scholarly journals qPCR assays for the detection of two western North American freshwater mussel species, Anodonta nuttalliana and Anodonta oregonensis, from environmental DNA

2018 ◽  
Author(s):  
Torrey W. Rodgers ◽  
Karen E. Mock

AbstractWe developed species-specific quantitative PCR assays for the detection of two freshwater mussel species native to the western North America, Anodonta nuttalliana and Anodonta oregonensis, from environmental DNA. These species have experienced dramatic declines over the last century, and are currently threatened in many portions of their range. Improved tools for detecting and monitoring these species are needed. Species-specificity and sensitivity of the assays was empirically tested in the lab, and both assays were also validated with field collected eDNA samples. We found that the assays we designed are species-specific, sensitive, and are effective for detecting Anodonta nuttalliana and Anodonta oregonensis from environmental DNA samples collected from streams and rivers. These assays will aid in the detection, monitoring, management, and conservation of these threatened species.

2020 ◽  
Author(s):  
Torrey W. Rodgers ◽  
Joseph C. Dysthe ◽  
Cynthia Tait ◽  
Thomas W. Franklin ◽  
Michael K. Schwartz ◽  
...  

AbstractWe developed multiplexed, species-specific, quantitative PCR assays for the detection of four freshwater mussel species native to western North America, Gonidea angulata, Margaritifera falcata, Anodonta nuttalliana and Anodonta oregonensis, from environmental DNA (eDNA). These species have experienced dramatic declines over the last century and are currently threatened in many portions of their ranges. Therefore, improved tools for detecting and monitoring these species are needed. Species-specificity and sensitivity of assays were empirically tested in the lab, and multiplex assays were also validated with field collected eDNA samples. All assays were species-specific, sensitive, and effective for detection from eDNA samples collected from streams and rivers. These assays will aid in the detection, monitoring, management, and conservation of these vulnerable species.


2015 ◽  
Vol 8 ◽  
pp. MBI.S29736 ◽  
Author(s):  
Kenjiro Nagamine ◽  
Guo-Chiuan Hung ◽  
Bingjie Li ◽  
Shyh-Ching Lo

Using Streptococcus pyogenes as a model, we previously established a stepwise computational workflow to effectively identify species-specific DNA signatures that could be used as PCR primer sets to detect target bacteria with high specificity and sensitivity. In this study, we extended the workflow for the rapid development of PCR assays targeting Enterococcus faecalis, Enterococcus faecium, Clostridium perfringens, Clostridium difficile, Clostridium tetani, and Staphylococcus aureus, which are of safety concern for human tissue intended for transplantation. Twenty-one primer sets that had sensitivity of detecting 5–50 fg DNA from target bacteria with high specificity were selected. These selected primer sets can be used in a PCR array for detecting target bacteria with high sensitivity and specificity. The workflow could be widely applicable for the rapid development of PCR-based assays for a wide range of target bacteria, including those of biothreat agents.


2020 ◽  
Author(s):  
Yassine Messaoud ◽  
Anya Reid ◽  
Nadezhda M. Tchebakova ◽  
Annika Hofgaard ◽  
Faouzi Messsaoud

Abstract BackgroundThe climate variables effect on tree growth in boreal and temperate forests has received increased interest in the global context of climate change. However, most studies are geographically limited and involved few tree species. Here, sixteen tree species across western North America were used to investigate tree response to climate change at the species range scale. MethodsForest inventory data from 36,944 stands established between 1600 and 1968 throughout western Canada and USA were summarized. Height growth (total height at breast-height age of 50 years) of healthy dominant and co-dominant trees were related to annual and summer temperatures, annual and summer Palmer Drought Severity Index (PDSI, and tree establishment date (ED). Climate-induced height growth patterns were then tested to determine links to spatial environment (soil conditions and geographic locations), species range (coastal, interior, and both ranges) and species traits (shade tolerance and leaf form), using linear mixed model for the global height growth and general linear model to test the height growth patterns for each species. ResultsIncrease of temperatures and PDSI had a positive effect on height growth for most of the study species, whereas Alaska yellow-cedar (Chamaecyparis nootkatensis, (D. Don) Spach) height growth declined with ED. All explaining variables and the interactions explained 59% of the total height growth variance. Although tree height growth response was species-specific, increased height growth during the 20th century was more pronounced for coastal ranged species, high shade tolerant species, and broadleaf species. Furthermore, height growth increase occurred mostly on rich soil, at the northernmost species range, and, unexpectedly, at lower elevations. A decline in height growth for some species further north and especially higher in elevation possibly related to increased cloudiness and precipitation. However, drought conditions remain in interior areas despite moving northward and upward that decrease height growth. ConclusionThese results highlight the general trend (species characteristics and range) and the species-specific height patterns, indicating the spatio-temporal complexity of the growth response to recent global climate change.


2012 ◽  
Vol 39 (7) ◽  
pp. 629 ◽  
Author(s):  
Zachary H. Olson ◽  
Jeffrey T. Briggler ◽  
Rod N. Williams

Context Environmental DNA, or eDNA, methods are a novel application of non-invasive genetic sampling in which DNA from organisms is detected via sampling of water or soil, typically for the purposes of determining the presence or absence of an organism. eDNA methods have the potential to revolutionise the study of rare or endangered taxa. Aims We evaluated the efficacy of eDNA sampling to detect populations of an amphibian of conservation concern, the eastern hellbender (Cryptobranchus a. alleganiensis), indirectly from their aquatic environments. Methods We developed species-specific primers, validated their specificity and sensitivity, and assessed the utility of our methods in silico and in laboratory trials. In the field, we collected water samples from three sites with known densities of hellbenders, and from one site where hellbenders do not occur. We filtered water samples, extracted DNA from filters, and assayed the extraction products for hellbender DNA by using polymerase chain reaction (PCR) and gel electrophoresis. Key results Our methods detected hellbenders at densities approaching the lowest of reported natural densities. The low-density site (0.16 hellbenders per 100 m2) yielded two positive amplifications, the medium-density site (0.38 hellbenders per 100 m2) yielded eight positive amplifications, and the high-density site (0.88 hellbenders per 100 m2) yielded 10 positive amplifications. The apparent relationship between density and detection was obfuscated when river discharge was considered. There was no amplification in any negative control. Conclusion eDNA methods may represent a cost-effective means by which to establish broad-scale patterns of occupancy for hellbenders. Implications eDNA can be considered a valuable tool for detecting many species that are otherwise difficult to study.


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