations is described. This assay which uses deuterium-labeled analogs of the phenprocoumon metabolites as internal standards has a lower limit of quantitation of 20 ng ml-1. Diazomethane is used to derivatize both metabolites and parent compound yielding along with the expected 4-methoxy derivative a minor amount of the 2-methoxychromone. Resolution of the methylated metabolites is accomplished by capillary gas chromatography.     

LC/MS analysis of NAD biosynthesis using stable isotope pyridine precursors

A liquid chromatographic-electrospray ionization ion trap mass spectrometry (LC/MS) method has been developed to measure the biosynthetic incorporation of specific precursors into NAD. The stable isotope-labeled precursors tryptophan, quinolinic acid, nicotinic acid, and nicotinamide were added to the media of human liver tumor cells (SK-HEP) grown in culture. The cells were harvested, the NAD was extracted, and the ratio of labeled to unlabeled NAD was measured using the newly developed LC/MS assay. The quantity of NAD formed from each precursor relative to an internal standard (fully labeled 13C, 15N-labeled NAD prepared from baker's yeast) was measured. The detection limit (signal-to-noise ratio 5:1) of the LC/MS method was 37 fmol (25 pg) of NAD and was linear from 20.0 ng to 25 pg. All reported NAD levels were normalized relative to cellular protein measurements. At 50 microM precursor concentrations, nicotinamide was the dominant precursor and NAD levels in the cell rose well above normal levels. Other precursors were minimally incorporated. The same methods were applied to NAD biosynthesized by macrophages derived from peripheral blood monocytes. However, the NAD concentration in macrophages was about 5% of that in SK-HEP cells and the incorporation of stable isotope-labeled substrates remained below measurable levels.     

Studies on accuracy of trichothecene multitoxin analysis using stable isotope dilution assays

Critical parameters in mycotoxin analysis were examined by using stable isotope-labelled tricho-thecenes. Sample weight was downsized to 1 g without loosing precision when sufficiently homogenized samples were taken for analysis. Complete extraction of trichothecenes could be achieved with a solvent mixture of acetonitrile+water (84+16; v+v) even without the use of stable isotope labelled standards. However, in particular for the analysis of deoxynivalenol the absolute amount of water in the solvent volume used for extraction appeared critical. Depending on the matrix a low water amount resulted in too low quantitative values when no stable isotope-labelled standards are applied to correct for incomplete extraction. In this case the used extraction volume had to be at least 10 ml for 1 g sample when acetonitrile + water (84+16; v+v) was used as extraction solvent. Losses during sample preparation using two different clean-up columns were not observed. On the contrary, matrix suppression in the ESI-interface of the LC-MS equipment was found to be a serious problem. Depending on the matrix, the latter effect resulted in considerably lower values for trichothecenes when no stable isotope-labelled standards were used to counterbalance this suppression. Presented at the 29th Mykotoxin-Workshop, Fellbach, Germany, May 14–16, 2007