Carbon source accounting for fish using combined DNA and stable isotope analyses in a regulated lowland river weir pool

Coralline barrens and benthic mega-invertebrates: An intimate connection

Despite considerable progress in understanding the transition from algal forests to coralline barrens, knowledge of coralline barren ecosystems in terms of community composition and functioning is still sparse and important gaps remain to be filled. Using a barren/forest patch system, we tested the hypothesis that the presence of coralline barren enhances the abundance and diversity of benthic mega-invertebrates. We also analysed trophic functional diversity through isotopic analyses of δ13C and δ15N. The distribution of benthic mega-invertebrates biomass differed markedly between coralline barren and algal forest, being more abundant and diverse in the barren state. Isotopic diversity metrics of the benthic mega-invertebrates assemblage indicated comparable trophic structure between the two states, although higher isotopic uniqueness in coralline barren was determined by sea urchins, especially A. lixula, and carnivorous starfish. We showed that in a patchy coralline barren/algal forest system, a more diversified benthic mega-invertebrates assemblage in the barren caused limited trophodynamic changes. This was possibly determined by the behaviour of some trophic groups such as filter feeders, deposit feeders and omnivores. Finally, our results evidence the close association between coralline barrens and benthic mega-invertebrates, contradicting the common view of coralline barrens as depauperate habitats with low diversity and productivity.

Changes in invertebrate food web structure between high- and low-productivity environments are driven by intermediate but not top-predator diet shifts

Predator-prey interactions shape ecosystem stability and are influenced by changes in ecosystem productivity. However, because multiple biotic and abiotic drivers shape the trophic responses of predators to productivity, we often observe patterns, but not mechanisms, by which productivity drives food web structure. One way to capture mechanisms shaping trophic responses is to quantify trophic interactions among multiple trophic groups and by using complementary metrics of trophic ecology. In this study, we combine two diet-tracing methods: diet DNA and stable isotopes, for two trophic groups (top predators and intermediate predators) in both low- and high-productivity habitats to elucidate where in the food chain trophic structure shifts in response to changes in underlying ecosystem productivity. We demonstrate that while top predators show increases in isotopic trophic position (δ15N) with productivity, neither their isotopic niche size nor their DNA diet composition changes. Conversely, intermediate predators show clear turnover in DNA diet composition towards a more predatory prey base in high-productivity habitats. Taking this multi-trophic approach highlights how predator identity shapes responses in predator-prey interactions across environments with different underlying productivity, building predictive power for understanding the outcomes of ongoing anthropogenic change.

Omics-based ecosurveillance uncovers the influence of estuarine macrophytes on sediment microbial function and metabolic redundancy in a tropical ecosystem

Vertical zonation within estuarine ecosystems can strongly influence microbial diversity and function by regulating competition, predation, and environmental stability. The degree to which microbial communities exhibit horizontal patterns through an estuary has received comparatively less attention. Here, we take a multi-omics ecosurveillance approach to study environmental gradients created by the transition between dominant vegetation types along a near pristine tropical river system (Wenlock River, Far North Queensland, Australia). The study sites included intertidal mudflats fringed by saltmarsh, mangrove or mixed soft substrata habitats. Collected sediments were analyzed for eukaryotes and prokaryotes using small sub-unit (SSU) rRNA gene amplicons to profile the relative taxonomic composition. Central carbon metabolism metabolites and other associated organic polar metabolites were analyzed using established metabolomics-based approaches, coupled with total heavy metals analysis. Eukaryotic taxonomic information was found to be more informative of habitat type. Bacterial taxonomy and community composition also showed habitat-specificity, with phyla Proteobacteria and Cyanobacteria strongly linked to mangroves and saltmarshes, respectively. In contrast, metabolite profiling was critical for understanding the biochemical pathways and expressed functional outputs in these systems that were tied to predicted microbial gene function (16S rRNA). A high degree of metabolic redundancy was observed in the bacterial communities, with the metabolomics data suggesting varying degrees of metabolic criticality based on habitat type. The predicted functions of the bacterial taxa combined with annotated metabolites accounted for the conservative perspective of microbial community redundancy against the putative metabolic pathway impacts in the metabolomics data. Coupling these data demonstrates that habitat-mediated estuarine gradients drive patterns of community diversity and metabolic function and highlights the real redundancy potential of habitat microbiomes. This information is useful as a point of comparison for these sensitive ecosystems and provides a framework for identifying potentially vulnerable or at-risk systems before they are significantly degraded.

Characterizing the spatial distributions of soil biota at a legacy base metal mine using environmental DNA

Characterizing the distribution of biota in response to contaminants is a critical element of site risk assessments. In this study we investigated the spatial distributions of biota and soil chemistry data in surface soil from Sunny Corner, a legacy base metal sulfide mine, Australia. Our results showed that copper (Cu), zinc (Zn), arsenic (As) and lead (Pb) in the surface soil exceeded Australian national soil quality guidelines and posed risks to the environment. Environmental (e)DNA metabarcoding of prokaryote and eukaryote composition confirmed the suggestion of environmental risk posed by these elements collectively explaining 72.9 % and 60.5 % of the total variation in the composition of soil prokaryotes and eukaryotes, respectively. Prokaryotic taxa from the phyla Gemmatimonadetes, Verrucomicrobia and Deinococcus-Thermus showed similar spatial patterns to As and Pb, and were positively correlated. Eukaryotic taxa from the phylum Chlorophyta had similar positive correlations with As and Pb in the soil. In contrast, Amoebozoa and Cercozoa, were sensitive to metals and metalloids, having higher relative abundances in soils with lower concentrations of contaminants. Our study shows that metabarcoding is a promising ecological approach for rapid, large scale assessment of contaminated and potentially impacted sites.

Impact assessment of ephemeral discharge of contamination downstream of two legacy base metal mines using environmental DNA

Mining and processing metalliferous ores can degrade the environment well beyond the footprint of the mine, particularly where on-site containment and post-mining remediation has been insufficient to prevent releases of solid and aqueous mine wastes. In this study, we investigated the potential of sediment and water chemistry coupled with environmental (e)DNA metabarcoding to evaluate discrete and cumulative ecological impacts of two legacy base metal (copper (Cu), zinc (Zn), lead (Pb)) mines (Peelwood and Cordillera) which discharge metals via ephemeral tributaries into perennial Peelwood Creek. Although the two mine streams exceeded Australian guidelines for sediment and freshwater quality for Cu, Zn and Pb, Peelwood Creek had relatively low sediment and water metal concentrations, suggesting a low potential for environmental toxicity. Although sediment and water chemistry defined the extent of biological impacts, metabarcoding showed that Peelwood and Cordillera mines had discrete impacts and Peelwood mine was the main source of contamination of Peelwood Creek. Metabarcoding showed that prokaryotes can be good indicators of metal contamination whereas eukaryotes did not reflect contamination impacts in Peelwood Creek. Metabarcoding results showed that benthic communities downstream of Cordillera mine were less impacted than those below Peelwood mine, suggesting that Peelwood mine should be considered for further remediation.

Application of environmental DNA for assessment of contamination downstream of a legacy base metal mine

Acid Rock Drainage (ARD) from legacy mines can negatively impact the biota in sediments and waters for tens of kilometers downstream. Here we used environmental (e)DNA metabarcoding to assess the impacts of metal contaminants on biota in sediment and water downstream of a legacy base metal sulfide mine in southeastern Australia, as exemplar of similar mines elsewhere. Concentrations of metals in water were below Australian water quality guideline values at 20 km downstream for copper (Cu), 40 km downstream for zinc (Zn) and 10 km downstream for lead (Pb). Sediment metal concentrations were below national guideline concentrations at 10 km downstream for Cu, 60 km downstream for Zn and 20 km downstream for Pb. In contrast, metabarcoding showed that biological communities from sediment samples at 10 km and 20 km downstream were similar to sites close to the mine and thus indicative of being impacted, despite metal concentrations being relatively low. As we illustrate, when combined with sediment and water chemistry, metabarcoding can provide more ecological robust perspective on the downstream effects of legacy mines, capturing the sensitivities of a diverse range of organisms.

Metabarcoding Reveals Changes in Benthic Eukaryote and Prokaryote Community Composition along a Tropical Marine Sediment Nickel Gradient

The Southeast Asia and Melanesia region has extensive nickel (Ni)-rich lateritic regoliths formed from the tropical weathering of ultramafic rocks. As the global demand for Ni continues to rise, these lateritic regoliths are increasingly being exploited for their economic benefit. Mining of these regoliths contributes to the enrichment of coastal sediments in trace metals, especially Ni. The present study used high-throughput sequencing (metabarcoding) to determine changes in eukaryote (18s v7 recombinant DNA [rDNA] and diatom-specific subregion of the 18s v4 rDNA) and prokaryote (16s v4 rDNA) community compositions along a sediment Ni concentration gradient offshore from a large lateritized ultramafic regolith in New Caledonia (Vavouto Bay). Significant changes in the eukaryote, diatom, and prokaryote community compositions were found along the Ni concentration gradient. These changes correlated most with the dilute-acid extractable concentration of Ni in the sediments, which explained 26, 23, and 19% of the variation for eukaryote, diatom, and prokaryote community compositions, respectively. Univariate analyses showed that there was no consistent change in indices of biodiversity, evenness, or richness. Diatom richness and diversity did, however, decrease as sediment acid extractable-Ni concentrations increased. Threshold indicator taxa analysis was conducted separately for each of the 3 targeted genes to detect changes in taxa whose occurrences decreased or increased along the acid extractable-Ni concentration gradient. Based on these data, 46 mg acid extractable-Ni/kg was determined as a threshold value where sensitive species began to disappear. In the case of the estuarine sediments offshore from lateritized ultramafic regolith in New Caledonia, this is recommended as an interim threshold value until further lines of evidence can contribute to a region-specific Ni sediment quality guideline value. Environ Toxicol Chem 2021;40:1894-1907. © 2021 SETAC.

Fish as predators and prey: DNA-based assessment of their role in food webs

Fish are both consumers and prey, and as such part of a dynamic trophic network. Measuring how they are trophically linked, both directly and indirectly, to other species is vital to comprehend the mechanisms driving alterations in fish communities in space and time. Moreover, this knowledge also helps to understand how fish communities respond to environmental change and delivers important information for implementing management of fish stocks. DNA-based methods have significantly widened our ability to assess trophic interactions in both marine and freshwater systems and they possess a range of advantages over other approaches in diet analysis. In this review we provide an overview of different DNA-based methods that have been used to assess trophic interactions of fish as consumers and prey. We consider the practicalities and limitations, and emphasize critical aspects when analysing molecular derived trophic data. We exemplify how molecular techniques have been employed to unravel food web interactions involving fish as consumers and prey. In addition to the exciting opportunities DNA-based approaches offer, we identify current challenges and future prospects for assessing fish food webs where DNA-based approaches will play an important role.

Individual dietary specialization reduces intraspecific competition, rather than feeding activity, in black amur bream (Megalobrama terminalis)

Individual specialization and high plasticity in feeding activity are common in natural populations. However, the role of these two in intraspecific competition is unclear. In this study, the rhythm of feeding activity, dietary composition, niche width, niche overlap, and individual specialization was explored in four different size groups of black amur bream (Megalobrama terminalis), using microscopic identification of foregut contents and stable isotope analysis (δ¹³C and δ¹⁵N) of dorsal muscle. Both methods observed ontogenetic shifts in dietary preference and individual specializations, and revealed that the total niche width of large individuals was greater than small individuals. Mixed linear models indicated that feeding activity was significantly influenced by time (p < 0.0001), and no significant changes among size groups was evident (p = 0.244). Niche overlaps revealed that there was intensive diet competition between different size groups of black amur bream. Individual specialization in small juveniles was likely to be stronger than sub-adult and adult groups. Pearson’s correlation analysis revealed that the individual specialization was positively correlated with mean diet similarity within a group. The results indicated that intraspecific competition is reduced mainly by individual dietary specialization, rather than shift in feeding activity.

Integration of palaeo-and-modern food webs reveal slow changes in a river floodplain wetland ecosystem

Large rivers, including the Murray River system in southeast Australia, are disturbed by many activities. The arrival of European settlers to Australia by the mid-1800s transformed many floodplain wetlands of the lower Murray River system. River impoundment and flow regulation in the late 1800s and, from the 1930s, resulted in species invasion, and elevated nutrient concentrations causing widespread eutrophication. An integrated palaeoecology, and palaeo-and-modern food web approach, incorporating mixing models, was undertaken to reveal changes in a regulated wetland (i.e. Kings Billabong). The lack of preserved sediment suggests the wetland was naturally intermittent before 1890. After this time, when used as a water retention basin, the wetland experienced net sediment accumulation. Subfossil cladocerans, and δ¹³C of Daphnia, chironomid, and bulk sediment, all reflected an early productive, likely clear water state and shifts in trophic state following river regulation in the 1930s. Food web mixing models, based on δ¹³C and δ¹⁵N in subfossil and modern Daphnia, fish, and submerged and emergent macrophytes, also indicated a shift in the trophic relationships between fish and Daphnia. By the 1970s, a new state was established but a further significant alteration of nitrogen and carbon sources, and trophic interactions, continued through to the early 2000s. A possible switch from Daphnia as a prey of Australian Smelt could have modified the food web of the wetland by c. 2006. The timing of this change corresponded to the expansion of emergent macrophytes possibly due to landscape level disruptions. The evidence of these changes suggests a need for a broader understanding of the evolution of wetlands for the management of floodplains in the region.

Macrofaunal control of microbial community structure in continental margin sediments

Through a process called "bioturbation," burrowing macrofauna have altered the seafloor habitat and modified global carbon cycling since the Cambrian. However, the impact of macrofauna on the community structure of microorganisms is poorly understood. Here, we show that microbial communities across bioturbated, but geochemically and sedimentologically divergent, continental margin sites are highly similar but differ clearly from those in nonbioturbated surface and underlying subsurface sediments. Solid- and solute-phase geochemical analyses combined with modeled bioturbation activities reveal that dissolved O₂ introduction by burrow ventilation is the major driver of archaeal community structure. By contrast, solid-phase reworking, which regulates the distribution of fresh, algal organic matter, is the main control of bacterial community structure. In nonbioturbated surface sediments and in subsurface sediments, bacterial and archaeal communities are more divergent between locations and appear mainly driven by site-specific differences in organic carbon sources.

The effect of dissolved nickel and copper on the adult coral Acropora muricata and its microbiome

The potential impacts of mining activities on tropical coastal ecosystems are poorly understood. In particular, limited information is available on the effects of metals on scleractinian corals which are foundation species that form vital structural habitats supporting other biota. This study investigated the effects of dissolved nickel and copper on the coral Acropora muricata and its associated microbiota. Corals collected from the Great Barrier Reef were exposed to dissolved nickel (45, 90, 470, 900 and 9050 μg Ni/L) or copper (4, 11, 32 and 65 μg Cu/L) in flow through chambers at the National Sea Simulator, Townsville, Qld, Australia. After a 96-h exposure DNA metabarcoding (16S rDNA and 18S rDNA) was undertaken on all samples to detect changes in the structure of the coral microbiome. The controls remained healthy throughout the study period. After 36 h, bleaching was only observed in corals exposed to 32 and 65 μg Cu/L and very high nickel concentrations (9050 μg Ni/L). At 96 h, significant discolouration of corals was only observed in 470 and 900 μg Ni/L treatments, the highest concentrations tested. While high concentrations of nickel caused bleaching, no changes in the composition of their microbiome communities were observed. In contrast, exposure to copper not only resulted in bleaching, but altered the composition of both the eukaryote and bacterial communities of the coral's microbiomes. Our findings showed that these effects were only evident at relatively high concentrations of nickel and copper, reflecting concentrations observed only in extremely polluted environments. Elevated metal concentrations have the capacity to alter the microbiomes which are inherently linked to coral health.

Jellyfish on the menu: mtDNA assay reveals scyphozoan predation in the Irish Sea

Localized outbreaks of jellyfish, known as blooms, cause a variety of adverse ecological and economic effects. However, fundamental aspects of their ecology remain unknown. Notably, there is scant information on the role jellyfish occupy in food webs: in many ecosystems, few or no predators are known. To identify jellyfish consumers in the Irish Sea, we conducted a molecular gut content assessment of 50 potential predators using cnidarian-specific mtDNA primers and sequencing. We show that jellyfish predation may be more common than previously acknowledged: uncovering many previously unknown jellyfish predators. A substantial proportion of herring and whiting were found to have consumed jellyfish. Rare ingestion was also detected in a variety of other species. Given the phenology of jellyfish in the region, we suggest that the predation was probably targeting juvenile stages of the jellyfish life cycle.

Laboratory Protocol for Genetic Gut Content Analyses of Aquatic Macroinvertebrates Using Group-specific rDNA Primers

Analyzing food webs is essential for a better understanding of ecosystems. For example, food web interactions can undergo severe changes caused by the invasion of non-indigenous species. However, an exact identification of field predator-prey interactions is difficult in many cases. These analyses are often based on a visual evaluation of gut content or the analysis of stable isotope ratios (δ¹⁵N and δ¹³C). Such methods require comprehensive knowledge about, respectively, morphologic diversity or isotopic signature from individual prey organisms, leading to obstacles in the exact identification of prey organisms. Visual gut content analyses especially underestimate soft bodied prey organisms, because maceration, ingestion and digestion of prey organisms make identification of specific species difficult. Hence, polymerase chain reaction (PCR) based strategies, for example the use of group-specific primer sets, provide a powerful tool for the investigation of food web interactions. Here, we describe detailed protocols to investigate the gut contents of macroinvertebrate consumers from the field using group-specific primer sets for nuclear ribosomal deoxyribonucleic acid (rDNA). DNA can be extracted either from whole specimens (in the case of small taxa) or out of gut contents of specimens collected in the field. Presence and functional efficiency of the DNA templates need to be confirmed directly from the tested individual using universal primer sets targeting the respective subunit of DNA. We also demonstrate that consumed prey can be determined further down to species level via PCR with unmodified group-specific primers combined with subsequent single strand conformation polymorphism (SSCP) analyses using polyacrylamide gels. Furthermore, we show that the use of different fluorescent dyes as labels enables parallel screening for DNA fragments of different prey groups from multiple gut content samples via automated fragment analysis.

Diet analysis of small mammal pests: A comparison of molecular and microhistological methods

Knowledge of what pest species are eating is important to determine their impact on stored food products and to plan management strategies accordingly. In this study, we investigated the food habits of 2 rodents, Rattus rattus (ship rat) and Mus musculus castaneus (house mouse) as well as an insectivore, Suncus murinus (shrew), present in human dwellings. Both a microhistological approach and a DNA barcoding approach were used in the present study. Following DNA extraction, amplification was performed using group-specific primers targeting birds, plants and invertebrates. Resulting polymerase chain reaction products were sequenced and analyzed to identify the different prey species present in the gut contents. The findings from the application of both techniques were in agreement, but the detection of prey type with each technique was different. The DNA barcoding approach gave greater species-level identification when compared to the microhistological method, especially for the invertebrate and avian prey. Overall, with both techniques, 23 prey taxa were identified in the gut contents of the 3 species, including 15 plants, 7 insects and a single bird species. We conclude that with a selection of suitable "barcode genes" and optimization of polymerase chain reaction protocols, DNA barcoding can provide more accurate and faster results. Prey detection from either technique alone can bias the dietary information. Hence, combining prey information of both microhistological analysis and DNA barcoding is recommended to study pest diet, especially if the pest is an omnivore or insectivore species.

Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats

Traditionally, microbial surveys investigating the effect of chronic anthropogenic pressure such as polyaromatic hydrocarbons (PAHs) contaminations consider just the alpha and beta diversity and ignore the interactions among the different taxa forming the microbial community. Here, we investigated the ecological relationships between the three domains of life (i.e., Bacteria, Archaea, and Eukarya) using 454 pyrosequencing on the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon) and the French Atlantic Ocean (Bay of Biscay and English Channel). Our approach provided a robust ecological framework for the partition of the taxa abundance distribution into 859 core Operational taxonomic units (OTUs) and 6629 satellite OTUs. OTUs forming the core microbial community showed the highest sensitivity to changes in environmental and contaminant variations, with salinity, latitude, temperature, particle size distribution, total organic carbon (TOC) and PAH concentrations as main drivers of community assembly. The core communities were dominated by Gammaproteobacteria and Deltaproteobacteria for Bacteria, by Thaumarchaeota, Bathyarchaeota and Thermoplasmata for Archaea and Metazoa and Dinoflagellata for Eukarya. In order to find associations among microorganisms, we generated a co-occurrence network in which PAHs were found to impact significantly the potential predator – prey relationship in one microbial consortium composed of ciliates and Actinobacteria. Comparison of network topological properties between contaminated and non-contaminated samples showed substantial differences in the network structure and indicated a higher vulnerability to environmental perturbations in the contaminated sediments.

Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments

Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta-diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales.

Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries

DNA-derived measurements of biological composition have the potential to produce data covering all of life, and provide a tantalizing proposition for researchers and managers. We used metabarcoding to compare benthic eukaryote composition from five estuaries of varying condition. In contrast to traditional studies, we found biotic richness was greatest in the most disturbed estuary, with this being due to the large volume of extraneous material (i.e. run-off from aquaculture, agriculture and other catchment activities) being deposited in the system. In addition, we found strong correlations between composition and a number of environmental variables, including nutrients, pH and turbidity. A wide range of taxa responded to these environmental gradients, providing new insights into their sensitivities to natural and anthropogenic stressors. Metabarcoding has the capacity to bolster current monitoring techniques, enabling the decisions regarding ecological condition to be based on a more holistic view of biodiversity.

DNA barcoding reveals novel insights into pterygophagy and prey selection in distichodontid fishes (Characiformes: Distichodontidae)

DNA barcoding was used to investigate dietary habits and prey selection in members of the African-endemic family Distichodontidae noteworthy for displaying highly specialized ectoparasitic fin-eating behaviors (pterygophagy). Fin fragments recovered from the stomachs of representatives of three putatively pterygophagous distichodontid genera (Phago, Eugnathichthys, and Ichthyborus) were sequenced for the mitochondrial gene co1. DNA barcodes (co1 sequences) were then used to identify prey items in order to determine whether pterygophagous distichodontids are opportunistic generalists or strict specialists with regard to prey selection and, whether as previously proposed, aggressive mimicry is used as a strategy for successful pterygophagy. Our findings do not support the hypothesis of aggressive mimicry suggesting instead that, despite the possession of highly specialized trophic anatomies, fin-eating distichodontids are opportunistic generalists, preying on fishes from a wide phylogenetic spectrum and to the extent of engaging in cannibalism. This study demonstrates how DNA barcoding can be used to shed light on evolutionary and ecological aspects of highly specialized ectoparasitic fin-eating behaviors by enabling the identification of prey species from small pieces of fins found in fish stomachs.

Sources of variation in small rodent trophic niche: new insights from DNA metabarcoding and stable isotope analysis

Intraspecific competition for food is expected to increase the trophic niche width of consumers, defined here as their diet diversity, but this process has been little studied in herbivores. Population densities of small rodents fluctuate greatly, providing a good study model to evaluate effects of competition on trophic niche. We studied resource use in five arctic small rodent populations of four species combining DNA metabarcoding of stomach contents and stable isotope analysis (SIA). Our results suggest that for small rodents, the most pronounced effect of competition on trophic niche is due to increased use of secondary habitats and to habitat-specific diets, rather than an expansion of trophic niche in primary habitat. DNA metabarcoding and SIA provided complementary information about the composition and temporal variation of herbivore diets. Combing these two approaches requires caution, as the underlying processes causing observed patterns may differ between methodologies due to different spatiotemporal scales.

Searching for the true diet of marine predators: incorporating Bayesian priors into stable isotope mixing models

Reconstructing the diet of top marine predators is of great significance in several key areas of applied ecology, requiring accurate estimation of their true diet. However, from conventional stomach content analysis to recent stable isotope and DNA analyses, no one method is bias or error free. Here, we evaluated the accuracy of recent methods to estimate the actual proportion of a controlled diet fed to a top-predator seabird, the Little penguin (Eudyptula minor). We combined published DNA data of penguins scats with blood plasma δ¹⁵N and δ¹³C values to reconstruct the diet of individual penguins fed experimentally. Mismatch between controlled (true) ingested diet and dietary estimates obtained through the separately use of stable isotope and DNA data suggested some degree of differences in prey assimilation (stable isotope) and digestion rates (DNA analysis). In contrast, combined posterior isotope mixing model with DNA Bayesian priors provided the closest match to the true diet. We provided the first evidence suggesting that the combined use of these complementary techniques may provide better estimates of the actual diet of top marine predators- a powerful tool in applied ecology in the search for the true consumed diet.

Intraguild predation in pioneer predator communities of alpine glacier forelands

Pioneer communities establishing themselves in the barren terrain in front of glacier forelands consist principally of predator species such as carabid beetles and lycosid spiders. The fact that so many different predators can co-inhabit an area with no apparent primary production was initially explained by allochthonous material deposited in these forelands. However, whether these populations can be sustained on allochthonous material alone is questionable and recent studies point towards this assumption to be flawed. Intraguild predation (IGP) might play an important role in these pioneer predator assemblages, especially in the very early successional stages where other prey is scarce. Here, we investigated IGP between the main predator species and their consumption of Collembola, an important autochthonous alternative prey, within a glacier foreland in the Ötztal (Austrian Alps). Multiplex PCR and stable isotope analysis were used to characterize the trophic niches in an early and late pioneer stage over 2 years. Results showed that intraguild prey was consumed by all invertebrate predators, particularly the larger carabid species. Contrary to our initial hypothesis, the DNA detection frequency of IGP prey was not significantly higher in early than in late pioneer stage, which was corroborated by the stable isotope analysis. Collembola were the most frequently detected prey in all of the predators, and the overall prey DNA detection patterns were consistent between years. Our findings show that IGP appears as a constant in these pioneer predator communities and that it remains unaffected by successional changes.

Application of DNA barcoding for identification of freshwater carnivorous fish diets: Is number of prey items dependent on size class for Micropterus salmoides?

Understanding predator–prey interactions is a major challenge in ecological studies. In particular, the accurate identification of prey is a fundamental requirement in elucidating food-web structure. This study took a molecular approach in determining the species identity of consumed prey items of a freshwater carnivorous fish (largemouth bass, Micropterus salmoides), according to their size class. Thirty randomly selected gut samples were categorized into three size classes, based on the total length of the bass. Using the universal primer for the mtDNA cytochrome oxidase I (COI) region, polymerase chain reaction (PCR) amplification was performed on unidentified gut contents and then sequenced after cloning. Two gut samples were completely empty, and DNA materials from 27 of 28 gut samples were successfully amplified by PCR (success rate: 96.4%). Sequence database navigation yielded a total of 308 clones, containing DNA from 26 prey items. They comprised four phyla, including seven classes, 12 orders, and 12 families based on BLAST and BOLD database searches. The results indicate that largemouth bass show selective preferences in prey item consumption as they mature. These results corroborate a hypothesis, presence of ontogenetic diet shift, derived through other methodological approaches. Despite the practical limitations inherent in DNA barcoding analysis, high-resolution (i.e., species level) identification was possible, and the predation patterns of predators of different sizes were identifiable. The utilization of this method is strongly recommended for determining specific predator–prey relationships in complex freshwater ecosystems.

Bias in diet determination: incorporating traditional methods in Bayesian mixing models

There are not “universal methods” to determine diet composition of predators. Most traditional methods are biased because of their reliance on differential digestibility and the recovery of hard items. By relying on assimilated food, stable isotope and Bayesian mixing models (SIMMs) resolve many biases of traditional methods. SIMMs can incorporate prior information (i.e. proportional diet composition) that may improve the precision in the estimated dietary composition. However few studies have assessed the performance of traditional methods and SIMMs with and without informative priors to study the predators’ diets. Here we compare the diet compositions of the South American fur seal and sea lions obtained by scats analysis and by SIMMs-UP (uninformative priors) and assess whether informative priors (SIMMs-IP) from the scat analysis improved the estimated diet composition compared to SIMMs-UP. According to the SIMM-UP, while pelagic species dominated the fur seal’s diet the sea lion’s did not have a clear dominance of any prey. In contrast, SIMM-IP’s diets compositions were dominated by the same preys as in scat analyses. When prior information influenced SIMMs’ estimates, incorporating informative priors improved the precision in the estimated diet composition at the risk of inducing biases in the estimates. If preys isotopic data allow discriminating preys’ contributions to diets, informative priors should lead to more precise but unbiased estimated diet composition. Just as estimates of diet composition obtained from traditional methods are critically interpreted because of their biases, care must be exercised when interpreting diet composition obtained by SIMMs-IP. The best approach to obtain a near-complete view of predators’ diet composition should involve the simultaneous consideration of different sources of partial evidence (traditional methods, SIMM-UP and SIMM-IP) in the light of natural history of the predator species so as to reliably ascertain and weight the information yielded by each method.

Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils

Floodplain ecosystems are characterized by alternating wet and dry phases and periodic inundation defines their ecological character. Climate change, river regulation and the construction of levees have substantially altered natural flooding and drying regimes worldwide with uncertain effects on key biotic groups. In southern Australia, we hypothesized that soil eukaryotic communities in climate change affected areas of a semi-arid floodplain would transition towards comprising mainly dry-soil specialist species with increasing drought severity. Here, we used 18S rRNA amplicon pyrosequencing to measure the eukaryote community composition in soils that had been depleted of water to varying degrees to confirm that reproducible transitional changes occur in eukaryotic biodiversity on this floodplain. Interflood community structures (3 years post-flood) were dominated by persistent rather than either aquatic or dry-specialist organisms. Only 2% of taxa were unique to dry locations by 8 years post-flood, and 10% were restricted to wet locations (inundated a year to 2 weeks post-flood). Almost half (48%) of the total soil biota were detected in both these environments. The discovery of a large suite of organisms able to survive nearly a decade of drought, and up to a year submerged supports the concept of inherent resilience of Australian semi-arid floodplain soil communities under increasing pressure from climatic induced changes in water availability.

Determining the diet of larvae of western rock lobster (Panulirus cygnus) using high-throughput DNA sequencing techniques

The Western Australian rock lobster fishery has been both a highly productive and sustainable fishery. However, a recent dramatic and unexplained decline in post-larval recruitment threatens this sustainability. Our lack of knowledge of key processes in lobster larval ecology, such as their position in the food web, limits our ability to determine what underpins this decline. The present study uses a high-throughput amplicon sequencing approach on DNA obtained from the hepatopancreas of larvae to discover significant prey items. Two short regions of the 18S rRNA gene were amplified under the presence of lobster specific PNA to prevent lobster amplification and to improve prey amplification. In the resulting sequences either little prey was recovered, indicating that the larval gut was empty, or there was a high number of reads originating from multiple zooplankton taxa. The most abundant reads included colonial Radiolaria, Thaliacea, Actinopterygii, Hydrozoa and Sagittoidea, which supports the hypothesis that the larvae feed on multiple groups of mostly transparent gelatinous zooplankton. This hypothesis has prevailed as it has been tentatively inferred from the physiology of larvae, captive feeding trials and co-occurrence in situ. However, these prey have not been observed in the larval gut as traditional microscopic techniques cannot discern between transparent and gelatinous prey items in the gut. High-throughput amplicon sequencing of gut DNA has enabled us to classify these otherwise undetectable prey. The dominance of the colonial radiolarians among the gut contents is intriguing in that this group has been historically difficult to quantify in the water column, which may explain why they have not been connected to larval diet previously. Our results indicate that a PCR based technique is a very successful approach to identify the most abundant taxa in the natural diet of lobster larvae.

Transcriptome analysis of a North American songbird, Melospiza melodia

An effective way to understand the genomics of divergence in non-model organisms is to use the transcriptome to identify genes associated with divergence. We examine the transcriptome of the song sparrow (Melospiza melodia) and contrast it with the avian models zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). We aimed to (i) obtain a functional annotation of a substantial portion of the song sparrow transcriptome; (ii) compare transcript divergence; (iii) efficiently characterize single nucleotide polymorphism/indel markers possibly fixed between song sparrow subspecies; and (iv) identify the most common set of transcripts in birds using the zebra finch as a reference. Using two individuals from each of three populations, whole-body mRNA was normalized and sequenced (110Mb total). The assembly yielded 38 539 contigs [N50 (the length–weighted median) = 482 bp]; 4574 were orthologous to both model genomes and 3680 are functionally annotated. This low-coverage scan of the song sparrow transcriptome revealed 29 982 SNPs/indels, 1402 fixed between populations and subspecies. Referencing zebra finch and chicken, we identified 43 and 5 fast-evolving genes, respectively. We also identified the most common set of transcripts present in birds with respect to zebra finch. This study provides new insight into songbird transcriptomes, and candidate markers identified here may help research in songbirds (oscine Passeriformes), a frequently studied group.

Difficulties barcoding in the dark: the case of crustacean stygofauna from eastern Australia

The eastern Australian aquifers remain mostly unexplored; however, recent surveys suggest that there could be substantial levels of subterranean biodiversity hidden in these aquifers. Groundwater fauna (stygofauna) is often characterised by short-range endemism. Furthermore, high levels of cryptic species, and lack of formal taxonomic descriptions and taxonomic expertise for many of the groups demand innovative approaches for assessing subterranean biodiversity. Here we evaluate the potential of using DNA barcoding as a rapid biodiversity assessment tool for the subterranean groundwater fauna of New South Wales, Australia. We experienced low amplification success using universal and more taxon-specific primers for PCR amplification of the barcoding gene (COI) in a range of crustacean stygofauna. Sequence comparisons of the most commonly used COI universal primers in selected crustacean taxa revealed high levels of variability. Our results suggest that successful amplification of the COI region from crustacean stygofauna is not straightforward using the standard ‘universal’ primers. We propose that the development of a multiprimer (taxon specific) and multigene approach for DNA barcode analyses, using next-generation sequencing methodologies, will help to overcome many of the technical problems reported here and provide a basis for using DNA barcoding for rapid biodiversity assessments of subterranean aquatic ecosystems.

Who is eating what: diet assessment using next generation sequencing

The analysis of food webs and their dynamics facilitates understanding of the mechanistic processes behind community ecology and ecosystem functions. Having accurate techniques for determining dietary ranges and components is critical for this endeavour. While visual analyses and early molecular approaches are highly labour intensive and often lack resolution, recent DNA-based approaches potentially provide more accurate methods for dietary studies. A suite of approaches have been used based on the identification of consumed species by characterization of DNA present in gut or faecal samples. In one approach, a standardized DNA region (DNA barcode) is PCR amplified, amplicons are sequenced and then compared to a reference database for identification. Initially, this involved sequencing clones from PCR products, and studies were limited in scale because of the costs and effort required. The recent development of next generation sequencing (NGS) has made this approach much more powerful, by allowing the direct characterization of dozens of samples with several thousand sequences per PCR product, and has the potential to reveal many consumed species simultaneously (DNA metabarcoding). Continual improvement of NGS technologies, on-going decreases in costs and current massive expansion of reference databases make this approach promising. Here we review the power and pitfalls of NGS diet methods. We present the critical factors to take into account when choosing or designing a suitable barcode. Then, we consider both technical and analytical aspects of NGS diet studies. Finally, we discuss the validation of data accuracy including the viability of producing quantitative data.

Barcoding a quantified food web: crypsis, concepts, ecology and hypotheses

The efficient and effective monitoring of individuals and populations is critically dependent on correct species identification. While this point may seem obvious, identifying the majority of the more than 100 natural enemies involved in the spruce budworm (Choristoneura fumiferana--SBW) food web remains a non-trivial endeavor. Insect parasitoids play a major role in the processes governing the population dynamics of SBW throughout eastern North America. However, these species are at the leading edge of the taxonomic impediment and integrating standardized identification capacity into existing field programs would provide clear benefits. We asked to what extent DNA barcoding the SBW food web would alter our understanding of the diversity and connectence of the food web and the frequency of generalists vs. specialists in different forest habitats. We DNA barcoded over 10% of the insects collected from the SBW food web in three New Brunswick forest plots from 1983 to 1993. For 30% of these specimens, we amplified at least one additional nuclear region. When the nodes of the food web were estimated based on barcode divergences (using molecular operational taxonomic units (MOTU) or phylogenetic diversity (PD)--the food web became much more diverse and connectence was reduced. We tested one measure of food web structure (the "bird feeder effect") and found no difference compared to the morphologically based predictions. Many, but not all, of the presumably polyphagous parasitoids now appear to be morphologically-cryptic host-specialists. To our knowledge, this project is the first to barcode a food web in which interactions have already been well-documented and described in space, time and abundance. It is poised to be a system in which field-based methods permit the identification capacity required by forestry scientists. Food web barcoding provided an effective tool for the accurate identification of all species involved in the cascading effects of future budworm outbreaks. Integrating standardized barcodes within food webs may ultimately change the face of community ecology. This will be most poignantly felt in food webs that have not yet been quantified. Here, more accurate and precise connections will be within the grasp of any researcher for the first time.

Utilization of stomach content DNA to determine diet diversity in piscivorous fishes

The objective of the study was to validate and apply DNA-based approaches to describe fish diets. Laboratory experiments were performed to determine the number of hours after ingestion that DNA could be reliably isolated from stomach content residues, particularly with small prey fishes (c. 1 cm, <0·75 g). Additionally, experiments were conducted at different temperatures to resolve temperature effects on digestion rate and DNA viability. The molecular protocol of cloning and sequencing was then applied to the analysis of stomach contents of wild fishes collected from the western basin of Lake Erie, Canada-U.S.A. The results showed that molecular techniques were more precise than traditional visual inspection and could provide insight into diet preferences for even highly digested prey that have lost all physical characteristics.

Comparing the performance of multiple mitochondrial genes in the analysis of Australian freshwater fishes

In this study, four mitochondrial genes (cytochrome oxidase I, ATPase, cytochrome b and control region) were amplified from most of the fish species found in the fresh waters of south-eastern Queensland, Australia. The performance of these different gene regions was compared in terms of their ability to cluster fish families together in a neighbour-joining tree, both individually by gene and in all combinations. The relative divergence rates of each of these genes were also calculated. The three coding genes (cytochrome oxidase I, ATPase and cytochrome b) recovered similar number of families and had broadly similar divergence rates. ATPase diverged a little more quickly than cytochrome oxidase I and cytochrome b slightly more slowly than cytochrome oxidase I. All two-gene combinations recovered the same number of families. Results from the control region were much more variable, and, although generally possessing more diversity than the other regions, were sometimes less variable.

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?