scholarly journals Improving the detection of rare native fish species in environmental DNA metabarcoding surveys

2021 ◽  
Vol 4 ◽  
Author(s):  
Jack Rojahn ◽  
Dianne Gleeson ◽  
Elise Furlan ◽  
Tim Haeusler ◽  
Jonas Bylemans
Keyword(s):  
Rare Species ◽  
Native Species ◽  
Environmental Dna ◽  
Detection Sensitivity ◽  
Native Fish ◽  
Sampling Effort ◽  
Maxent Model ◽  
Detection Probabilities ◽  
Blocking Primer ◽  
The Impact

The presence of threatened or endangered species often strongly influences management and conservation decisions. Within the Murray–Darling Basin (MDB), Australia, the presence of threatened native fish affects the management and allocation of water resources. These decisions are currently based on traditional fisheries data and a predictive MaxEnt model. However, it is important to verify the model's predictive power given the implication it may have, but this requires methods with a high detection sensitivity for rare species. Although the use of environmental DNA (eDNA) metabarcoding achieves a higher detection sensitivity compared with traditional methods, earlier surveys in the MDB have shown that the highly abundant and invasive common carp (Cyprinus carpio) can reduce detection probabilities for rare species. Consequently, a polymerase chain reaction (PCR) blocking primer designed to block the amplification of carp eDNA could increase the detection probabilities for rare native species while simultaneously reducing the required sampling effort and survey costs. Although PCR blocking primers are often used in ancient DNA and dietary studies, no aquatic eDNA metabarcoding study to date has evaluated the potential benefits of using PCR blocking primers. A laboratory and field‐based pilot study was used to address this knowledge gap and assess the impact of a blocking primer on the detection probabilities of native species and the minimum sampling effort required. Results showed that the inclusion of the blocking primer increased the detection probabilities for native species by 10–20% and reduced the minimum required sampling effort by 25–50%. These findings provide important insights into possible methods for optimizing eDNA metabarcoding surveys for the detection of rare aquatic species.

scholarly journals Environmental DNA Based Surveillance for the Highly Invasive Carpet Sea Squirt Didemnum vexillum: A Targeted Single-Species Approach

2021 ◽  
Vol 8 ◽  
Author(s):  
Iveta Matejusova ◽  
Jennifer Graham ◽  
Fiona Bland ◽  
Jean-Pierre Lacaze ◽  
Guillaume Herman ◽  
...  
Keyword(s):  
Water Samples ◽  
Native Species ◽  
Limit Of Detection ◽  
Sampling Site ◽  
Monitoring Program ◽  
Environmental Dna ◽  
Qpcr Assay ◽  
Didemnum Vexillum ◽  
Sampling Points ◽  
The Impact

The presence and diversity of marine non-native species, the number of new invasions, and the impact on native communities and habitats are important metrics used to assess the health of marine ecosystems. Monitoring for marine non-native species, using traditional approaches such as rapid assessment surveys (RASs), requires taxonomic expertise and may still fail to detect rare or inconspicuous species. This study reports a validation process for a quantitative PCR (qPCR) assay based on the cytochrome oxidase 1 gene, designed to detect highly invasive tunicate Didemnum vexillum by targeting environmental DNA (eDNA) present in water samples. The D. vexillum qPCR assay showed high sensitivity, with the threshold limit of detection (LOD) and modeled LOD3 (based on triplicate qPCR reactions) estimated as 9.187 and 1.117 copies reaction–1, respectively and the limit of quantification (LOQ) was calculated as 18 copies reaction–1. Analyses of water samples collected from selected Pacific oyster farms and recreational marinas in Scotland showed 100% concordance between the historical data on presence of D. vexillum from RASs and detection of D. vexillum eDNA. Consistency of detection of D. vexillum eDNA among different sampling points within each infected sampling site varied, ranging between 100% positive throughout the site to some sampling points testing “negative” or only as “suspected” for D. vexillum. Sites with lower within-site detection consistency included sites with a low density of D. vexillum as reported by RASs or were sites undergoing D. vexillum management. The present pilot monitoring program demonstrates the potential to generate important data on presence of D. vexillum. This program will be scaled up across large geographic regions and used in the first instance to focus and target the traditional RASs to D. vexillum eDNA-positive sites in a cost-effective way, with an aim to verify the species presence by visual observation and direct Sanger sequencing of positive qPCR products.

scholarly journals Trophic Niche Overlap between Invasive and Indigenous Fish in a Northwest Reservoir of China

Water ◽  
2021 ◽  
Vol 13 (23) ◽  
pp. 3459
Author(s):  
Jie Wei ◽  
Zhulan Nie ◽  
Fenfen Ji ◽  
Longhui Qiu ◽  
Jianzhong Shen
Keyword(s):  
Invasive Species ◽  
Fish Species ◽  
Native Species ◽  
Niche Overlap ◽  
Niche Width ◽  
Native Fish ◽  
Tarim River ◽  
Tarim River Basin ◽  
Indigenous Species ◽  
The Impact

The Kizil reservoir in the Tarim River basin is an important habitat for the native Schizothoracinae fish (including Aspiorhynchus laticeps, Schizothorax biddulphi, Schizothorax eurystomus, Schizothorax intermedius and Schizothorax barbatus). Unfortunately, these species are threatened by many exotic fish, such as Ctenopharyngodon idellus, Silurus asotus. As an isolated habitat, the Kizil reservoir is an ideal area for studying biological invasions. However, the impact of invasive species on indigenous species in this reservoir remains unknown. In this study, the niche width and niche overlap between invasive and indigenous species in Kizil reservoir were studied based on stable isotope analysis. The results showed that niche width of two invasive species, S. asotus and C. idellus, was larger than that of native fish species, which confirmed the hypotheses that successful invaders have larger niche width. The niche overlap analysis showed that the two invasive species had high niche overlap with native fish species, which meant that there might be intensive interspecific competitions between them. The invasion of non-native species could be the main reason for the decrease of native species in the Kizil reservoir.

scholarly journals Escapes of non-native fish from flooded aquaculture facilities: the case of Paranapanema River, southern Brazil

2018 ◽  
Vol 35 ◽  
pp. 1-6 ◽  
Author(s):  
Armando César Rodrigues Casimiro ◽  
Diego Azevedo Zoccal Garcia ◽  
Ana Paula Vidotto-Magnoni ◽  
John Robert Britton ◽  
Angelo Antonio Agostinho ◽  
...  
Keyword(s):  
River Basin ◽  
Native Species ◽  
Biodiversity Loss ◽  
Native Fish ◽  
Southern Brazil ◽  
Fish Farms ◽  
Native Fishes ◽  
Aquaculture Facilities ◽  
The Impact ◽  
Large Floods

Non-native species are a major driver of biodiversity loss. Aquaculture activities play a key role in introductions, including the escape of fishes from fish farm facilities. Here, the impact of flooding due to El Niño rains in 2015/2016 in the Lower and Middle Paranapanema River basin, southern Brazil, was investigated by evaluating fish escapes from 12 fish farms. The flooding resulted in the escape of approximately 1.14 million fishes into the river, encompassing 21 species and three hybrids. Non-native species were the most abundant escapees, especially Oreochromisniloticus (Linnaeus, 1758) and Coptodonrendalli (Boulenger, 1897) (96% of all fish). Only seven native fishes were in the escapee fauna, comprising 1% of all fish. Large floods, coupled with inadequate biosecurity, thus resulted in considerable inputs of non-native fish into this already invaded system.

scholarly journals Advancing improvement in riverine water quality caused a non-native fish species invasion and native fish fauna recovery

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Łukasz Głowacki ◽  
Andrzej Kruk ◽  
Tadeusz Penczak
Keyword(s):  
Water Quality ◽  
Fish Species ◽  
Native Species ◽  
Interference Competition ◽  
Fish Fauna ◽  
Species Traits ◽  
Native Fish ◽  
Biological Degradation ◽  
Species Invasion ◽  
Prussian Carp

AbstractThe knowledge of biotic and abiotic drivers that put non-native invasive fishes at a disadvantage to native ones is necessary for suppressing invasions, but the knowledge is scarce, particularly when abiotic changes are fast. In this study, we increased this knowledge by an analysis of the biomass of most harmful Prussian carp Carassius gibelio in a river reviving from biological degradation. The species' invasion followed by the invasion's reversal occurred over only two decades and were documented by frequent monitoring of fish biomass and water quality. An initial moderate improvement in water quality was an environmental filter that enabled Prussian carp’s invasion but prevented the expansion of other species. A later substantial improvement stimulated native species’ colonization of the river, and made one rheophil, ide Leuciscus idus, a significant Prussian carp’s replacer. The redundancy analysis (RDA) of the dependence of changes in the biomass of fish species on water quality factors indicated that Prussian carp and ide responded in a significantly opposite way to changes in water quality in the river over the study period. However, the dependence of Prussian carp biomass on ide biomass, as indicated by regression analysis and analysis of species traits, suggests that the ecomorphological similarity of both species might have produced interference competition that contributed to Prussian carp’s decline.

scholarly journals The value of quantitative environmental DNA analyses for the management of invasive and endangered native fish

2021 ◽  
Author(s):  
Jack Rojahn ◽  
Luke Pearce ◽  
Dianne M. Gleeson ◽  
Richard P. Duncan ◽  
Dean M. Gilligan ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Native Fish ◽  
Dna Analyses

scholarly journals Diet composition of the invasive red-whiskered bulbul Pycnonotus jocosus in Mauritius

2010 ◽  
Vol 26 (3) ◽  
pp. 347-350 ◽  
Author(s):  
Jannie Fries Linnebjerg ◽  
Dennis M. Hansen ◽  
Nancy Bunbury ◽  
Jens M. Olesen
Keyword(s):  
Invasive Species ◽  
Introduced Species ◽  
Native Species ◽  
Diet Composition ◽  
Ecological Perspective ◽  
Positive Interactions ◽  
Invasional Meltdown ◽  
Ecological Processes ◽  
Successful Establishment ◽  
The Impact

Disruption of ecosystems is one of the biggest threats posed by invasive species (Mack et al. 2000). Thus, one of the most important challenges is to understand the impact of exotic species on native species and habitats (e.g. Jones 2008). The probability that entire ‘invasive communities’ will develop increases as more species establish in new areas (Bourgeois et al. 2005). For example, introduced species may act in concert, facilitating one another's invasion, and increasing the likelihood of successful establishment, spread and impact. Simberloff & Von Holle (1999) introduced the term ‘invasional meltdown’ for this process, which has received widespread attention since (e.g. O'Dowd 2003, Richardson et al. 2000, Simberloff 2006). Positive interactions among introduced species are relatively common, but few have been studied in detail (Traveset & Richardson 2006). Examples include introduced insects and birds that pollinate and disperse exotic plants, thereby facilitating the spread of these species into non-invaded habitats (Goulson 2003, Mandon-Dalger et al. 2004, Simberloff & Von Holle 1999). From a more general ecological perspective, the study of interactions involving introduced and invasive species can contribute to our knowledge of ecological processes – for example, community assembly and indirect interactions.

scholarly journals Temporal resolution of single-photon responses in primate rod photoreceptors and limits imposed by cellular noise

2019 ◽  
Vol 121 (1) ◽  
pp. 255-268 ◽  
Author(s):  
Greg D. Field ◽  
Valerie Uzzell ◽  
E. J. Chichilnisky ◽  
Fred Rieke
Keyword(s):  
Temporal Resolution ◽  
Moving Objects ◽  
Single Photon ◽  
Night Vision ◽  
Detection Sensitivity ◽  
Sensory Receptor ◽  
Rod Photoreceptor ◽  
Scotopic Vision ◽  
Central Processing ◽  
The Impact

Sensory receptor noise corrupts sensory signals, contributing to imperfect perception and dictating central processing strategies. For example, noise in rod phototransduction limits our ability to detect light, and minimizing the impact of this noise requires precisely tuned nonlinear processing by the retina. But detection sensitivity is only one aspect of night vision: prompt and accurate behavior also requires that rods reliably encode the timing of photon arrivals. We show here that the temporal resolution of responses of primate rods is much finer than the duration of the light response and identify the key limiting sources of transduction noise. We also find that the thermal activation rate of rhodopsin is lower than previous estimates, implying that other noise sources are more important than previously appreciated. A model of rod single-photon responses reveals that the limiting noise relevant for behavior depends critically on how rod signals are pooled by downstream neurons. NEW & NOTEWORTHY Many studies have focused on the visual system’s ability to detect photons, but not on its ability to encode the relative timing of detected photons. Timing is essential for computations such as determining the velocity of moving objects. Here we examine the timing precision of primate rod photoreceptor responses and show that it is more precise than previously appreciated. This motivates an evaluation of whether scotopic vision approaches limits imposed by rod temporal resolution.

Toward functional proteomics of alveolar macrophages

2005 ◽  
Vol 288 (4) ◽  
pp. L585-L595 ◽  
Author(s):  
Haifeng M. Wu ◽  
Ming Jin ◽  
Clay B. Marsh
Keyword(s):  
Alveolar Macrophages ◽  
Large Scale ◽  
Cell Types ◽  
Mononuclear Phagocyte ◽  
Detection Sensitivity ◽  
Current Status ◽  
Blood Monocytes ◽  
Protein Patterns ◽  
Additional Information ◽  
The Impact

Alveolar macrophages (AM) belong to a phenotype of macrophages with distinct biological functions and important pathophysiological roles in lung health and disease. The molecular details determining AM differentiation from blood monocytes and AM roles in lung homeostasis are largely unknown. With the use of different technological platforms, advances in the field of proteomics have made it possible to search for differences in protein expression between AM and their precursor monocytes. Proteome features of each cell type provide new clues into understanding mononuclear phagocyte biology. In-depth analyses using subproteomics and subcellular proteomics offer additional information by providing greater protein resolution and detection sensitivity. With the use of proteomic techniques, large-scale mapping of phosphorylation differences between the cell types have become possible. Furthermore, two-dimensional gel proteomics can detect germline protein variants and evaluate the impact of protein polymorphisms on an individual's susceptibility to disease. Finally, surface-enhanced laser desorption and ionization (SELDI) time-of-flight mass spectrometry offers an alternative method to recognizing differences in protein patterns between AM and monocytes or between AM under different pathological conditions. This review details the current status of this field and outlines future directions in functional proteomic analyses of AM and monocytes. Furthermore, this review presents viewpoints of integrating proteomics with translational topics in lung diseases to define the mechanisms of disease and to uncover new diagnostic and therapeutic targets.

scholarly journals Airborne environmental DNA metabarcoding detects more diversity, with less sampling effort, than a traditional plant community survey

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Mark D. Johnson ◽  
Mohamed Fokar ◽  
Robert D. Cox ◽  
Matthew A. Barnes
Keyword(s):  
Plant Community ◽  
Plant Communities ◽  
Traditional Method ◽  
Environmental Dna ◽  
Single Species ◽  
Community Survey ◽  
Sampling Effort ◽  
Sampling Campaign ◽  
Dna Metabarcoding ◽  
Human Health Impacts

Abstract Background Airborne environmental DNA (eDNA) research is an emerging field that focuses on the detection of species from their genetic remnants in the air. The majority of studies into airborne eDNA of plants has until now either focused on single species detection, specifically only pollen, or human health impacts, with no previous studies surveying an entire plant community through metabarcoding. We therefore conducted an airborne eDNA metabarcoding survey and compared the results to a traditional plant community survey. Results Over the course of a year, we conducted two traditional transect-based visual plant surveys alongside an airborne eDNA sampling campaign on a short-grass rangeland. We found that airborne eDNA detected more species than the traditional surveying method, although the types of species detected varied based on the method used. Airborne eDNA detected more grasses and forbs with less showy flowers, while the traditional method detected fewer grasses but also detected rarer forbs with large showy flowers. Additionally, we found the airborne eDNA metabarcoding survey required less sampling effort in terms of the time needed to conduct a survey and was able to detect more invasive species than the traditional method. Conclusions Overall, we have demonstrated that airborne eDNA can act as a sensitive and efficient plant community surveying method. Airborne eDNA surveillance has the potential to revolutionize the way plant communities are monitored in general, track changes in plant communities due to climate change and disturbances, and assist with the monitoring of invasive and endangered species.

scholarly journals The first unified inventory of non-native fishes of the South Caucasian countries, Armenia, Azerbaijan, and Georgia

2021 ◽  
pp. 32
Author(s):  
Tatia Kuljanishvili ◽  
Levan Mumladze ◽  
Bella Japoshvili ◽  
Namig Mustafayev ◽  
Shaig Ibrahimov ◽  
...  
Keyword(s):  
Black Sea ◽  
Fish Species ◽  
Caspian Sea ◽  
Native Species ◽  
Biological Diversity ◽  
Native Fish ◽  
The Black Sea ◽  
The South ◽  
In The Wild ◽  
Native Fishes

The South Caucasus (SC) region is recognized for its high biological diversity and various endemic animal taxa. The area has experienced many fish introductions over the years, but the overall information about non-native fishes in the three SC countries, Armenia, Azerbaijan, and Georgia did not exist. Although these three countries belong to the Kura River drainage, Caspian Sea basin (only the western half of Georgia drains into the Black Sea), the legislative framework for each country regarding introduction of non-native fish species and their treatment is different and poorly developed. The goal of the present study was to make an initial inventory of non-native fish species in the three SC countries, and summarize the existing knowledge as a basis for future risk assessment models and formulation of regional management policies. Here, we present a unified list of 27 non-native species recorded in the wild in Armenia, Azerbaijan, and Georgia. Among these 27 species, eight were translocated from the Black Sea basin to the Caspian Sea basin. Out of these 27 non-native fishes, 15 species have become established (three of them being considered invasive) and six fish species could not survive in the wild.

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