Improved Methods for Capture,Extraction, and Quantitative Assay of Environmental DNA from Asian Bigheaded Carp (Hypophthalmichthys spp.)

Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.     

Trophic reorganization of native planktivorous fishes at different density extremes of bigheaded carps in the Illinois and Mississippi rivers,USA

The widespread introduction of non-native fishes has contributed to freshwater ecosystems being considered among the most altered ecosystems globally. Of particular concern are invasive planktivorous fishes (e.g., silver carp Hypophthalmichthys molitrix and bighead carp H. nobilis, collectively known as bigheaded carps) that have the potential to modify basal food web structure and compete for planktonic resources with native planktivores and young-of-year fishes. Bigheaded carps have proliferated throughout the Mississippi River basin, creating an outsized potential for resource competition with native fishes. Studies have showed niche overlap between bigheaded carps and native planktivores is generally high but that overlap varies among rivers. Importantly, niche overlap has not been assessed for density extremes of bigheaded carps within a river to determine whether trophic niches changed as a result of the invasion. The objectives of this study were to determine whether (1) silver and/or bighead carps share a similar isotopic niche with four native planktivores, and (2) that association varies ecologically (i.e., low- and high-densities of bigheaded carps) and spatially (i.e., between rivers). Our results generally show high trophic overlap among species, suggesting potential direct resource competition. Niche overlap was higher in study reaches with low densities of bigheaded carps compared to reaches with high densities, presumably due to intense resource competition and limiting of resources under high densities of bigheaded carps. Across density extremes, trophic reorganization by bigmouth buffalo (Ictiobus cyprinellus) was divergent from other native planktivores. Species-specific responses may be due to subtle differences in feeding strategies, degree of planktivory, food selectivity, and correlated food size distributions.

     

Aspects of Embryonic and Larval Development in Bighead Carp Hypophthalmichthys nobilis and Silver Carp Hypophthalmichthys molitrix

As bighead carp Hypophthalmichthys nobilis and silver carp H . molitrix (the bigheaded carps) are poised to enter the Laurentian Great Lakes and potentially damage the region’s economically important fishery, information on developmental rates and behaviors of carps is critical to assessing their ability to establish sustainable populations within the Great Lakes basin. In laboratory experiments, the embryonic and larval developmental rates, size, and behaviors of bigheaded carp were tracked at two temperature treatments, one “cold” and one “warm”. Developmental rates were computed using previously described stages of development and the cumulative thermal unit method. Both species have similar thermal requirements, with a minimum developmental temperature for embryonic stages of 12.1° C for silver carp and 12.9° C for bighead carp, and 13.3° C for silver carp larval stages and 13.4° C for bighead carp larval stages. Egg size differed among species and temperature treatments, as egg size was larger in bighead carp, and “warm" temperature treatments. The larvae started robust upwards vertical swimming immediately after hatching, interspersed with intervals of sinking. Vertical swimming tubes were used to measure water column distribution, and ascent and descent rates of vertically swimming fish. Water column distribution and ascent and descent rates changed with ontogeny. Water column distribution also showed some diel periodicity. Developmental rates, size, and behaviors contribute to the drift distance needed to fulfill the early life history requirements of bigheaded carps and can be used in conjunction with transport information to assess invasibility of a river.     

Bigheaded carps (<Emphasis Type="Italic">Hypophthalmichthys</Emphasis> spp.) at the edge of their invaded range: using hydroacoustics to assess population parameters and the efficacy of harvest as a control strategy in a large North American river

The threat posed by bigheaded carps (Hypophthalmichthys spp.) to novel ecosystems has focused efforts on preventing further range expansion; upstream progression in the Illinois River is a major concern due to its connection with the uninvaded Great Lakes. In addition to an electric barrier system, commercial harvest of silver carp (H. molitrix) and bighead carp (H. nobilis) in the upper river is intended to reduce propagule pressure and prevent range expansion. To quantify demographics and evaluate harvest efficacy, the upper river was sampled between 2012 and 2015 using mobile hydroacoustic methods. Reach-specific densities, size structures and species compositions varied interannually but the advancing population was characterized longitudinally as small-bodied, silver carp-dominated at the highest densities downstream, shifting to large-bodied, bighead carp-dominated at the low-density population front. The use of hydroacoustic sampling for harvest evaluation was validated in backwater lakes; there was a significant positive correlation between density estimates and the corresponding harvest catch-per-unit-effort of bigheaded carps. Localized densities of bigheaded carps were reduced by up to 64.4 % immediately post-harvest but generally rebounded within weeks. However, annual sampling of the entire upper river indicated that density of bigheaded carps decreased by over 40 % (between 2012 and 2013) and subsequently remained stable (between 2013 and 2014). The annual harvest of bigheaded carps increased during this period (from 45,192 to 102,453 individuals), in years of contrasting discharge conditions. At this spatiotemporal scale, harvest appears to have contributed to initial reduction, and subsequent maintenance of, bigheaded carps density levels, but discharge likely plays an important role (e.g., through immigration) in determining the extent of its impact. Mobile hydroacoustic sampling enabled robust quantification of the population over varying spatial scales and density gradients, highlighting the potential of this approach as an assessment tool for invasive fishes in riverine environments.     

Tag retention and survival of juvenile bighead carp implanted with a dummy acoustic tag at three temperatures

Bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix (together, the bigheaded carps) are invasive fishes in North America that have resulted in substantial negative effects on native fish communities and aquatic ecosystems. Movement and behavior of adult bigheaded carps has been studied previously using telemetry, while similar studies with juvenile bigheaded carps have yet to be attempted. Recent technological advances in telemetry transmitters has increased the availability of tags sufficiently small enough to implant in juvenile carps. However, the effects of surgical implantation of telemetry tags on juvenile bigheaded carps have not been evaluated. We determined tag retention and survival associated with surgical implantation of acoustic telemetry tags into juvenile bighead carp (range 128–152 mm total length) at three temperatures (13, 18, and 23°C). In addition, we assessed the effect of surgically implanted transmitters on the fitness, defined as changes in weight or critical swimming speed, of carp implanted with transmitters. Survival was high among tagged fish (85%) with 47% of tags retained at the conclusion of the 45‐day study. No substantial decline in fitness of the fish was observed in tagged fish compared to untagged fish.     

Mitochondrial Genome Sequencing and Development of Genetic Markers for the Detection of DNA of Invasive Bighead and Silver Carp (Hypophthalmichthys nobilis and H. molitrix) in Environmental Water Samples from the United States

Invasive Asian bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) pose a substantial threat to North American aquatic ecosystems. Recently, environmental DNA (eDNA), genetic material shed by organisms into their environment that can be detected by non-invasive sampling strategies and genetic assays, has gained recognition as a tool for tracking the invasion front of these species toward the Great Lakes. The goal of this study was to develop new species-specific conventional PCR (cPCR) and quantitative (qPCR) markers for detection of these species in North American surface waters. We first generated complete mitochondrial genome sequences from 33 bighead and 29 silver carp individuals collected throughout their introduced range. These sequences were aligned with those from other common and closely related fish species from the Illinois River watershed to identify and design new species-specific markers for the detection of bighead and silver carp DNA in environmental water samples. We then tested these genetic markers in the laboratory for species-specificity and sensitivity. Newly developed markers performed well in field trials, did not have any false positive detections, and many markers had much higher detection rates and sensitivity compared to the markers currently used in eDNA surveillance programs. We also explored the use of multiple genetic markers to determine whether it would improve detection rates, results of which showed that using multiple highly sensitive markers should maximize detection rates in environmental samples. The new markers developed in this study greatly expand the number of species-specific genetic markers available to track the invasion front of bighead and silver carp and will improve the resolution of these assays. Additionally, the use of the qPCR markers developed in this study may reduce sample processing time and cost of eDNA monitoring for these species.     

Influence of environmental factors and individual traits on the diet of non-native hybrid bigheaded carp (Hypophthalmichthys molitrix × H. nobilis) in Lake Balaton,Hungary

Planktivorous silver carp and bighead carp (collectively, the bigheaded carps) have been stocked worldwide and their invasion has caused severe impacts on many freshwater ecosystems. Exploiting the chance provided by the specific hybrid bigheaded carp stock in Lake Balaton (Hungary) covering the entire morphological range between the two species (including gill raker morphology), we implemented a comprehensive study (1) to reveal the feeding habits of hybrid bigheaded carps living in a mesotrophic, lacustrine habitat and (2) to assess how biotic and abiotic environmental factors and gill raker morphology affect diet composition. We found that all bigheaded carps utilized primarily zooplankton and neglected the scarce and inefficiently digestible phytoplankton, irrespective of gill raker morphology. Moreover, we observed strikingly high levels of inorganic debris consumption, but the proportion of inorganic matter in the guts was not associated directly with the concentration of suspended inorganic particles. Variance in the diet composition of bigheaded carps was related mostly to environmental factors, including the wind-induced resuspension of inorganic particles and seasonally variable availability of food resources. In conclusion, the effects of abiotic environmental factors and available food resources could overwhelm the effect of gill raker morphology in shaping the feeding habits of bigheaded carps.

     

Development of microsatellite DNA markers of silver carp (Hypophthalmichthys molitrix) and their cross‐species application in bighead carp (Aristichthys nobilis)

Forty‐four microsatellite DNA markers were developed for silver carp, and used to investigate polymorphisms of 41 wild silver carps and seven wild bighead carps collected from Jingzhou fragment of Yangtze River. In silver carp, 40 markers were polymorphic. A total of 297 alleles were detected at 40 polymorphic loci. The number of alleles per locus varied from two to 16 with an average of 7.4 and the expected heterozygosities of each locus ranged from 0.07 to 0.91 with an average of 0.69. All markers amplified both silver carp and bighead carp DNAs.     

Detecting the movement and spawning activity of bigheaded carps with environmental DNA

Bigheaded carps are invasive fishes threatening to invade the Great Lakes basin and establish spawning populations, and have been monitored using environmental DNA (eDNA). Not only does eDNA hold potential for detecting the presence of species, but may also allow for quantitative comparisons like relative abundance of species across time or space. We examined the relationships among bigheaded carp movement, hydrography, spawning and eDNA on the Wabash River, IN, USA. We found positive relationships between eDNA and movement and eDNA and hydrography. We did not find a relationship between eDNA and spawning activity in the form of drifting eggs. Our first finding demonstrates how eDNA may be used to monitor species abundance, whereas our second finding illustrates the need for additional research into eDNA methodologies. Current applications of eDNA are widespread, but the relatively new technology requires further refinement.     

Modelling bioenergetic and population-level impacts of invasive bigheaded carps (Hypophthalmichthys spp.) on native paddlefish (Polyodon spathula) in backwaters of the lower Mississippi River

1. While invasions of large rivers by exotic fish species are well documented, assessing actual or potential impacts on native species is a challenge. Rapid assessments may be possible through the application of a combination of bioenergetic and population dynamic models.
2. Paddlefish (Polyodon spathula) is a native species in the central USA with a history of population decline due to waterway development and overharvesting for roe. It is not known whether paddlefish are impacted by resource competition from invasive bigheaded carp populations, including silver (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis), which have expanded dramatically in the Mississippi River.
3. We used bioenergetic models to project the potential impact of invasive silver and bighead carp on zooplankton density and paddlefish somatic growth in backwater habitat. Bioenergetic outputs were translated to impacts on fecundity, becoming inputs for 50-year metapopulation simulations of backwater habitat connected to the main-stem Mississippi River by episodic flood events.
4. Competition with carp reduced growth and increased the risk of population decline for paddlefish. Impacts increased disproportionately with increased carp abundance and were further exacerbated in scenarios with increased diet overlap or decreased zooplankton abundance.
5. We also analysed paddlefish condition data collected at sites near the lower Mississippi River with varying histories of carp invasion. These data give credence to the bioenergetic model output; paddlefish had reduced body condition at sites with long-established, high-density carp populations.
6. We conclude that invasive bigheaded carps have great potential to reduce paddlefish growth, fecundity, and abundance. The pairing of bioenergetics and population models is likely to be broadly useful in assessing the risks posed by other invasive species.

     

Swimming performance of adult bighead carp Hypophthalmichthys nobilis (Richardson, 1845) and silver carp H. molitrix (Valenciennes, 1844)

Although the movement of invasive bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) in the Upper Mississippi River system is dependent on their ability to swim through its numerous lock‐and‐dams, the swimming performance of adults of these species is at present unknown. Using a large (2,935‐L) mobile swim tunnel, the swimming performance of adult bighead and adult silver carp was quantified at water velocities that challenged them to exhibit either prolonged and/or burst swimming (76–244 cm/s) with fatigue times of less than 10 min. Simple log‐linear models best described the relative swim speed to fatigue relationships for both species. Under these conditions, the swimming performances of adult bighead and silver carp were similar to several species of adult fishes native to the Mississippi River system, but relatively low (<3 total body lengths per second, TL/s) compared to previously studied juveniles and sub‐adult bigheaded carps (3–15 TL/s). The decline in endurance with water velocity was three times greater in bighead carp (slope = ?2.98) than in silver carp (slope = ?1.01) and the predictive ability of the bighead model was appreciably better than the silver carp model. The differences in adult swimming performance between the two species were coincident with behavioral differences (e.g. breaching in silver carp but not in bighead carp). The swimming performance data of adult bighead and silver carp can now be used to evaluate whether their passage through manmade river structures including the gates of lock‐and‐dams in the Upper Mississippi River might be reduced.     

Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish

Few studies have examined capture and extraction methods for environmental DNA (eDNA) to identify techniques optimal for detection and quantification. In this study, precipitation, centrifugation and filtration eDNA capture methods and six commercially available DNA extraction kits were evaluated for their ability to detect and quantify common carp (Cyprinus carpio) mitochondrial DNA using quantitative PCR in a series of laboratory experiments. Filtration methods yielded the most carp eDNA, and a glass fibre (GF) filter performed better than a similar pore size polycarbonate (PC) filter. Smaller pore sized filters had higher regression slopes of biomass to eDNA, indicating that they were potentially more sensitive to changes in biomass. Comparison of DNA extraction kits showed that the MP Biomedicals FastDNA SPIN Kit yielded the most carp eDNA and was the most sensitive for detection purposes, despite minor inhibition. The MoBio PowerSoil DNA Isolation Kit had the lowest coefficient of variation in extraction efficiency between lake and well water and had no detectable inhibition, making it most suitable for comparisons across aquatic environments. Of the methods tested, we recommend using a 1.5 μm GF filter, followed by extraction with the MP Biomedicals FastDNA SPIN Kit for detection. For quantification of eDNA, filtration through a 0.2–0.6 μm pore size PC filter, followed by extraction with MoBio PowerSoil DNA Isolation Kit was optimal. These results are broadly applicable for laboratory studies on carps and potentially other cyprinids. The recommendations can also be used to inform choice of methodology for field studies.     

Phenotypic plasticity in the spawning traits of bigheaded carp (Hypophthalmichthys spp.) in novel ecosystems

1. Bigheaded carp, including both silver (Hypophthalmichthys molitrix) and bighead (H. nobilis) carp, are successful invasive fishes that threaten global freshwater biodiversity. High phenotypic plasticity probably contributes to their success in novel ecosystems, although evidence of plasticity in several spawning traits has hitherto been largely anecdotal or speculative. 2. We collected drifting eggs from a Midwestern U.S.A. river from June to September 2011 and from April to June 2012 to investigate the spawning traits of bigheaded carp in novel ecosystems. 3. Unlike reports from the native range, the presence of drifting bigheaded carp eggs was not related to changes in hydrological regime or mean daily water temperature. Bigheaded carp also exhibited protracted spawning, since we found drifting eggs throughout the summer and as late as 1 September 2011. Finally, we detected bigheaded carp eggs in a river reach where the channel is c. 30 m wide with a catchment area of 4579 km², the smallest stream in which spawning has yet been documented. 4. Taken with previous observations of spawning traits that depart from those observed within the native ranges of both bighead and silver carp, our findings provide direct evidence that bigheaded carp exhibit plastic spawning traits in novel ecosystems that may facilitate invasion and establishment in a wider range of river conditions than previously envisaged.     

Using marketing to fish‐down bigheaded carp (Hypophthalmichthys spp.) in the United States: Eliminating the negative brand name, “carp”

Invasive bigheaded carp species (Hypophthalmichthys spp.) from Asia have experienced rapid range expansion and population explosions in rivers of the United States resulting in ecosystem damage currently being witnessed and documented by fishery biologists. In addition, silver carp (H. molitrix) present a danger of injury and death to unsuspecting boaters, water skiers or recreational fishers due to their propensity to jump in response to boat motor noise. Fishing‐down bigheaded carp populations for human consumption will reduce environmental damage and potential human injury and mortality until other control measures become available. The name “carp” conveys an extremely negative brand name for purposes of product marketing. We suggest that the silver carp be renamed by the professional scientific community to silverfin (a trademarked name currently used in culinary circles) and the bighead carp (H. nobilis) to bighead. The suggested common names changes represent a simple, albeit small step to reducing bigheaded carp population numbers based on sound product naming strategies developed and used in marketing science.     

Long-term changes in fish community structure in relation to the establishment of Asian carps in a large floodplain river

The Upper Mississippi River System, including the Illinois River, has been invaded by a number of nonnative species including silver carp Hypophthalmichthys molitirx and bighead carp H. nobilis, collectively referred to here as Asian carps. Silver carp densities in the Illinois River have increased dramatically and now represent some of the highest densities of wild silver carp anywhere in the world. Asian carps have the potential to alter existing ecosystems by consuming planktonic resources and therefore, could have the ability to alter existing fish communities as most fishes are dependent on planktonic resources during early development. However, identifying the relationship of fish community structure to the establishment of Asian carps has yet to be thoroughly investigated. Using long-term fish community data collected by the Upper Mississippi River Restoration’s Long Term Resource Monitoring element, we investigate changes in fish community structure pre- and post-establishment of Asian carps. Significant differences in the pre- and post-establishment communities were observed for the majority of gears and habitats. Species contributing to changes between establishment periods included most sportfish species and catostomids, which were less abundant post-establishment of Asian carps, while shortnose gar, grass carp, and emerald shiner were more abundant. While our analyses show Asian carps are likely contributing to major differences in fish community structure, future research and long-term monitoring should investigate the mechanisms and interactions responsible for community changes as well as identifying any potential concurrent or confounding factors such as changes in river hydrology or sedimentation.     

The Relationship between the Distribution of Common Carp and Their Environmental DNA in a Small Lake

Although environmental DNA (eDNA) has been used to infer the presence of rare aquatic species, many facets of this technique remain unresolved. In particular, the relationship between eDNA and fish distribution is not known. We examined the relationship between the distribution of fish and their eDNA (detection rate and concentration) in a lake. A quantitative PCR (qPCR) assay for a region within the cytochrome b gene of the common carp (Cyprinus carpio or ‘carp’), an ubiquitous invasive fish, was developed and used to measure eDNA in Lake Staring (MN, USA), in which both the density of carp and their distribution have been closely monitored for several years. Surface water, sub-surface water, and sediment were sampled from 22 locations in the lake, including areas frequently used by carp. In water, areas of high carp use had a higher rate of detection and concentration of eDNA, but there was no effect of fish use on sediment eDNA. The detection rate and concentration of eDNA in surface and sub-surface water were not significantly different (p≥0.5), indicating that eDNA did not accumulate in surface water. The detection rate followed the trend: high-use water > low-use water > sediment. The concentration of eDNA in sediment samples that were above the limit of detection were several orders of magnitude greater than water on a per mass basis, but a poor limit of detection led to low detection rates. The patchy distribution of eDNA in the water of our study lake suggests that the mechanisms that remove eDNA from the water column, such as decay and sedimentation, are rapid. Taken together, these results indicate that effective eDNA sampling methods should be informed by fish distribution, as eDNA concentration was shown to vary dramatically between samples taken less than 100 m apart.     

Reproductive condition and occurrence of intersex in bighead carp and silver carp in the Missouri River

Little is known about the reproductive biology of the exotic bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix in the Missouri River. In order to fill this gap in understanding, herein is described the reproductive condition of these Asian carps. Evidence is presented which indicates that bighead and silver carp in the Missouri River have a protracted spawning period that extends from early spring through fall and some individual bighead and silver carp are spawning multiple times during a reproductive season. Although bighead and silver carps are successfully maturing and spawning in the Missouri River some reproductive abnormalities such as intersex, atresia, and sterility were observed. Knowledge of the reproductive activity of these invasive carps may be useful to resource managers tasked with their control. Furthermore, the reproductive abnormalities observed should be considered when evaluating the environmental condition of the Missouri River relative to supporting a healthy fish fauna.     

Temperature dependent effects of carbon dioxide on avoidance behaviors in bigheaded carps

Effective behavioral deterrents are needed to prevent aquatic invasive species from entering novel ecosystems. One deterrent strategy that shows promise is elevated carbon dioxide (CO₂) concentrations in water which can alter the behavior of freshwater fishes, including invasive bigheaded carps (Hypophthalmichthys spp.). However, few studies have evaluated behavioral responses to elevated CO₂ concentrations at different water temperatures. The objective of this study was to quantify CO₂ concentrations needed to achieve avoidance (voluntary response) and narcosis (involuntary response observed by loss of equilibrium) behaviors in silver carp (H. molitrix) and bighead carp (H. nobilis) at 5, 15, and 25 °C. Overall, silver carp and bighead carp displayed avoidance and narcosis behaviors to CO₂ at each water temperature, however bighead carp responded at higher CO₂ concentrations than silver carp. Behavioral avoidance and narcosis were observed at approximately 40% lower CO₂ concentrations in 5 °C water relative to 25 °C suggesting considerable influence of water temperature on a CO₂ stimulus for both species. Results indicate that fluctuating water temperature (e.g., spatial and temporal variation across management sites) can influence how fish respond to elevated CO₂, and may usefully be considered when applying CO₂ as a behavioral deterrent.