scholarly journals Environmental DNA enables detection of terrestrial mammals from forest pond water

2016 ◽  
Author(s):  
Masayuki Ushio ◽  
Hisato Fukuda ◽  
Toshiki Inoue ◽  
Kobayashi Makoto ◽  
Osamu Kishida ◽  
...  
Keyword(s):  
Water Samples ◽  
Cervus Nippon ◽  
Environmental Dna ◽  
Terrestrial Ecosystems ◽  
Illumina Miseq ◽  
Pcr Primers ◽  
Pond Water ◽  
Universal Primers ◽  
Taxonomic Assignment ◽  
Terrestrial Mammals

Terrestrial animals must have frequent contact with water to maintain their lives, implying that environmental DNA (eDNA) originating from terrestrial animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR primers (MiMammal, a modified version of fish universal primers) for metabarcoding mammalian eDNA. After verifying the primers’ usefulness in silico and using water samples from zoo cages of animals with known species compositions, we collected five 500-ml water samples from ponds in two cool-temperate forests in Hokkaido, northern Japan. Using eDNA extracted from the water samples, we constructed amplicon libraries using MiMammal primers for Illumina MiSeq sequencing. MiMammal metabarcoding yielded a total of 75,214 reads, which we then subjected to data pre-processing and taxonomic assignment. We thereby detected species of mammals common to the sampling areas, including deer (Cervus nippon), mouse (Mus musculus), vole (Myodes rufocanus), raccoon (Procyon lotor), rat (Rattus norvegicus) and shrew (Sorex unguiculatus). Previous applications of the eDNA metabarcoding approach have mostly been limited to aquatic/semiaquatic systems, but the results presented here show that the approach is also promising even in forest mammal biodiversity surveys.

scholarly journals Demonstration of the potential of environmental DNA as a tool for the detection of avian species

2017 ◽  
Author(s):  
Masayuki Ushio ◽  
Koichi Murata ◽  
Tetsuya Sado ◽  
Isao Nishiumi ◽  
Masamichi Takeshita ◽  
...  
Keyword(s):  
Water Samples ◽  
Bird Species ◽  
Environmental Dna ◽  
Pcr Primers ◽  
Bird Communities ◽  
Avian Species ◽  
Universal Primers ◽  
Functional Roles ◽  
Detection And Identification ◽  
Miseq Platform

AbstractBirds play unique functional roles in the maintenance of ecosystems, such as pollina-tion and seed dispersal, and thus monitoring bird communities (e.g., monitoring bird species diversity) is a first step towards avoiding undesirable consequences of anthro-pogenic impacts on bird communities. In the present study, we hypothesized that birds, regardless of their main habitats, must have frequent contact with water and that tissues that contain their DNA that persists in the environment (environmental DNA; eDNA) could be used to detect the presence of avian species. To this end, we applied a set of universal PCR primers (MiBird, a modified version of fish/mammal universal primers) for metabarcoding avian eDNA. We confirmed the versatility of MiBird primers by performing in silico analyses and by amplifying DNAs extracted from bird tissues. Analyses of water samples from zoo cages of birds with known species composition suggested that the use of MiBird primers combined with the Il-lumina MiSeq platform could successfully detect avian species from water samples. Additionally, analysis of water samples collected from a natural pond detected five avian species common to the sampling areas. The present findings suggest that avian eDNA metabarcoding would be a complementary detection/identification tool in cases where visual detection and identification of bird species is difficult.

scholarly journals Environmental DNA enables detection of terrestrial mammals from forest pond water

2017 ◽  
Vol 17 (6) ◽  
pp. e63-e75 ◽  
Author(s):  
Masayuki Ushio ◽  
Hisato Fukuda ◽  
Toshiki Inoue ◽  
Kobayashi Makoto ◽  
Osamu Kishida ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Pond Water ◽  
Terrestrial Mammals ◽  
Forest Pond

scholarly journals Aquatic biofilms can act as natural environmental DNA samplers

2021 ◽  
Vol 4 ◽  
Author(s):  
Sinziana Rivera ◽  
Valentin Vasselon ◽  
Frederic Rimet ◽  
Agnès Bouchez
Keyword(s):  
Water Samples ◽  
Ecological Status ◽  
Fish Communities ◽  
Morphological Characteristics ◽  
Environmental Dna ◽  
Reference Database ◽  
Macroinvertebrate Communities ◽  
Taxonomic Assignment ◽  
Novel Approach ◽  
Single Matrix

Diatoms, macroinvertebrates and fish communities are widely used for the assessment of the ecological status of rivers and lakes. Metabarcoding studies of these communities are usually performed from “bulk” samples in the case of diatoms and macroinvertebrates; and from water samples in the case of fish. Recent studies, suggest that aquatic biofilms can physically act as environmental catchers of environmental DNA (eDNA) (e.g. Mariani et al. 2019). Thus, we propose an alternative metabarcoding approach to study macroinvertebrates and fishes directly from this matrix. The capacity of aquatic biofilms to catch macroinvertebrate eDNA was tested from a previous study in Mayotte Island were both biofilm samples and macroinvertebrate morphological inventories were available at same river sites (Rivera et al. 2021). First, macroinvertebrate specimens were identified based on their morphological characteristics. Second, DNA was extracted from biofilms, and macroinvertebrate communities were targeted using a standard COI barcode. The resulting morphological and molecular inventories were compared. Our results showed that both methods provided comparable structures and diversities for macroinvertebrate communities when using unassigned OTUs suggesting that macroinvertebrate DNA is present in biofilms and representative of the communities. However, after taxonomic assignment of OTUs, diversity and richness were no longer correlated. Indeed, many constraints were observed as the need for: a) more specific primers to avoid co-amplification of untargeted taxa inhabiting biofilms, b) primers targeting shorter barcodes to sequence more easily degraded eDNA that may be captured in biofilms, and c) a reference database well adapted to our tropical study sites. Finally, even if the results of this first study were encouraging, we wanted to test the biofilm approach on organisms that do not inhabit this environmental matrix in order to be able to distinguish between intra or extra-cellular DNA. Based on these observations, a second study looking for a fish eDNA signal in aquatic biofilms was performed. Environmental biofilm and water samples were collected in parallel at littoral sites at Lake Geneva. DNA was extracted from these samples, and fish communities were targeted using a standard 12S barcode. The molecular inventories derived from the biofilm and the water samples were compared. Both methods provide comparable floristic lists, providing a novel approach for ecological studies related to fish phenology using eDNA in biofilms. Our results open the door to the study of diatoms, macroinvertebrates and fish communities through metabarcoding from a single matrix reducing sampling efforts and costs.

scholarly journals eDNA metabarcoding outperforms traditional fisheries sampling and reveals fine-scale heterogeneity in a temperate freshwater lake

2020 ◽  
Author(s):  
Rebecca R Gehri ◽  
Wesley A. Larson ◽  
Kristen Gruenthal ◽  
Nicholas Sard ◽  
Yue Shi
Keyword(s):  
Community Composition ◽  
Lake Water ◽  
Water Samples ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
Aquatic Systems ◽  
Taxonomic Resolution ◽  
Universal Primers ◽  
Great Promise ◽  
Fish Diversity

AbstractUnderstanding biodiversity in aquatic systems is critical to ecological research and conservation efforts, but accurately measuring species richness using traditional methods can be challenging. Environmental DNA (eDNA) metabarcoding, which uses high-throughput sequencing and universal primers to amplify DNA from multiple species present in an environmental sample, has shown great promise for augmenting results from traditional sampling to characterize fish communities in aquatic systems. Few studies, however, have compared exhaustive traditional sampling with eDNA metabarcoding of corresponding water samples at a small spatial scale. We intensively sampled Boardman Lake (137 ha) in Michigan, USA from May to June in 2019 using gill and fyke nets and paired each net set with lake water samples collected in triplicate. We analyzed water samples using eDNA metabarcoding with 12S and 16S fish-specific primers and compared estimates of fish diversity among methods. In total, we set 60 nets and analyzed 180 1 L lake water samples. We captured a total of 12 fish species in our traditional gear and detected 40 taxa in the eDNA water samples, which included all the species observed in nets. The 12S and 16S assays detected a comparable number of taxa, but taxonomic resolution varied between the two genes. In our traditional gear, there was a clear difference in the species selectivity between the two net types, and there were several species commonly detected in the eDNA samples that were not captured in nets. Finally, we detected spatial heterogeneity in fish community composition across relatively small scales in Boardman Lake with eDNA metabarcoding, but not with traditional sampling. Our results demonstrated that eDNA metabarcoding was substantially more efficient than traditional gear for estimating community composition, highlighting the utility of eDNA metabarcoding for assessing species diversity and informing management and conservation.

scholarly journals Concentration and quantification of Tilapia tilapinevirus from water using a simple iron flocculation coupled with probe-based RT-qPCR

2021 ◽  
Author(s):  
Suwimon Taengphu ◽  
Pattanapon Kayansamruaj ◽  
Yasuhiko Kawato ◽  
Jerome Delamare-Deboutteville ◽  
Chadag Vishnumurthy Mohan ◽  
...  
Keyword(s):  
Water Samples ◽  
Detection System ◽  
Environmental Dna ◽  
Pond Water ◽  
Disease Forecasting ◽  
Early Disease ◽  
River Water Samples ◽  
Specificity And Sensitivity ◽  
Qpcr Method ◽  
Detection And Quantification

Tilapia tilapinevirus (also known as tilapia lake virus, TiLV) is an important virus responsible for die-off of farmed tilapia globally. Detection and quantification of the virus from environmental DNA/RNA (eDNA/eRNA) using pond water represents a potential, noninvasive routine approach for pathogen monitoring and early disease forecasting in aquaculture systems. Here, we report a simple iron flocculation method for viral concentration from water combined with a newly developed hydrolysis probe quantitative RT-qPCR method for detection and quantification of TiLV. The RT-qPCR method targeting a conserved region of TiLV genome segment 9 has a detection limit of 10 viral copies per uL of template. The method had a 100% analytical specificity and sensitivity for TiLV. The optimized iron flocculation method was able to recover 16.11 +/- 3.3% of virus from water samples spiked with viral cultures. During disease outbreak cases from an open-caged system and a closed hatchery system, both tilapia and water samples were collected for detection and quantification of TiLV. The results revealed that TiLV was detected from both clinically sick fish and asymptomatic fish. Most importantly, the virus was successfully detected from water samples collected from different locations in the affected farms e.g. river water samples from affected cages (8.50 x 102 to 2.79 x 104 copies/L) and fish-rearing water samples, sewage, and reservoir (4.29 x 102 to 3.53 x 103 copies/L) from affected and unaffected ponds of the hatchery. In summary, this study suggests that the eRNA detection system using iron flocculation coupled with probe based-RT-qPCR is feasible for concentration and quantification of TiLV from water. This approach might be useful for noninvasive monitoring of TiLV in tilapia aquaculture systems and facilitating appropriate decisions on biosecurity interventions needed.

Investigation of Some Water Quality Parameters of Pond Water under Mymensingh Municipality

2015 ◽  
Vol 8 (1) ◽  
pp. 85-89
Author(s):  
F Zannat ◽  
MA Ali ◽  
MA Sattar
Keyword(s):  
Water Quality ◽  
Water Samples ◽  
Chemical Properties ◽  
Pond Water ◽  
Quality Parameters ◽  
Water Quality Parameters ◽  
Urban Region ◽  
Mn Toxicity ◽  
Ph Values ◽  
Drinking Water Standard

A study was conducted to evaluate the water quality parameters of pond water at Mymensingh Urban region. The water samples were collected from 30 ponds located at Mymensingh Urban Region during August to October 2010. The chemical analyses of water samples included pH, EC, Na, K, Ca, S, Mn and As were done by standard methods. The chemical properties in pond water were found pH 6.68 to 7.14, EC 227 to 700 ?Scm-1, Na 15.57 to 36.00 ppm, K 3.83 to 16.16 ppm, Ca 2.01 to 7.29 ppm, S 1.61 to 4.67 ppm, Mn 0.33 to 0.684 ppm and As 0.0011 to 0.0059 ppm. The pH values of water samples revealed that water samples were acidic to slightly alkaline in nature. The EC value revealed that water samples were medium salinity except one sample and also good for irrigation. According to drinking water standard Mn toxicity was detected in pond water. Considering Na, Ca and S ions pond water was safe for irrigation and aquaculture. In case of K ion, all the samples were suitable for irrigation but unsuitable for aquaculture.J. Environ. Sci. & Natural Resources, 8(1): 85-89 2015

A Multiplex PCR Assay Mediated by Universal Primers for the Detection of Adulterated Meat in Mutton

2019 ◽  
Vol 82 (2) ◽  
pp. 325-330 ◽  
Author(s):  
WANWAN LIU ◽  
XIAONAN WANG ◽  
JING TAO ◽  
BANGSHENG XI ◽  
MAN XUE ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Detection System ◽  
Meat Products ◽  
Pcr Primers ◽  
Rapid Identification ◽  
Food Samples ◽  
Detection Sensitivity ◽  
Universal Primers ◽  
Multiplex Pcr Assay ◽  
Multiple Pcr

ABSTRACT This study aimed to establish a multiplex PCR detection system mediated by “universal primers,” which would be able to determine whether mutton meat contained nonmutton ingredients from rats, foxes, and ducks. Based on the sequence variation of specific mitochondrial genes, nine different multiplex PCR primers were designed, and four kinds of meat products were rapidly identified by electrophoresis using an optimized multiplex PCR system based on the molecular weight differences of the amplified products. Multiplex PCR applications optimized for meat food source from food samples for testing was used to verify the accuracy of the identification method. The results showed that the primers in multiple PCR system mediated by universal primers could be used for the rapid identification of rat, fox, duck, and sheep meat in mutton products, and the detection sensitivity could reach 0.05 ng/μL. The identification of food samples validated the practical value of this method. Therefore, a multiplex PCR system mediated by universal primers was established, which can be used to quickly identify the origin of animal ingredients from rats, foxes, and ducks in mutton products.

scholarly journals Dental functional traits of mammals resolve productivity in terrestrial ecosystems past and present

2012 ◽  
Vol 279 (1739) ◽  
pp. 2793-2799 ◽  
Author(s):  
Liping Liu ◽  
Kai Puolamäki ◽  
Jussi T. Eronen ◽  
Majid M. Ataabadi ◽  
Elina Hernesniemi ◽  
...  
Keyword(s):  
Net Primary Productivity ◽  
Terrestrial Ecosystems ◽  
Functional Trait ◽  
Geological Time ◽  
Crown Height ◽  
Short Term ◽  
Functional Interpretation ◽  
Terrestrial Mammals ◽  
Terrestrial Biomes ◽  
The Relationship

We have recently shown that rainfall, one of the main climatic determinants of terrestrial net primary productivity (NPP), can be robustly estimated from mean molar tooth crown height (hypsodonty) of mammalian herbivores. Here, we show that another functional trait of herbivore molar surfaces, longitudinal loph count, can be similarly used to extract reasonable estimates of rainfall but also of temperature, the other main climatic determinant of terrestrial NPP. Together, molar height and the number of longitudinal lophs explain 73 per cent of the global variation in terrestrial NPP today and resolve the main terrestrial biomes in bivariate space. We explain the functional interpretation of the relationships between dental function and climate variables in terms of long- and short-term demands. We also show how the spatially and temporally dense fossil record of terrestrial mammals can be used to investigate the relationship between biodiversity and productivity under changing climates in geological time. The placement of the fossil chronofaunas in biome space suggests that they most probably represent multiple palaeobiomes, at least some of which do not correspond directly to any biomes of today's world.

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