scholarly journals Treated like dirt: Robust forensic and ecological inferences from soil eDNA after challenging sample storage

2021 ◽  
Author(s):  
Tobias Guldberg Frøslev ◽  
Rasmus Ejrnæs ◽  
Anders Johannes Hansen ◽  
Hans Henrik Bruun ◽  
Ida Broman Nielsen ◽  
...  
Keyword(s):  
Community Composition ◽  
Storage Temperature ◽  
Habitat Type ◽  
Environmental Dna ◽  
Storage Conditions ◽  
Taxonomic Composition ◽  
Marker Genes ◽  
Original Sample ◽  
Storage Duration ◽  
Soil Microbiota

Biodiversity of soil microbiota is routinely assessed with environmental DNA-based methods, among which amplification and massive parallel sequencing of marker genes (eDNA metabarcoding) is the most common. Soil microbiota may for example be investigated in relation to biodiversity research or as a tool in forensic investigations. After sampling, the taxonomic composition of soil biotic communities may change. In order to minimize community changes after sampling, it is desirable to reduce biological activity, e.g. by freezing immediately after sampling. However, this may be impossible due to remoteness of study sites or, in forensic cases, where soil has been attached to a questioned item for protracted periods of time. Here we investigated the effect of storage duration and conditions on the assessment of the soil biota with eDNA metabarcoding. We extracted eDNA from freshly collected soil samples and again from the same samples after storage under contrasting temperature conditions. We used five different primer sets targeting bacteria, fungi, protists (cercozoans), general eukaryotes, and plants. For these groups, we quantified differences in richness, evenness and community composition. Subsequently, we tested whether we could correctly infer habitat type and original sample identity after storage using a large reference dataset. We found increased community composition differences with extended storage time and with higher storage temperature. However, for samples stored less than 28 days at a maximum of 20 C, changes were generally insignificant. Classification models could successfully assign most stored samples to their exact location of origin and correct habitat type even after weeks of storage. Even samples showing larger compositional changes generally retained the original sample as the best match (relative similarity). Our results show that for most biodiversity and forensic applications, storage of samples for days and even several weeks may not be a problem, if storage temperature does not exceed 20 C. Even after suboptimal storage conditions, significant patterns can be reproduced.

scholarly journals The effect of silica desiccation under different storage conditions on filter-immobilized environmental DNA

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Michael J. Allison ◽  
Jessica M. Round ◽  
Lauren C. Bergman ◽  
Ali Mirabzadeh ◽  
Heather Allen ◽  
...  
Keyword(s):  
Silica Gel ◽  
Storage Temperature ◽  
Environmental Dna ◽  
Cost Effective ◽  
Storage Conditions ◽  
Systematic Evaluation ◽  
Silica Bead ◽  
Gel Beads ◽  
Polymerase Chain

Abstract Objective Silica gel beads have promise as a non-toxic, cost-effective, portable method for storing environmental DNA (eDNA) immobilized on filter membranes. Consequently, many ecological surveys are turning to silica bead filter desiccation rather than ethanol preservation. However, no systematic evaluation of silica bead storage conditions or duration past 1 week has been published. The present study evaluates the quality of filter-immobilized eDNA desiccated with silica gel under different storage conditions for over a year using targeted quantitative real-time polymerase chain reaction (qPCR)-based assays. Results While the detection of relatively abundant eDNA target was stable over 15 months from either ethanol- or silica gel-preserved filters at − 20 and 4 °C, silica gel out-performed ethanol preservation at 23 °C by preventing a progressive decrease in eDNA sample quality. Silica gel filter desiccation preserved low abundance eDNA equally well up to 1 month regardless of storage temperature (18, 4, or − 20 °C). However only storage at − 20 °C prevented a noticeable decrease in detectability at 5 and 12 months. The results indicate that brief storage of eDNA filters with silica gel beads up to 1 month can be successfully accomplished at a range of temperatures. However, longer-term storage should be at − 20 °C to maximize sample integrity.

Effects of Storage Duration on Biodiesel Properties Derived from Waste Cooking Oil

2014 ◽  
Vol 554 ◽  
pp. 494-499 ◽  
Author(s):  
Amir Khalid ◽  
Norazwan Azman ◽  
Hanis Zakaria ◽  
Bukhari Manshoor ◽  
Izzuddin Zaman ◽  
...  
Keyword(s):  
Water Content ◽  
Fossil Fuels ◽  
Storage Temperature ◽  
Acid Value ◽  
Waste Cooking Oil ◽  
Storage Conditions ◽  
Storage Duration ◽  
Oil Reserves ◽  
Cooking Oil ◽  
Different Temperatures

The reduction of world oil reserves fossil fuels and increasing environmental concerns significantly influences the popularity of biodiesel as an alternative diesel. This research investigates the effects of storage duration of variant blending waste cooking oil ratio under different storage temperature on fuel properties. The biodiesel samples were stored at different temperatures and were monitored at regular interval over a period of 70 days. Blending of biodiesel was varied from 5vol % (WCO5) ~15vol% (WCO15) and storage temperature from 24°C~35°C. These samples were monitored on a weekly and the effects of storage conditions on properties of biodiesel such as density, kinematics viscosity, acid value, water content and flash point of biodiesel were discussed in detail. The observation of biodiesel shows that the increasing of storage duration of biodiesel derived from waste cocking oil influences to the increasing of density, kinematics viscosity, acid value and water content.

Root freezing tolerance and vitality of Norway spruce and Scots pine seedlings; influence of storage duration, storage temperature, and prestorage root freezing

1994 ◽  
Vol 24 (12) ◽  
pp. 2477-2484 ◽  
Author(s):  
Anders Lindström ◽  
Eva Stattin
Keyword(s):  
Norway Spruce ◽  
Scots Pine ◽  
Freezing Tolerance ◽  
Storage Temperature ◽  
Frozen Storage ◽  
Storage Conditions ◽  
Freezing Injury ◽  
Storage Duration ◽  
Storage Container ◽  
Pine Seedlings

This study investigated the effect of different cold storage conditions on (i) root freezing tolerance of Norway spruce (Piceaabies (L.) Karst.) and Scots pine (Pinussylvestris L.) and (ii) the vitality of seedlings that suffered freezing injury to roots prior to storage. Container-grown seedlings, 1 year old, were stored from the end of October to April in three environments with different root temperatures: outdoor storage (−0.5 to 11.0 °C), cool storage (0.7 to 3.7 °C), or frozen storage (−5.0 to −3.8 °C). Root freezing tolerance was determined prior to storage in October and during storage in January and March. Maximum root freezing tolerance for both species occurred in January, when over 50% of spruce and pine seedlings survived 2 h exposure to −25 and −20 °C, respectively. At this time, roots of frozen-stored spruce were significantly more freezing tolerant than outdoor-stored seedlings, whereas storage environment had no significant effect on pine. Freezing tolerance in roots of both species decreased from January to March in all test environments but to a lesser extent at the subzero temperatures in the frozen storage. Root freezing to −10, −15, or −20 °C in late October before storage resulted in reduced poststorage survival of seedlings in April. Pine was more adversely affected (0–13% survival) than spruce (0–85% survival). Freezing of roots prior to storage caused the lowest survival with frozen storage.

scholarly journals Dependence of fat acidity value on wheat grain storage conditions

2020 ◽  
Vol 17 ◽  
pp. 00107
Author(s):  
I. A. Kechkin ◽  
V. A. Ermolaev ◽  
M. V. Ivanov ◽  
A. I. Romanenko ◽  
E. A. Gurkovskaya
Keyword(s):  
Storage Temperature ◽  
Storage Period ◽  
Acid Value ◽  
Storage Conditions ◽  
Air Humidity ◽  
Wheat Grain ◽  
Storage Duration ◽  
Long Term Storage ◽  
Relative Air Humidity

The article presents the dependence of the fat acidity value (FAV) on the values of humidity and temperature, the relationship between the storage duration for wheat grain and FAV. To establish the expiration date of wheat grain during long-term storage, the author of the article considered the fat acid value (FAV) in mg of KOH. Storage temperature and relative air humidity in a desiccator affect the change (growth) of fat acidity value. The greatest changes occurred at 6th, 7th and 8th months of storage at a relative air humidity of more than 65 % and temperatures above 20 °C. At a storage temperature of 10 °C, in all cases the growth of FAV remained insignificant and was within the limits of determination accuracy. It is noted that when the relative humidity was below 60 %, while the temperature was the same as in the previous case, the FAV of wheat grain was practically unchanged through the 6-month storage period.

scholarly journals The Effect of Silica Desiccation Under Different Storage Conditions on Filter-Immobilized Environmental DNA

2020 ◽  
Author(s):  
Michael J Allison ◽  
Jessica M Round ◽  
Lauren C Bergman ◽  
Ali Mirabzadeh ◽  
Heather Allen ◽  
...  
Keyword(s):  
Silica Gel ◽  
Storage Temperature ◽  
Environmental Dna ◽  
Cost Effective ◽  
Storage Conditions ◽  
Systematic Evaluation ◽  
Silica Bead ◽  
Gel Beads ◽  
Polymerase Chain

Abstract Objective Silica gel beads have promise as a non-toxic, cost-effective, portable method for storing environmental DNA (eDNA) immobilized on filter membranes. Consequently, many ecological surveys are turning to silica bead filter desiccation rather than ethanol preservation. However, no systematic evaluation of silica bead storage conditions or duration past one week has been published. The present study evaluates the quality of filter-immobilized eDNA desiccated with silica gel under different storage conditions for over a year using targeted quantitative real-time polymerase chain reaction (qPCR)-based assays. Results While the detection of relatively abundant eDNA target was stable over 15 months from either ethanol- or silica gel-preserved filters at -20 and 4oC, silica gel out-performed ethanol preservation at 23oC by preventing a progressive decrease in eDNA sample quality. Silica gel filter desiccation preserved low abundance eDNA equally well up to 1 month regardless of storage temperature (18, 4, or -20oC). However only storage at -20oC prevented a noticeable decrease in detectability at 5 and 12 months. The results indicate that brief storage of eDNA filters with silica gel beads up to one month can be successfully accomplished at a range of temperatures. However, longer-term storage should be at -20oC to maximize sample integrity.

scholarly journals Changes of Physicochemical Properties of Starch Syrups Recommended for Winter Feeding of Honeybees during Storage

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 374
Author(s):  
Teresa Szczęsna ◽  
Ewa Waś ◽  
Piotr Semkiw ◽  
Piotr Skubida ◽  
Katarzyna Jaśkiewicz ◽  
...  
Keyword(s):  
Chemical Composition ◽  
Physicochemical Properties ◽  
Physicochemical Parameters ◽  
Storage Temperature ◽  
Storage Conditions ◽  
Different Temperatures ◽  
And Storage ◽  
Bee Colonies ◽  
Temperature Time ◽  
Winter Feeding

The aim of this study was to determine the influence of storage temperature and time on physicochemical parameters of starch syrups recommended for the winter feeding of bee colonies. The studies included commercially available three starch syrups and an inverted saccharose syrup that were stored at different temperatures: ca. 20 °C, 10–14 °C, and ca. 4 °C. Physicochemical parameters of fresh syrups (immediately after purchase) and syrups after 3, 6, 9, 12, 15, 18, 21, and 24 months of storage at the abovementioned temperatures were measured. It was observed that the rate of unfavorable changes in chemical composition of starch syrups and the inverted saccharose syrup, mainly the changes in the 5-hydroxymethylfurfural (HMF) content, depended on the type of a syrup and storage conditions (temperature, time). Properties of tested starch syrups intended for winter feeding of bees stored at ca. 20 °C maintained unchanged for up to 6 months, whereas the same syrups stored at lower temperatures (10–14 °C) maintained unchanged physicochemical parameters for about 12 months. In higher temperatures, the HMF content increased. To date, the influence of this compound on bees has not been thoroughly investigated.

scholarly journals Corrigendum to: PEMA: a flexible pipeline for environmental DNA metabarcoding analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes

GigaScience ◽  
2020 ◽  
Vol 9 (12) ◽  
Author(s):  
Haris Zafeiropoulos ◽  
Ha Quoc Viet ◽  
Katerina Vasileiadou ◽  
Antonis Potirakis ◽  
Christos Arvanitidis ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Environmental Dna ◽  
Marker Genes ◽  
18S Ribosomal Rna ◽  
Dna Metabarcoding

scholarly journals Growth and enterotoxin production of Bacillus cereus in cow, goat, and sheep milk

2014 ◽  
Vol 83 (10) ◽  
pp. S3-S8 ◽  
Author(s):  
Lenka Necidová ◽  
Šárka Bursová ◽  
Alena Skočková ◽  
Bohdana Janštová ◽  
Pavla Prachařová ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Storage Temperature ◽  
Goat Milk ◽  
Storage Conditions ◽  
Cow Milk ◽  
Enzyme Linked Immunosorbent Assay ◽  
Plate Method ◽  
Milk Samples ◽  
Sheep Milk ◽  
Enterotoxin Production

The aim of this study was to compare Bacillus cereus growth rates and diarrhoeal enterotoxin production in raw and pasteurized goat, sheep, and cow milk in terms of storage conditions. Milk samples were inoculated with B. cereus (CCM 2010), which produces diarrhoeal enterotoxins. Enterotoxin production was tested by ELISA (Enzyme-Linked Immunosorbent Assay), and the count of B. cereus was determined by the plate method. With raw cow milk, B. cereus growth and enterotoxin production can be completely suppressed; in raw goat and sheep milk, enterotoxin was produced at 22 °C. In pasteurized cow, goat, and sheep milk, the B. cereus count increased under all storage conditions, with more rapid growth being observed at 15 °C (sheep milk) and 22 °C (cow and goat milk). Enterotoxin presence was detected at 15 °C and 22 °C, and with pasteurized cow milk also at 8 °C. Our model experiments have determined that B. cereus multiplication and subsequent enterotoxin production depend on storage temperature and milk type.

scholarly journals Influence of Different Filling, Cooling, and Storage Conditions on the Growth of Alicyclobacillus acidoterrestris CRA7152 in Orange Juice

2009 ◽  
Vol 75 (23) ◽  
pp. 7409-7416 ◽  
Author(s):  
Ana Cláudia N. F. Spinelli ◽  
Anderson S. Sant'Ana ◽  
Salatir Rodrigues-Junior ◽  
Pilar R. Massaguer
Keyword(s):  
Orange Juice ◽  
Storage Temperature ◽  
Growth Parameters ◽  
Storage Conditions ◽  
Inoculum Level ◽  
Alicyclobacillus Acidoterrestris ◽  
Time Required ◽  
Cold Point ◽  
And Storage ◽  
A Current

ABSTRACT The prevention of spoilage by Alicyclobacillus acidoterrestris is a current challenge for fruit juice and beverage industries worldwide due to the bacterium's acidothermophilic growth capability, heat resistance, and spoilage potential. This study examined the effect of storage temperature on A. acidoterrestris growth in hot-filled orange juice. The evolution of the A. acidoterrestris population was monitored under six different storage conditions after pasteurization (at 92°C for 10 s), maintenance at 85°C for 150 s, and cooling with water spray to 35°C in about 30 min and using two inoculum levels: <101 and 101 spores/ml. Final cooling and storage conditions were as follows: treatment 1, 30°C for the bottle cold point and storage at 35°C; treatment 2, 30°C for 48 h and storage at 35°C; treatment 3, 25°C for the bottle cold point and storage at 35°C; treatment 4, 25°C for 48 h and storage at 35°C; treatment 5, storage at 20°C (control); and treatment 6, filling and storage at 25°C. It was found that only in treatment 5 did the population remain inhibited during the 6 months of orange juice shelf life. By examining treatments 1 to 4, it was observed that A. acidoterrestris predicted growth parameters were significantly influenced (P < 0.05) either by inoculum level or cooling and storage conditions. The time required to reach a 104 CFU/ml population of A. acidoterrestris was considered to be an adequate parameter to indicate orange juice spoilage by A. acidoterrestris. Therefore, hot-filled orange juice should be stored at or below 20°C to avoid spoilage by this microorganism. This procedure can be considered a safe and inexpensive alternative to other treatments proposed earlier.

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