scholarly journals Effects of Microbial Activity and Environmental Parameters on the Degradation of Extracellular Environmental DNA from a Eutrophic Lake

2019 ◽  
Vol 16 (18) ◽  
pp. 3339 ◽  
Author(s):  
Nur Syahidah Zulkefli ◽  
Keon-Hee Kim ◽  
Soon-Jin Hwang
Keyword(s):  
Microbial Activity ◽  
Degradation Rate ◽  
Abiotic Factors ◽  
Environmental Parameters ◽  
Environmental Dna ◽  
Eutrophic Lake ◽  
Freshwater Ecosystems ◽  
Extracellular Dna ◽  
Biotic And Abiotic Factors ◽  
Positive Effects

Extracellular DNA (exDNA) pool in aquatic environments is a valuable source for biomonitoring and bioassessment. However, degradation under particular environmental conditions can hamper exDNA detectability over time. In this study, we analyzed how different biotic and abiotic factors affect the degradation rate of extracellular environmental DNA using 16S rDNA sequences extracted from the sediment of a eutrophic lake and Anabaena variabilis cultured in the laboratory. We exposed the extracted exDNA to different levels of temperature, light, pH, and bacterial activity, and quantitatively analyzed the concentration of exDNA during 4 days. The solution containing bacteria for microbial activity treatment was obtained from the lake sediment using four consecutive steps of filtration; two mesh filters (100 μm and 60 μm mesh) and two glass fiber filters (2.7 μm and 1.2 μm pore-sized). We found that temperature individually and in combination with bacterial abundance had significant positive effects on the degradation of exDNA. The highest degradation rate was observed in samples exposed to high microbial activity, where exDNA was completely degraded within 1 day at a rate of 3.27 day−1. Light intensity and pH had no significant effects on degradation rate of exDNA. Our results indicate that degradation of exDNA in freshwater ecosystems is driven by the combination of both biotic and abiotic factors and it may occur very fast under particular conditions.

Quantifying Shedding and Degradation Rates of Environmental DNA (eDNA) from Pacific Crown-of-thorns Seastar (Acanthaster cf. Solaris)

2021 ◽  
Author(s):  
Sarah Lok Ting Kwong ◽  
Cecilia Villacorta-Rath ◽  
Jason Doyle ◽  
Sven Uthicke
Keyword(s):  
Degradation Rate ◽  
Abiotic Factors ◽  
Feeding Activity ◽  
Environmental Dna ◽  
Aquatic Environments ◽  
Early Life Stages ◽  
Factors Affecting ◽  
Degradation Rates ◽  
Population Outbreaks ◽  
Two Temperatures

Abstract Population outbreaks of the corallivorous crown-of-thorns seastar (CoTS; Acanthaster spp.) are significant threats to the Indo-Pacific reefs. Although recent research demonstrated that environmental DNA (eDNA) techniques could improve CoTS monitoring and management, the interpretation of surveillance results has been limited by uncertainties about eDNA dynamics in aquatic environments. Here, we aimed to identify biotic and abiotic factors affecting the shedding and degradation rates of CoTS eDNA. Using laboratory-raised 8-month-old juvenile CoTS, aquarium experiments were conducted to test the effect of two temperatures (24 and 28°C) and three feeding treatments (no food, food available and food inaccessible) on eDNA shedding rate. Additionally, CoTS eDNA degradation rate was quantified under three temperatures (24, 26 and 28°C). We found that eDNA shedding rate was affected by feeding treatment (p < 0.0001) but not temperature. Specifically, the shedding rate under food accessible treatment was about 7 times higher than that of food inaccessible treatment (p < 0.0001), whereas the presence of coral reduced the shedding rate by half (food inaccessible vs no food, p = 0.0249). Degradation of CoTS eDNA was rapid (half-life = 14h) and not affected by temperature. Our results demonstrated that feeding activity increased eDNA release, but some of the released DNA was lost potentially due to binding to coral surface mucus layer or skeleton. The rapid degradation rate indicated that results of eDNA surveillance likely reflects recent and local occurrence of CoTS. Although further testing is needed, this study provided support for using eDNA as a novel detection tool for early life stages of CoTS on coral reefs.

scholarly journals Effect of biotic and abiotic factors on the production and degradation of fish environmental DNA: An experimental evaluation

2021 ◽  
Author(s):  
Isabeau Caza‐Allard ◽  
Martin Laporte ◽  
Guillaume Côté ◽  
Julien April ◽  
Louis Bernatchez
Keyword(s):  
Experimental Evaluation ◽  
Abiotic Factors ◽  
Environmental Dna ◽  
Biotic And Abiotic Factors

scholarly journals The impact of invertebrate pests on pasture persistence and their interrelationship with biotic and abiotic factors

2011 ◽  
Vol 15 ◽  
pp. 109-117
Author(s):  
S.M. Zydenbos ◽  
B.I.P. Barratt ◽  
N.L. Bell ◽  
C.M. Ferguson ◽  
P.J. Gerard ◽  
...  
Keyword(s):  
Soil Fertility ◽  
Plant Pathogens ◽  
Management Practices ◽  
Abiotic Factors ◽  
Insect Damage ◽  
Long Term Effects ◽  
Pasture Management ◽  
Biotic And Abiotic Factors ◽  
Positive Effects ◽  
The Impact

New Zealand pastures are host to a range of native and exotic invertebrates. Many of these are pests that feed on the sown plant species, often causing plant death and deterioration in the productivity and persistence of the sward. While most research has focused on pest biology and control, studies of plant productivity show dramatic acute (short-medium term) and chronic (longterm) effects. For example, grass grub has been reported to cause 50% losses to ryegrass swards and Argentine stem weevil can cause a 20% loss of productivity, but the long term effects through loss of the sown species and changes in composition can be even more severe. Insect damage can be exacerbated by other biotic (e.g. weed invasion, grazing animals, plant pathogens) or abiotic factors (e.g. climate, soil fertility) to further reduce plant persistence. Some biotic and abiotic factors may interact with insect pests to have positive effects on pasture persistence, e.g. biocontrol agents that reduce pest density or addition of fertiliser to enable plants to recover from insect damage. For many pasture pests, knowledge of their ecology is based on research from over 20 years ago that, while still valid, needs to be updated to account for modern intensive pasture management practices, such as intensive grazing with a lack of reseeding, and new cultivars. To improve pasture persistence, integrated research programmes are needed that examine the relative importance of all factors contributing to plant survival and develop strategies to mitigate their effects. Keywords: Argentine stem weevil, black beetle, clover root weevil, drought, grass grub, grazing pressure, manuka beetle, nematodes, pasture persistence, pasture quality, pasture yield, porina, soil fertility, striped chafer.

scholarly journals Development of environmental DNA surveillance for the threatened crucian carp (Carassius carassius)

2018 ◽  
Author(s):  
Lynsey R Harper ◽  
Nathan P Griffiths ◽  
Lori Lawson Handley ◽  
Carl D Sayer ◽  
Daniel S Read ◽  
...  
Keyword(s):  
Copy Number ◽  
Crucian Carp ◽  
Abiotic Factors ◽  
Environmental Dna ◽  
Carassius Carassius ◽  
Catch Per Unit Effort ◽  
Dna Copy Number ◽  
Species Detection ◽  
Biotic And Abiotic Factors ◽  
Macrophyte Cover

The crucian carp (Carassius carassius) is one of few fish species associated with small ponds in the UK. These populations contain genetic diversity not found in Europe and are important to conservation efforts for the species, which has declined across its range. Detection and monitoring of extant crucian carp populations are crucial for conservation success. Environmental DNA (eDNA) analysis could be very useful in this respect as a rapid, cost-efficient monitoring tool. We developed a species-specific quantitative PCR (qPCR) assay for eDNA surveillance of crucian carp to enable non-invasive, large-scale distribution monitoring. We compared fyke netting and eDNA at ponds with (N = 10) and without (N = 10) crucian carp for presence-absence detection and relative abundance estimation, specifically whether DNA copy number reflected catch-per-unit-effort (CPUE) estimate. We examined biotic and abiotic influences on eDNA detection and quantification, and compared qPCR to standard PCR. Notably, eDNA occurrence and detection probabilities in relation to biotic and abiotic factors were estimated using a hierarchical occupancy model. eDNA analysis achieved 90% detection for crucian carp (N = 10), failing in only one pond where presence was known. We observed an overall positive trend between DNA copy number and CPUE estimate, but this was not significant. Macrophyte cover decreased the probability of eDNA occurrence at ponds, whereas CPUE and conductivity had positive and negative influences on eDNA detection probability in qPCR replicates respectively. Conductivity also had a negative effect on DNA copy number, but copy number increased with temperature and percentage of macrophyte cover. PCR was comparable to qPCR for species detection and may provide semi-quantitative information. Our results demonstrate that eDNA could enable detection of crucian carp populations in ponds and benefit ongoing conservation efforts, but imperfect species detection in relation to biotic and abiotic factors and eDNA workflow requires further investigation. Nonetheless, we have established an eDNA framework for crucian carp and sources of imperfect detection which future investigations can build upon.

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