Rapid molecular detection of invasive species in ballast and harbor water by integrating environmental DNA and light transmission spectroscopy

Invasive species introduced via the ballast water of commercial ships cause enormous environmental and economic damage worldwide. Accurate monitoring for these often microscopic and morphologically indistinguishable species is challenging but critical for mitigating damages. We apply eDNA sampling, which involves the filtering and subsequent DNA extraction of microscopic bits of tissue suspended in water, to ballast and harbor water sampled during a commercial ship's 1400 km voyage through the North American Great Lakes. Using a lab-based gel electrophoresis assay and a rapid, field-ready light transmission spectroscopy (LTS) assay, we test for the presence of two invasive species: quagga (Dreissena bugensis) and zebra (D. polymorpha) mussels. Furthermore, we spiked a set of uninfested ballast and harbor samples with zebra mussel tissue to further test each assay's detection capabilities. In unmanipulated samples, zebra mussel was not detected, while quagga mussel was detected in all samples at a rate of 85% for the gel assay and 100% for the LTS assay. In the spiked experimental samples, both assays detected zebra mussel in 94% of spiked samples and 0% of negative controls. Overall, these results demonstrate that eDNA sampling is effective for monitoring ballast-mediated invasions and that LTS has the potential for rapid, field-based detection.

Use of structured expert judgment to forecast invasions by bighead and silver carp in Lake Erie

Identifying which nonindigenous species will become invasive and forecasting the damage they will cause is difficult and presents a significant problem for natural resource management. Often, the data or resources necessary for ecological risk assessment are incomplete or absent, leaving environmental decision makers ill equipped to effectively manage valuable natural resources. Structured expert judgment (SEJ) is a mathematical and performance-based method of eliciting, weighting, and aggregating expert judgments. In contrast to other methods of eliciting and aggregating expert judgments (where, for example, equal weights may be assigned to experts), SEJ weights each expert on the basis of his or her statistical accuracy and informativeness through performance measurement on a set of calibration variables. We used SEJ to forecast impacts of nonindigenous Asian carp (Hypophthalmichthys spp.) in Lake Erie, where it is believed not to be established. Experts quantified Asian carp biomass, production, and consumption and their impact on 4 fish species if Asian carp were to become established. According to experts, in Lake Erie Asian carp have the potential to achieve biomass levels that are similar to the sum of biomasses for several fishes that are harvested commercially or recreationally. However, the impact of Asian carp on the biomass of these fishes was estimated by experts to be small, relative to long term average biomasses, with little uncertainty. Impacts of Asian carp in tributaries and on recreational activities, water quality, or other species were not addressed. SEJ can be used to quantify key uncertainties of invasion biology and also provide a decision-support tool when the necessary information for natural resource management and policy is not available.

The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol-chloroform-isoamyl alcohol DNA extraction

Current research targeting filtered macrobial environmental DNA (eDNA) often relies upon cold ambient temperatures at various stages, including the transport of water samples from the field to the laboratory and the storage of water and/or filtered samples in the laboratory. This poses practical limitations for field collections in locations where refrigeration and frozen storage is difficult or where samples must be transported long distances for further processing and screening. This study demonstrates the successful preservation of eDNA at room temperature (20 °C) in two lysis buffers, CTAB and Longmire's, over a 2-week period of time. Moreover, the preserved eDNA samples were seamlessly integrated into a phenol-chloroform-isoamyl alcohol (PCI) DNA extraction protocol. The successful application of the eDNA extraction to multiple filter membrane types suggests the methods evaluated here may be broadly applied in future eDNA research. Our results also suggest that for many kinds of studies recently reported on macrobial eDNA, detection probabilities could have been increased, and at a lower cost, by utilizing the Longmire's preservation buffer with a PCI DNA extraction.

Evolution of invasive traits in nonindigenous species: increased survival and faster growth in invasive populations of rusty crayfish (Orconectes rusticus)

The importance of evolution in enhancing the invasiveness of species is not well understood, especially in animals. To evaluate evolution in crayfish invasions, we tested for differences in growth rate, survival, and response to predators between native and invaded range populations of rusty crayfish (Orconectes rusticus). We hypothesized that low conspecific densities during introductions into lakes would select for increased investment in growth and reproduction in invasive populations. We reared crayfish from both ranges in common garden experiments in lakes and mesocosms, the latter in which we also included treatments of predatory fish presence and food quality. In both lake and mesocosm experiments, O. rusticus from invasive populations had significantly faster growth rates and higher survival than individuals from the native range, especially in mesocosms where fish were present. There was no influence of within-range collection location on growth rate. Egg size was similar between ranges and did not affect crayfish growth. Our results, therefore, suggest that growth rate, which previous work has shown contributes to strong community-level impacts of this invasive species, has diverged since O. rusticus was introduced to the invaded range. This result highlights the need to consider evolutionary dynamics in invasive species mitigation strategies.

Out-of-sample validation for structured expert judgment of Asian carp establishment in Lake Erie

Structured expert judgment (SEJ) is used to quantify the uncertainty of nonindigenous fish (bighead carp [Hypophthalmichthys nobilis] and silver carp [H. molitrix]) establishment in Lake Erie. The classical model for structured expert judgment model is applied. Forming a weighted combination (called a decision maker) of experts' distributions, with weights derived from performance on a set of calibration variables from the experts' field, exhibits greater statistical accuracy and greater informativeness than simple averaging with equal weights. New methods of cross validation are applied and suggest that performance characteristics relative to equal weighting could be predicted with a small number (1-2) of calibration variables. The performance-based decision maker is somewhat degraded on out-of-sample prediction, but remained superior to the equal weight decision maker in terms of statistical accuracy and informativeness.

Geographic selection bias of occurrence data influences transferability of invasive Hydrilla verticillata distribution models

Due to socioeconomic differences, the accuracy and extent of reporting on the occurrence of native species differs among countries, which can impact the performance of species distribution models. We assessed the importance of geographical biases in occurrence data on model performance using Hydrilla verticillata as a case study. We used Maxent to predict potential North American distribution of the aquatic invasive macrophyte based upon training data from its native range. We produced a model using all available native range occurrence data, then explored the change in model performance produced by omitting subsets of training data based on political boundaries. We also compared those results with models trained on data from which a random sample of occurrence data was omitted from across the native range. Although most models accurately predicted the occurrence of H. verticillata in North America (AUC > 0.7600), data omissions influenced model predictions. Omitting data based on political boundaries resulted in larger shifts in model accuracy than omitting randomly selected occurrence data. For well-documented species like H. verticillata, missing records from single countries or ecoregions may minimally influence model predictions, but for species with fewer documented occurrences or poorly understood ranges, geographic biases could misguide predictions. Regardless of focal species, we recommend that future species distribution modeling efforts begin with a reflection on potential spatial biases of available occurrence data. Improved biodiversity surveillance and reporting will provide benefit not only in invaded ranges but also within under-reported and unexplored native ranges.

Environmental conditions influence eDNA persistence in aquatic systems

Environmental DNA (eDNA) surveillance holds great promise for improving species conservation and management. However, few studies have investigated eDNA dynamics under natural conditions, and interpretations of eDNA surveillance results are clouded by uncertainties about eDNA degradation. We conducted a literature review to assess current understanding of eDNA degradation in aquatic systems and an experiment exploring how environmental conditions can influence eDNA degradation. Previous studies have reported macrobial eDNA persistence ranging from less than 1 day to over 2 weeks, with no attempts to quantify factors affecting degradation. Using a SYBR Green quantitative PCR assay to observe Common Carp ( Cyprinus carpio ) eDNA degradation in laboratory mesocosms, our rate of Common Carp eDNA detection decreased over time. Common Carp eDNA concentration followed a pattern of exponential decay, and observed decay rates exceeded previously published values for aquatic macrobial eDNA. Contrary to our expectations, eDNA degradation rate declined as biochemical oxygen demand, chlorophyll, and total eDNA (i.e., from any organism) concentration increased. Our results help explain the widely divergent, previously published estimates for eDNA degradation. Measurements of local environmental conditions, consideration of environmental influence on eDNA detection, and quantification of local eDNA degradation rates will help interpret future eDNA surveillance results.

Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments

In many North American rivers, populations of multiple species of non-native cyprinid fishes are present, including black carp (Mylpharyngodon piceus), grass carp (Ctenopharyngodon idella), bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), common carp (Cyprinus carpio), and goldfish (Carassius auratus). All six of these species are found in the Mississippi River basin and tracking their invasion has proven difficult, particularly where abundance is low. Knowledge of the location of the invasion front is valuable to natural resource managers because future ecological and economic damages can be most effectively prevented when populations are low. To test the accuracy of environmental DNA (eDNA) as an early indicator of species occurrence and relative abundance, we applied eDNA technology to the six non-native cyprinid species putatively present in a 2.6 river mile stretch of the Chicago (IL, USA) canal system that was subsequently treated with piscicide. The proportion of water samples yielding positive detections increased with relative abundance of the six species, as indicated by the number of carcasses recovered after poisoning. New markers for black carp, grass carp, and a common carp/goldfish are reported and details of the marker testing to ensure specificity are provided.

Global Introductions of Crayfishes: Evaluating the Impact of Species Invasions on Ecosystem Services

Impacts of nonindigenous crayfishes on ecosystem services exemplify the mixture of positive and negative effects of intentionally introduced species. Global introductions for aquaculture and ornamental purposes have begun to homogenize naturally disjunct global distributions of crayfish families. Negative impacts include the loss of provisioning (e.g., reductions in edible native species, reproductive interference or hybridization with native crayfishes), regulatory (e.g., lethal disease spread, increased costs to agriculture and water management), supporting (e.g., large changes in ecological communities), and cultural (e.g., loss of festivals celebrating native crayfish) services. Where quantification of impacts exists (e.g., Procambarus clarkii and Pacifastacus leniusculus in Europe), regulations now prohibit introduction and spread of crayfishes, indicating that losses of ecosystem services have outweighed gains. Recent research advances such as predicting invasiveness, predicting spread, improved detection and control, and bioeconomic analysis to increase cost-effectiveness of management could be employed to reduce future losses of ecosystem services.

DNA-based species detection capabilities using laser transmission spectroscopy

Early detection of invasive species is critical for effective biocontrol to mitigate potential ecological and economic damage. Laser transmission spectroscopy (LTS) is a powerful solution offering real-time, DNA-based species detection in the field. LTS can measure the size, shape and number of nanoparticles in a solution and was used here to detect size shifts resulting from hybridization of the polymerase chain reaction product to nanoparticles functionalized with species-specific oligonucleotide probes or with the species-specific oligonucleotide probes alone. We carried out a series of DNA detection experiments using the invasive freshwater quagga mussel (Dreissena bugensis) to evaluate the capability of the LTS platform for invasive species detection. Specifically, we tested LTS sensitivity to (i) DNA concentrations of a single target species, (ii) the presence of a target species within a mixed sample of other closely related species, (iii) species-specific functionalized nanoparticles versus species-specific oligonucleotide probes alone, and (iv) amplified DNA fragments versus unamplified genomic DNA. We demonstrate that LTS is a highly sensitive technique for rapid target species detection, with detection limits in the picomolar range, capable of successful identification in multispecies samples containing target and non-target species DNA. These results indicate that the LTS DNA detection platform will be useful for field application of target species. Additionally, we find that LTS detection is effective with species-specific oligonucleotide tags alone or when they are attached to polystyrene nanobeads and with both amplified and unamplified DNA, indicating that the technique may also have versatility for broader applications.

Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA

Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, ‘early detection and rapid response’; (ii) for conserving imperilled native species, ‘protection of biodiversity hotspots’; and (iii) for assessing biosecurity risk, ‘an ounce of prevention equals a pound of cure.’ However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism’s DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next-generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.

Combining perturbations and parameter variation to influence mean first passage times

Perturbations are relatively large shocks to state variables that can drive transitions between stable states, while drift in parameter values gradually alters equilibrium magnitudes. This latter effect can lead to equilibrium bifurcation, the generation, or annihilation of equilibria. Equilibrium annihilations reduce the number of equilibria and so are associated with catastrophic population collapse. We study the combination of perturbations and parameter drift, using a two-species intraguild predation (IGP) model. For example, we use bifurcation analysis to understand how parameter drift affects equilibrium number, showing that both competition and predation rates in this model are bifurcating parameters. We then introduce a stochastic process to model the effects of population perturbations. We demonstrate how to evaluate the joint effects of perturbations and drift using the common currency of mean first passage time to transitions between stable states. Our methods and results are quite general, and for example, can relate to issues in both pest control and sustainable harvest. Our results show that parameter drift (1) does not importantly change the expected time to reach target points within a basin of attraction, but (2) can dramatically change the expected time to shift between basins of attraction, through its effects on equilibrium resilience.

Quantitative and rapid DNA detection by laser transmission spectroscopy

Laser transmission spectroscopy (LTS) is a quantitative and rapid in vitro technique for measuring the size, shape, and number of nanoparticles in suspension. Here we report on the application of LTS as a novel detection method for species-specific DNA where the presence of one invasive species was differentiated from a closely related invasive sister species. The method employs carboxylated polystyrene nanoparticles functionalized with short DNA fragments that are complimentary to a specific target DNA sequence. In solution, the DNA strands containing targets bind to the tags resulting in a sizable increase in the nanoparticle diameter, which is rapidly and quantitatively measured using LTS. DNA strands that do not contain the target sequence do not bind and produce no size change of the carboxylated beads. The results show that LTS has the potential to become a quantitative and rapid DNA detection method suitable for many real-world applications.

Limitations of gravity models in predicting the spread of Eurasian watermilfoil

The effects of non-native invasive species are costly and environmentally damaging, and resources to slow their spread and reduce their effects are scarce. Models that accurately predict where new invasions will occur could guide the efficient allocation of resources to slow colonization. We assessed the accuracy of a model that predicts the probability of colonization of lakes in Wisconsin by Eurasian watermilfoil (Myriophyllum spicatum). We based this predictive model on 9 years (1990-1999) of sequence data of milfoil colonization of lakes larger than 25 ha (n =1803). We used milfoil colonization sequence data from 2000 to 2006 to test whether the model accurately predicted the number of lakes that actually were colonized from among the 200 lakes identified as being most likely to be colonized. We found that a lake's predicted probability of colonization was not correlated with whether a lake actually was colonized. Given the low predictability of colonization of specific lakes, we compared the efficacy of preventing milfoil from leaving occupied sites, which does not require predicting colonization probability, with protecting vacant sites from being colonized, which does require predicting colonization probability. Preventing organisms from leaving colonized sites reduced the likelihood of spread more than protecting vacant sites. Although we focused on the spread of a single species in a particular region, our results show the shortcomings of gravity models in predicting the spread of numerous non-native species to a variety of locations via a wide range of vectors.

Semisubmersible oil platforms: understudied and potentially major vectors of biofouling-mediated invasions

Biofouling has long been recognised as a major pathway for the introduction of non-indigenous species. This study records the decapods and stomatopod crustaceans fouling a semisubmersible oil platform dry docked for hull cleaning in Jurong Port, Singapore. Of the 25 species of decapods identified, 13 were non-indigenous and represent new records to Singapore waters. Of these, the crabs Glabropilumnus seminudus and Carupa tenuipes are known to be invasive in other parts of the world. The stomatopod, Gonodactylaceus randalli, is the first mantis shrimp recorded in a biofouling community. The richness and diversity of this fouling community, consisting of many vagile species, highlights the difference between platforms and ships. With the expansion of maritime oil and gas exploration, the threat posed by an expanded fleet of semisubmersible oil platforms translocating non-indigenous fouling communities across biogeographical boundaries is very serious. Scientists, policy-makers, and stakeholders should turn their attention to this growing problem.