scholarly journals Degradation modeling of water environmental DNA: Experiments on multiple DNA sources in pond and seawater

2020 ◽  
Author(s):  
Tatsuya Saito ◽  
Hideyuki Doi
Keyword(s):  
Environmental Dna ◽  
Degradation Process ◽  
Exponential Model ◽  
Natural Environments ◽  
Multiple Sources ◽  
Marine Habitats ◽  
Fundamental Information ◽  
Degradation Rates ◽  
Free Cells ◽  
Degradation Models

ABSTRACTEnvironmental DNA (eDNA) methods have been developed to detect organism distribution and abundance/biomass in various environments. eDNA degradation is critical for eDNA evaluation. However, the dynamics and mechanisms of eDNA degradation are largely unknown, especially when considering different eDNA sources, e.g., cells and fragmental DNA. We experimentally evaluated the degradation rates of eDNA derived from multiple sources, including fragmental DNA, free cells, and inhabiting species. We conducted the experiment with pond and seawater to evaluate the differences between freshwater and marine habitats. We quantified the eDNA copies of free cells, fragmental DNA, and inhabiting species (Cyprinus carpio in the pond and Trachurus japonicus in the sea). Our results show that eDNA derived from both cells and fragmental DNA decreased exponentially in both the sea and pond samples. The degradation of eDNA from inhabiting species showed similar behavior to the cell-derived eDNA. We evaluated three degradation models with different assumptions and degradation steps and found that a simple exponential model is effective in most cases. Our findings on cell- and fragmental DNA-derived eDNA provide fundamental information about the eDNA degradation process and can be applied to elucidate eDNA behavior in natural environments.

scholarly journals Effect of salinity and water dilution on environmental DNA degradation in freshwater environments

2021 ◽  
Author(s):  
Tatsuya Saito ◽  
Hideyuki Doi
Keyword(s):  
Degradation Rate ◽  
Salt Water ◽  
Environmental Dna ◽  
Degradation Process ◽  
Pond Water ◽  
Dna Degradation ◽  
Free Cell ◽  
Natural Environments ◽  
Fundamental Information ◽  
Water Dilution

Environmental DNA (eDNA) analysis methods have been developed to detect the distribution and abundance/biomass of organisms in various environments. eDNA generally degrades quickly, thus the study of eDNA degradation is critical for eDNA evaluation. However, there have only been a few studies of eDNA degradation experiments in which the salt concentration and water dilution were controlled. In this study, the effects of degradation were experimentally evaluated by controlling the salinity and water dilution of pond water. An experiment was conducted to evaluate the effects of salinity and dilution on eDNA detection with fragmental eDNA and free cell-derived eDNA using pond water, diluted pond water, and saline pond water. We quantified the eDNA copies of free cells, fragmental DNA, and the eDNA from Cyprinus carpio. In both the diluted and saline pond water, we found that the degradation rate of eDNA was much slower than that in pond water. Furthermore, the DNA concentration did not exponentially decrease in both the saline purified water and purified water samples. For the lower degradation rate in salt water, we interpreted that salts may affect DNA degradation factors such as microbe compositions and activities. The effect of salinity and dilution on eDNA detection provides fundamental information about the degradation process of eDNA, which is essential to understand the behavior of eDNA in natural environments.

scholarly journals Degradation factors of environmental DNA evaluated by experiments and meta-analysis

2021 ◽  
Vol 4 ◽  
Author(s):  
Tatsuya Saito ◽  
Hideyuki Doi
Keyword(s):  
Water Temperature ◽  
Degradation Rate ◽  
Meta Analysis ◽  
Environmental Dna ◽  
Resident Species ◽  
Multiple Sources ◽  
Related Factors ◽  
Marine Habitats ◽  
Amplicon Length ◽  
Degradation Rates

Environmental DNA (eDNA) methods have been developed to detect organisms' distributions and abundance/biomass in various environments. eDNA degradation is critical for eDNA evaluation, but, the dynamics and mechanisms of eDNA degradation are largely unknown, especially when considering different eDNA sources, e.g., cell-derived and fragmental DNA. In this study, we conducted the degradation experiments (Saito and Doi 2020a) and a meta-analysis (Saito and Doi 2020b). Firstly, we experimentally evaluated the degradation rates of eDNA derived from multiple sources, including fragmental DNA (the DNA of internal positive control, IPC), free cells from Oncorhynchus kisutch, and the resident species (Saito and Doi 2020a). We conducted the experiments with pond and seawater to evaluate the differences between freshwater and marine habitats. Our results showed that eDNA derived from the both cells and fragmental DNA decreased exponentially in the both sea and pond samples. The degradation of eDNA from the resident species showed similar behavior to the cell-derived eDNA. As a meta-analysis, we complied the degradation rates of eDNA in laboratory experiment and field studies from 28 studies (Saito and Doi 2020b). We also collected the related factors, including water sources, water temperature, DNA regions, and PCR amplicon lengths of the measured DNA. Our results suggested that water temperature and amplicon length were significantly related to the degradation rate of eDNA. From the simulation based on the 95% quantile model, we predicted the maximum degradation rate of eDNA in various combinations of water temperature and PCR amplicon length.

Examination for Degradation Paths of Butyltin Compounds in Natural Waters

1992 ◽  
Vol 25 (11) ◽  
pp. 117-124 ◽  
Author(s):  
N. Watanabe ◽  
S. Sakai ◽  
H. Takatsuki
Keyword(s):  
Glass Fiber ◽  
Half Life ◽  
Natural Waters ◽  
Sea Water ◽  
Degradation Process ◽  
Distilled Water ◽  
Degradation Rates ◽  
Clean Area ◽  
Butyltin Compounds ◽  
Sun Light

Examination of individual degradation paths (biodegradation and photolysis) of butyltin compounds (especially tributyltin: TBT) in natural waters was performed. Biodegradation of TBT and dibutyltin (DBT) in an unfiltered sea water in summer is rather fast; their half life is about a week. But pretreatment with glass fiber filter makes the half life of TBT much longer (about 80 days). Photolysis of TBT in sea water by sun light is rapid (half life is about 0.5 days), and faster than in distilled water or in fresh water. Degradation rates of each process for TBT are calculated in various conditions of sea water, and contribution rates are compared. Biodegradation will be the main degradation process in an “SS-rich” area such as a marina, but photolysis will exceed that in a “clean” area. Over all half lives of TBT in sea water vary from 6 days to 127 days considering seasons and presence of SS.

scholarly journals Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tatsuhiko Hoshino ◽  
Ryohei Nakao ◽  
Hideyuki Doi ◽  
Toshifumi Minamoto
Keyword(s):  
Fish Species ◽  
High Throughput Sequencing ◽  
Correlation Coefficients ◽  
Environmental Dna ◽  
Digital Pcr ◽  
Absolute Quantification ◽  
Taqman Probe ◽  
Individual Species ◽  
Natural Environments ◽  
Target Sequence

AbstractThe combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5′ end of the target sequence during the first DNA synthesis. Here, we applied qSeq to eDNA analysis to test its effectiveness in biodiversity monitoring. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.

Bacterial microencapsulation with three algal polysaccharides

1997 ◽  
Vol 43 (11) ◽  
pp. 1091-1095 ◽  
Author(s):  
Terry B. Hammill ◽  
Ronald L. Crawford
Keyword(s):  
Aqueous Medium ◽  
Guar Gum ◽  
Cell Suspensions ◽  
Type I ◽  
Type Ii ◽  
Degradation Rates ◽  
Degrading Bacteria ◽  
Free Cells ◽  
Algal Polysaccharides ◽  
Pressure Nozzle

Methods for encapsulating pollutant-degrading bacteria into microbeads of carrageenan type I, carrageenan type II, and guar gum are described. Cell suspensions in solutions of encapsulating agents were passed through a low-pressure nozzle into an aqueous medium. The resultant aerosols polymerized to form microbeads that ranged in diameter from 2–70 μm. Pentachlorophenol degradation experiments with an encapsulated Sphingomonas sp. showed degradation rates similar to those seen using free cells. These results describe three additional matrices for the microencapsulation of bacteria that have potential for use in bioremediation processes.Key words: Sphingomonas, pentachlorophenol, immobilization, encapsulation, bioremediation.

scholarly journals Estimation accuracy of species abundance based on environmental DNA with relation to its production source, state, and assay methodology suggested by meta-analyses

2021 ◽  
Author(s):  
Toshiaki Jo ◽  
Hiroki Yamanaka
Keyword(s):  
Meta Analysis ◽  
Empirical Studies ◽  
Species Abundance ◽  
Environmental Dna ◽  
Efficient Estimation ◽  
Estimation Accuracy ◽  
Accurate Estimation ◽  
Abundance Estimation ◽  
Natural Environments ◽  
Promising Tool

Environmental DNA (eDNA) analysis is a promising tool for non-disruptive and cost-efficient estimation of species abundance. However, its practical applicability in natural environments is limited because it is unclear whether eDNA concentrations actually represent species abundance in the field. Although the importance of accounting for eDNA dynamics, such as transport and degradation, has been discussed, the influences of eDNA characteristics, including production source and state, and methodology, including collection and quantification strategy and abundance metrics, on the accuracy of eDNA-based abundance estimation were entirely overlooked. We conducted a meta-analysis using 56 previous eDNA literature and investigated the relationships between the accuracy (R2) of eDNA-based abundance estimation and eDNA characteristics and methodology. Our meta-regression analysis found that R2 values were significantly lower for crustaceans than fish, suggesting that less frequent eDNA production owing to their external morphology and physiology may impede accurate estimation of their abundance via eDNA. Moreover, R2 values were positively associated with filter pore size, indicating that selective collection of larger-sized eDNA, which is typically fresher, could improve the estimation accuracy of species abundance. Furthermore, R2 values were significantly lower for natural than laboratory conditions, while there was no difference in the estimation accuracy among natural environments. Our findings shed a new light on the importance of what characteristics of eDNA should be targeted for more accurate estimation of species abundance. Further empirical studies are required to validate our findings and fully elucidate the relationship between eDNA characteristics and eDNA-based abundance estimation.

scholarly journals Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats

2019 ◽  
Vol 34 (3) ◽  
pp. 697-710 ◽  
Author(s):  
Eva Egelyng Sigsgaard ◽  
Felipe Torquato ◽  
Tobias Guldberg Frøslev ◽  
Alec B. M. Moore ◽  
Johan Mølgård Sørensen ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Marine Habitats

scholarly journals Responses in the Inferior Colliculus of the Guinea Pig to Concurrent Harmonic Series and the Effect of Inactivation of Descending Controls

2010 ◽  
Vol 103 (4) ◽  
pp. 2050-2061 ◽  
Author(s):  
Kyle T. Nakamoto ◽  
Trevor M. Shackleton ◽  
Alan R. Palmer
Keyword(s):  
Guinea Pig ◽  
Auditory Cortex ◽  
Inferior Colliculus ◽  
Sound Level ◽  
Harmonic Series ◽  
Natural Environments ◽  
Multiple Sources ◽  
Spike Response ◽  
Relative Level ◽  
Communication Calls

One of the fundamental questions of auditory research is how sounds are segregated because, in natural environments, multiple sounds tend to occur at the same time. Concurrent sounds, such as two talkers, physically add together and arrive at the ear as a single input sound wave. The auditory system easily segregates this input into a coherent percept of each of the multiple sources. A common feature of speech and communication calls is their harmonic structure and in this report we used two harmonic complexes to study the role of the corticofugal pathway in the processing of concurrent sounds. We demonstrate that, in the inferior colliculus (IC) of the anesthetized guinea pig, deactivation of the auditory cortex altered the temporal and/or the spike response to the concurrent, monaural harmonic complexes. More specifically, deactivating the auditory cortex altered the representation of the relative level of the complexes. This suggests that the auditory cortex modulates the representation of the level of two harmonic complexes in the IC. Since sound level is a cue used in the segregation of auditory input, the corticofugal pathway may play a role in this segregation.

scholarly journals A Dynamic Failure Time Degradation-Based Model

Symmetry ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 1532
Author(s):  
Abdulhakim A. Albabtain ◽  
Mansour Shrahili ◽  
Lolwa Alshagrawi ◽  
Mohamed Kayid
Keyword(s):  
Hazard Rate ◽  
Failure Time ◽  
Degradation Process ◽  
Residual Lifetime ◽  
Time To Failure ◽  
Lifetime Distributions ◽  
Mean Residual Lifetime ◽  
Aging Properties ◽  
Degradation Models ◽  
Characterization Property

A novel methodology for modelling time to failure of systems under a degradation process is proposed. Considering the method degradation may have influenced the failure of the system under the setup of the model several implied lifetime distributions are outlined. Hazard rate and mean residual lifetime of the model are obtained and a numerical situation is delineated to calculate their amounts. The problem of modelling the amount of degradation at the failure time is also considered. Two monotonic aging properties of the model is secured and a characterization property of the symmetric degradation models is established.

Modeling and Optimization of Photocatalytic Degradation of Methylene Blue Using Lanthanum Vanadate

2020 ◽  
Vol 1008 ◽  
pp. 97-103
Author(s):  
Mahmoud Samy ◽  
Mona G. Ibrahim ◽  
Mohamed Gar Alalm ◽  
Manabu Fujii
Keyword(s):  
Methylene Blue ◽  
Photocatalytic Degradation ◽  
Removal Efficiency ◽  
Textile Industry ◽  
Degradation Process ◽  
Optimum Conditions ◽  
Photo Degradation ◽  
Operational Conditions ◽  
Degradation Rates ◽  
Effects Of Ph

Methylene blue (MB) is one of the commonly used dyes in the textile industry and can be used as a model pollutant for the textile industry wastewater. In this work, the photocatalytic degradation of MB by synthesized nanoparticles of lanthanum vanadate (LaVO4) was assessed. The effects of pH, initial MB concentration and catalyst dose on the removal performance of MB were investigated and measuring the optimum values of these operational conditions was performed using response surface methodology (RSM). Catalyst dose of 0.43 g/L, initial MB concentration of 5.0 mg/L, and pH of 6.86 were found to be the optimum conditions in reaction time of 60 min. A mathematical model was formed to relate the removal efficiency of MB to the aforementioned operating parameters. The removal efficiency of MB was 91% without any scavengers at a catalyst dose of 0.3 g/L, pH of 7 and initial MB concentration of 10 mg/L. The trapping experiments confirmed the participation of different reactive species in the photo-degradation process. The degradation rates of MB were 91%, 86%, 81%, 77.70% and 72% in five successive runs using LaVO4.

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