Name: cortisol extraction from sturgeon fin and jawbone matrices
Uploaded: 2019-09-10T13:00:00
Description: Watch this Scientific Journal Video about Cortisol Extraction from Sturgeon Fin and Jawbone Matrices at JoVE.com

This work was conducted with the support of the Cooperative Research Program for Agriculture Science &#38; Technology Development (Project title: Livestock productivity change analysis with climate change, Project No. PJ012771), Rural Development Administration, Republic of Korea. Also, this study was supported by a grant (No. PJ01344604) from the Animal Nutrition &#38; Physiology Team, National Institute of Animal Science, RDA, Seoul, Republic of Korea. The authors gratefully acknowledge Persian Gesture CEO Mohammad Hassan Salmanzadeh and his team, who provided fish from the three sturgeon species examined in this study.

The following experimental procedures and methods were approved by the Animal Welfare and Ethics Authority of Kangwon National University, Chuncheon, Republic of Korea.
1. Fin collection
<ol>
	<li>Capture the sturgeon gently using a net to minimize injury and stress.</li>
	<li>Rinse the fish carefully with fresh water and then wipe the body surface with an absorbent towel prior to euthanasia.</li>
	<li>Hit the head of the fish using a plastic hammer such that the fish is stunned or loses con...

<ol>
	<li>Meyer, J. S., Novak, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hair+cortisol:+a+novel+biomarker+of+hypothalamic-pituitary-+adrenocortical+activity.">Hair cortisol: a novel biomarker of hypothalamic-pituitary- adrenocortical activity.</a> Endocrinology. 153, 4120-4127 (2012).</li><li>Ghassemi Nejad, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+cortisol+study:+facial+hair+and+nails.">A cortisol study: facial hair and nails.</a> Journal of Steroids Hormonal Sciences. 7, 1-5 (2016).</li><li>Meyer, J. S., Novak, M. 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Ph.D. dissertation. , (2018).</li><li>Carbajal, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cortisol+detection+in+fish+scales+by+enzyme+immunoassay:+biochemical+and+methodological+validation.">Cortisol detection in fish scales by enzyme immunoassay: biochemical and methodological validation.</a> Journal of Applied Ichthyology. 34, 1-4 (2018).</li><li>Bertotto, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alternative+matrices+for+cortisol+measurement+in+fish.">Alternative matrices for cortisol measurement in fish.</a> Aquaculture Research. 41, 1261-1267 (2010).</li><li>Ghassemi Nejad, J., Jeong, C., Shahsavarani, H., Sung, I. K., Lee, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Embedded+dental+cortisol+content:+a+pilot+study.">Embedded dental cortisol content: a pilot study.</a> Endocrinology &amp; Metabolic Syndrome. 5, 240 (2016).</li><li>Pankhurst, N. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+endocrinology+of+stress+in+fish:+an+environmental+perspective.">The endocrinology of stress in fish: an environmental perspective.</a> General and Comparative Endocrinology. 170, 265-275 (2011).</li><li>Ghassemi Nejad, J., Kim, W. B., Lee, B. H., Sung, K. 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H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Review+of+factors+influencing+stress+hormones+in+fish+and+wildlife.">Review of factors influencing stress hormones in fish and wildlife.</a> Journal of Nature Conservation. 21, 309-318 (2013).</li><li>Aerts, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Scales+tell+a+story+on+the+stress+history+of+fish.">Scales tell a story on the stress history of fish.</a> PLoS One. 10, e0123411 (2015).</li><li>Heimb&#252;rge, S., Kanitz, E., Otten, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+use+of+hair+cortisol+for+the+assessment+of+stress+in+animals.">The use of hair cortisol for the assessment of stress in animals.</a> General and Comparative Endocrinology. , 10-17 (2019).</li><li>Ghassemi Nejad, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparing+hair+cortisol+concentrations+from+various+body+sites+and+serum+cortisol+in+Holstein+lactating+cows+and+heifers+during+thermal+comfort+zone.">Comparing hair cortisol concentrations from various body sites and serum cortisol in Holstein lactating cows and heifers during thermal comfort zone.</a> Journal of Veterinary Behavior: Clinical and Application Research. 30, 92-95 (2019).</li><li>Bussy, U., Wassink, L., Scribner, K. 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A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stress+in+fishes:+a+diversity+of+responses+with+particular+reference+to+changes+in+circulating+corticosteroids.">Stress in fishes: a diversity of responses with particular reference to changes in circulating corticosteroids.</a> Integrative and Comparative Biology. 42, 517-525 (2002).</li><li>Ghassemi Nejad, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measuring+hair+and+blood+cortisol+in+sheep+and+dairy+cattle+using+RIA+and+ELISA+assay:+a+comparison.">Measuring hair and blood cortisol in sheep and dairy cattle using RIA and ELISA assay: a comparison.</a> Biological Rhythm Research. Accepted. , (2019).</li></ol>

Sturgeon is sometimes called a &#34;living fossil&#34; because it has exhibited few adaptations throughout past millennia. The sturgeon genus Acipenser contains 27 species that produce caviar; however, three species (beluga, baerii, and sevruga) produce most of the global caviar supply. Sturgeon are vulnerable to over-fishing and interference in their natural habitat and are therefore more critically endangered than any other group of species. Sturgeon belong to the oldest group of living vertebrates, which has ...

Cortisol is a reliable indicator of animal stress. Cortisol extraction provides a valid framework for researchers to monitor stress levels and general patterns in stressors. For example, previous studies have conducted methodological validation of hair cortisol measurements using various methods in humans1,2, monkeys3,4, cattle5, sheep6, and goldfish7,8. In fish species, cortisol measurements in matrices such as scales, skin mucus, feces, and blood9 have been shown to provide information on fish health. When blood sampling is problematic or scales are lacking, alternative matrices for cortisol extraction are needed. In fish, alternative matrices can include the jawbone, a hard tissue&#160;similar to the human tooth10.
The development of new matrices and validated techniques to determine fish stress levels is of particular interest to the caviar industry, where sturgeon can experience prolonged exposure to environmental stress factors11. The sex of sturgeon cannot be determined before 2 years of age, and sturgeon do not have scales. Because cortisol gradually accumulates in solid matrices during the growth stage2,7,12, long-term cortisol accumulation data from hard matrices such as fins and jawbones could provide insight into stress levels at different growth stages. In contrast, blood cortisol levels provide a snapshot of stress levels at the time of death and cannot accurately represent stress during long-term rearing conditions13,14. With increasing competition in the caviar market, new approaches to improve stress conditions for the production of healthier eggs among sturgeon species during long-term rearing (8-12 years or longer) are an increasingly important area of research. Due to the high cost of sturgeon, harvested samples are extremely costly ($8,000-15,000 per mature fish depending on species and growth stage), a limiting factor for research projects. However, the development of an appropriate technique for cortisol extraction from sturgeon fins and jawbones could be usefully applied both to fish farming systems and in wild fish to improve the quality and harvest of sturgeon eggs for both consumption and conservation.
As well as providing reliable results6, the selection of an appropriate cortisol extraction technique is of critical importance to ensure that other compounds present in the matrix during sample preparation do not confound the output, which might lead to inconsistent results. It is equally important to determine whether fin and jawbone cortisol levels are influenced by hormone levels in the surrounding water. Heimb&#252;rge et al.15 suggested that a number of factors may influence cortisol levels including age, sex, pregnancy, season, color12, and body region from which cortisol is extracted16. However, little information is available on the effects of washing solvents on cortisol extraction in fish body matrices8, and none on these effects in sturgeon, except for sturgeon eggs17.
Although analyzing baseline cortisol levels from the fins and jawbones of sturgeon requires that the fish be euthanized, this approach does not entail the invasive techniques required for blood sampling in live sturgeon. Fin and jawbone samples are easily collected, and extraction from these tissues can be performed rapidly. Similarly, hormone extraction and analysis are straightforward and require little specialized equipment.
In this study, we present a new and easily applied technique for the extraction, washing, and determination of cortisol from fish fins and jawbones, with the aim of determining whether cortisol levels measured from these matrices can be reliably used as stress indicators. The advantages of this technique include an easy and non-invasive8 approach, less data variation, and reliable output1,6,8,17; the technique is applicable to fish species without scales such as sturgeon. The technique requires slaughter of the fish, selection of appropriate washing solvents2,4, proper grinding of samples3,5, professional enzyme-linked immunosorbent assay (ELISA) application5,7, and extensive knowledge of the incorporation of cortisol sources into solid matrices6.
We applied two different washing solvents (ultrapure water and isopropanol) to obtain basal cortisol levels in fins from three sturgeon species: beluga (Huso huso), Siberian (Acipenser baerii), and sevruga (A. stellatus), under standard environmental conditions for each species. Jawbones of H. huso were also used to evaluate stress in sturgeon. This is the first study to measure cortisol levels in sturgeon jawbones. The results of this study will provide comparative cortisol data for sturgeon species in the early growth stage (~1 year) prior to sex determination.

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cortisol extraction from sturgeon fin and jawbone matrices

The aims of this study were to develop a technique for the extraction of cortisol from sturgeon fins using two washing solvents (water and isopropanol) and quantify any differences in fin cortisol levels among three main sturgeon species. Fins were harvested from 19 sacrificed sturgeons including seven beluga (Huso huso), seven Siberian (Acipenser baerii), and five sevruga (A. stellatus). The sturgeons were raised in Iranian farms for 2 years (2017-2018), and cortisol extraction analysis was conducted in South Korea (January-February 2019). Jawbones from five H. huso were also used for cortisol extraction. Data were analyzed using the general linear model (GLM) procedure in the SAS environment. The intra- and inter-assay coefficients of variation were 14.15 and 7.70, respectively. Briefly, the cortisol extraction technique involved washing the samples (300 &#177; 10 mg) with 3 mL of solvent (ultrapure water and isopropanol) twice, rotation at 80&#160;rpm for 2.5 min, air-drying the washed samples at room temperature (22-28 &#176;C) for 7 days, further drying the samples using a bead beater at 50 Hz for 32 min and grinding them into powder, applying 1.5 mL methanol to the dried powder (75 &#177; 5 mg), and slow rotation (40 rpm) for 18 h at room temperature with continuous mixing. Following extraction, samples were centrifuged (9,500 x g for 10 min), and 1 mL supernatant was transferred into a new microcentrifuge tube (1.5 mL), incubated at 38 &#176;C to evaporate the methanol, and analyzed via enzyme-linked immunosorbent assay (ELISA). No differences were observed in fin cortisol levels among species or in fin and jawbone cortisol levels between washing solvents. The results of this study demonstrate that the sturgeon jawbone matrix is a promising alternative stress indicator to solid matrices.

The presented fin cortisol extraction technique was developed and confirmed in this study using three sturgeon species. Cortisol levels obtained using ultrapure water and isopropanol as washing solvents were compared (Figure 2). Cortisol from H. huso jawbones was examined to determine whether sturgeon jawbones might be used as an alternative matrix to fins. The effects of washing solvent, sturgeon species, and their interaction are shown in T...

Watch this Scientific Journal Video about Cortisol Extraction from Sturgeon Fin and Jawbone Matrices at JoVE.com

Cortisol Extraction from Sturgeon Fin and Jawbone Matrices

In this study, we present a protocol for cortisol extraction from the fin and jawbone of sturgeon species. Fin and jawbone cortisol levels were further examined by comparing two washing solvents followed by ELISA assays. This study piloted the feasibility of jawbone cortisol as a novel stress indicator.

The aims of this study were to develop a technique for the extraction of cortisol from sturgeon fins using two washing solvents (water and isopropanol) ...

Our method introduces a novel alternative stress indicator that could be a platform for numerous future studies for measuring cortisol in new non plot and hair matrices. The advantages of this technique are its simplicity and its ability to be used to evaluate stress levels even in slaughtered animals. Establishing a relationship between high cortisol levels and healthy animals or humans using this technique can help with the diagnosis of some diseases.This method can also be used to study centuries old biological samples such as these old fossils to evaluate stress levels within the sample life span. For cortisol extraction, weigh out 300 plus or minus 10 milligrams of each sample on a digital analytical scale with a 0.0001 accuracy before placing the samples into individual 15 milliliter conical tubes. Add three milliliters of isopropanol to each sample tube and rotate the tubes at 80 rotations per minute for 2.5 minutes to wash out the cortisol and to remove any potential external contamination.After the last wash, air dry the samples at room temperature for seven days before washing the samples three more times as demonstrated using fresh ultra pure water for each wash. Weigh out 75 plus or minus five milligrams of dried fin or jawbone sample and use a bead beater to finally grind the sample at 50 hertz for 32 minutes. Then, deliver 1.5 milliliters of methanol to each tube of powdered fin or jawbone and place the samples on a tube rotator at 40 rotations per minute for 18 hours at room temperature.Following cortisol extraction, sediment the sample tissues by centrifugation. And transfer the top one milliliter of the yellowish, organic cortisol containing layer from each sample into individual 1.5 milliliter micro-centrifuged tubes. Dry the cortisol samples at 38 degrees Celsius in a fume hood overnight to evaporate the methanol.The next morning, add 400 microliters of PBS to each tube and vortex and centrifuge the samples to collect the cortisol. For ELISA Analysis, load 25 microliters of each extracted standard cortisol sample and control in duplicate into the appropriate wells of a 96 well ELISA plate. Load 25 microliters of Assay diluent into two wells to serve as the zero and into each non specific binding well.Mix 15 microliters of enzyme conjugate with 24 milliliters of Assay diluent and add 200 microliters of conjugate to each well. Mix the plate on a rotator for five minutes at 500 rotations per minute. Followed by a one hour incubation at room temperature.At the end of the incubation, wash the plate four times with 300 microliters of 1x Wash Buffer per well. Quickly inverting the plate over the sink after each wash to discard the buffer and blotting the plate on a stack of paper towels. After the last wash, add 200 microliters of TMB substrate solution to each well and place the plate onto the rotator for five minutes at 500 rotations per minute.After mixing, incubate the plate for 25 minutes at room temperature protected from light. At the end of the incubation, add 50 microliters of stop solution to each well. And mix the plate contents on the rotator for three minutes at 500 rotations per minute or until all of the wells have turned from green to yellow.Then, read the optical density of the samples and use the micro plate software to convert the cortisol levels in each sample to picograms per milligram. In this representative analysis, cortisol levels tended to be higher in fin samples washed with isopropanol than in those washed with water, but no significant differences in fin cortisol levels were observed among sturgeon species. There was no significant interaction between washing solvents and sturgeon species.Examination of cortisol from H.Huso jawbones to determine whether sturgeon jawbones might be used as an alternative matrix to fins revealed that the washing solvent had no significant effect on the cortisol level measured in H.Huso's sturgeon. Further, the data revealed a high similarity among the fins of three sturgeon species tested and in H.Huso jawbones. It is important to use the bead beater to grind the samples into fine powder and to use an appropriate commercial ELISA Assay Kit for a successful cortisol measurement.This method can also be used for detecting cortisol in teeth and other hard matrices as cortisol level measurements provide important information about how the environment affects animal biology. The method could be used as a new approach to assessing cortisol levels in human child milk teeth and in pediatric endocrinology, psycho biology, behavioral, archeological, and forensic studies.

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Environment

Helminth Collection and Identification from Wildlife

Wild animals are commonly parasitized by a wide range of helminths. The four major types of helminths are &#34;roundworms&#34; (nematodes), &#34;thorny-headed worms&#34; (acanthocephalans), &#34;flukes&#34; (trematodes), and &#34;tapeworms&#34; (cestodes). The optimum method for collecting helminths is to examine a host that has been dead less than 4-6 hr since most helminths will still be alive. A thorough necropsy should be conducted and all major organs examined. Organs are washed over a 106 &#956;m sieve under running water and contents examined under a stereo microscope. All helminths are counted and a representative number are fixed (either in 70% ethanol, 10% buffered formalin, or alcohol-formalin-acetic acid). For species identification, helminths are either cleared in lactophenol (nematodes and small acanthocephalans) or stained (trematodes, cestodes, and large acanthocephalans) using Harris&#39; hematoxylin or Semichon&#39;s carmine. Helminths are keyed to species by examining different structures (e.g. male spicules in nematodes or the rostellum in cestodes). The protocols outlined here can be applied to any vertebrate animal. They require some expertise on recognizing the different organs and being able to differentiate helminths from other tissue debris or gut contents. Collection, preservation, and staining are straightforward techniques that require minimal equipment and reagents. Taxonomic identification, especially to species, can be very time consuming and might require the submission of specimens to an expert or DNA analysis.

Wild animals are commonly parasitized by a wide range of helminths.&#160; The four major types of helminths are &#8220;roundworms&#8221; (nematodes), &#8220;thorny-headed worms&#8221; (acanthocephalans), &#8220;flukes&#8221; (trematodes), and &#8220;tapeworms&#8221; (cestodes).&#160; Here we describe how helminths are collected from a vertebrate animal and how they are preserved and taxonomically identified.&#160;

Wild animals are commonly parasitized by a wide range of helminths. The four major types of helminths are &#34;roundworms&#34; (nematodes), ...

Sediment Core Sectioning and Extraction of Pore Waters under Anoxic Conditions

We demonstrate a method for sectioning sediment cores and extracting pore waters while maintaining oxygen-free conditions. A simple, inexpensive system is built and can be transported to a temporary work space close to field sampling site(s) to facilitate rapid analysis. Cores are extruded into a portable glove bag, where they are sectioned and each 1-3 cm thick section (depending on core diameter) is sealed into 50 ml centrifuge tubes. Pore waters are separated with centrifugation outside of the glove bag and then returned to the glove bag for separation from the sediment. These extracted pore water samples can be analyzed immediately. Immediate analyses of redox sensitive species, such as sulfide, iron speciation, and arsenic speciation indicate that oxidation of pore waters is minimal; some samples show approximately 100% of the reduced species, e.g. 100% Fe(II) with no detectable Fe(III). Both sediment and pore water samples can be preserved to maintain chemical species for further analysis upon return to the laboratory.

A protocol for sectioning sediment cores and extracting pore waters under anoxic conditions in order to permit analysis of redox sensitive species in both solids and fluids is presented.

We demonstrate a method for sectioning sediment cores and extracting pore waters while maintaining oxygen-free conditions. A simple, inexpensive system is ...

A Simple Method for Automated Solid Phase Extraction of Water Samples for Immunological Analysis of Small Pollutants

A new method for solid phase extraction (SPE) of environmental water samples is proposed. The developed prototype is cost-efficient and user friendly, and enables to perform rapid, automated and simple SPE. The pre-concentrated solution is compatible with analysis by immunoassay, with a low organic solvent content. A method is described for the extraction and pre-concentration of natural hormone 17&#946;-estradiol in 100 ml water samples. Reverse phase SPE is performed with octadecyl-silica sorbent and elution is done with 200 &#181;l of methanol 50% v/v. Eluent is diluted by adding di-water to lower the amount of methanol. After preparing manually the SPE column, the overall procedure is performed automatically within 1 hr. At the end of the process, estradiol concentration is measured by using a commercial enzyme-linked immune-sorbent assay (ELISA). 100-fold pre-concentration is achieved and the methanol content in only 10% v/v. Full recoveries of the molecule are achieved with 1 ng/L spiked de-ionized and synthetic sea water samples.

A protocol for the extraction and pre-concentration of estradiol from water samples by using an automated and miniaturized system is presented.

A new method for solid phase extraction (SPE) of environmental water samples is proposed. The developed prototype is cost-efficient and user friendly, and ...

Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR

Real Time Polymerase Chain Reaction also known as quantitative PCR (q-PCR) is a widely used tool in microbial ecology to quantify gene abundances of taxonomic and functional groups in environmental samples. Used in combination with a reverse transcriptase reaction (RT-q-PCR), it can also be employed to quantify gene transcripts. q-PCR makes use of highly sensitive fluorescent detection chemistries that allow quantification of PCR amplicons during the exponential phase of the reaction. Therefore, the biases associated with &#39;end-point&#39; PCR detected in the plateau phase of the PCR reaction are avoided. A protocol to quantify bacterial 16S rRNA genes and transcripts from coastal sediments via real-time PCR is provided. First, a method for the co-extraction of DNA and RNA from coastal sediments, including the additional steps required for the preparation of DNA-free RNA, is outlined. Second, a step-by-step guide for the quantification of 16S rRNA genes and transcripts from the extracted nucleic acids via q-PCR and RT-q-PCR is outlined. This includes details for the construction of DNA and RNA standard curves. Key considerations for the use of RT-q-PCR assays in microbial ecology are included.

A protocol to quantify bacterial 16S rRNA genes and transcripts from coastal sediments via real-time PCR is provided. The methodology includes the co-extraction of DNA and RNA; preparation of DNA-free RNA; and 16S rRNA gene and transcript quantification via RT-q-PCR, including standard curve construction.

Real Time Polymerase Chain Reaction also known as quantitative PCR (q-PCR) is a widely used tool in microbial ecology to quantify gene abundances of ...

Alternative Method of Removing Otoliths from Sturgeon

Extracting the otoliths (ear bones) from fish that have very thick skulls can be difficult and very time consuming. The common practice of making a transverse vertical incision on the top of the skull with a hand or electrical saw may damage the otolith if not performed correctly. Sturgeons (Acipenseridae) are one family in particular that have a very large and thick skull. A new laboratory method entering the brain cavity from the ventral side of the fish to expose the otoliths was easier than other otolith extraction methods found in the literature. Methods reviewed in the literature are designed for the field and are more efficient at processing large quantities of fish quickly. However, this new technique was designed to be more suited for a laboratory setting when time is not pressing and successful extraction from each specimen is critical. The success of finding and removing otoliths using this technique is very high and does not compromise the structure in any manner. This alternative technique is applicable to other similar fish species for extracting the otoliths.

The goal of the protocol is to show an effective method to extract the otoliths from sturgeon carcasses.

Extracting the otoliths (ear bones) from fish that have very thick skulls can be difficult and very time consuming. The common practice of making a ...

Extraction and Analysis of Microbial Phospholipid Fatty Acids in Soils

Phospholipid fatty acids (PLFAs) are key components of microbial cell membranes. The analysis of PLFAs extracted from soils can provide information about the overall structure of terrestrial microbial communities. PLFA profiling has been extensively used in a range of ecosystems as a biological index of overall soil quality, and as a quantitative indicator of soil response to land management and other environmental stressors.
The standard method presented here outlines four key steps: 1. lipid extraction from soil samples with a single-phase chloroform mixture, 2. fractionation using solid phase extraction columns to isolate phospholipids from other extracted lipids, 3. methanolysis of phospholipids to produce fatty acid methyl esters (FAMEs), and 4. FAME analysis by capillary gas chromatography using a flame ionization detector (GC-FID). Two standards are used, including 1,2-dinonadecanoyl-sn-glycero-3-phosphocholine (PC(19:0/19:0)) to assess the overall recovery of the extraction method, and methyl decanoate (MeC10:0) as an internal standard (ISTD) for the GC analysis.

Phospholipid fatty acids provide information about the structure of soil microbial communities. We present methods for extraction from soil samples with a single-phase chloroform mixture, fractionation of extracted lipids using solid phase extraction columns, and methanolysis to produce fatty acid methyl esters, which are analyzed by capillary gas chromatography.

Phospholipid fatty acids (PLFAs) are key components of microbial cell membranes. The analysis of PLFAs extracted from soils can provide information about ...

Extraction of Structural Extracellular Polymeric Substances from Aerobic Granular Sludge

To evaluate and develop methodologies for the extraction of gel-forming extracellular polymeric substances (EPS), EPS from aerobic granular sludge (AGS) was extracted using six different methods (centrifugation, sonication, ethylenediaminetetraacetic acid (EDTA), formamide with sodium hydroxide (NaOH), formaldehyde with NaOH and sodium carbonate (Na2CO3) with heat and constant mixing). AGS was collected from a pilot wastewater treatment reactor. The ionic gel-forming property of the extracted EPS of the six different extraction methods was tested with calcium ions (Ca2+). From the six extraction methods used, only the Na2CO3 extraction could solubilize the hydrogel matrix of AGS. The alginate-like extracellular polymers (ALE) recovered with this method formed ionic gel beads with Ca2+. The Ca2+-ALE beads were stable in EDTA, formamide with NaOH and formaldehyde with NaOH, indicating that ALE are one part of the structural polymers in EPS. It is recommended to use an extraction method that combines physical and chemical treatment to solubilize AGS and extract structural EPS.

The protocol provides a methodology to solubilize aerobic granular sludge in order to extract alginate-like extracellular polymers (ALE).

To evaluate and develop methodologies for the extraction of gel-forming extracellular polymeric substances (EPS), EPS from aerobic granular sludge (AGS) ...

Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA

Recent studies demonstrated the use of environmental DNA (eDNA) from fishes to be appropriate as a non-invasive monitoring tool. Most of these studies employed disk fiber filters to collect eDNA from water samples, although a number of microbial studies in aquatic environments have employed filter cartridges, because the cartridge has the advantage of accommodating large water volumes and of overall ease of use. Here we provide a protocol for filtration of water samples using the filter cartridge and extraction of eDNA from the filter without having to cut open the housing. The main portions of this protocol consists of 1) filtration of water samples (water volumes &#8804;4 L or &gt;4 L); (2) extraction of DNA on the filter using a roller shaker placed in a preheated incubator; and (3) purification of DNA using a commercial kit. With the use of this and previously-used protocols, we perform metabarcoding analysis of eDNA taken from a huge aquarium tank (7,500 m3) with known species composition, and show the number of detected species per library from the two protocols as the representative results. This protocol has been developed for metabarcoding eDNA from fishes, but is also applicable to eDNA from other organisms.

We describe a protocol for filtration of water samples with a filter cartridge and extraction of environmental DNA (eDNA) without having to cut open the housing to remove the filter. This protocol is developed for metabarcoding eDNA from fishes, but is also applicable to eDNA from other organisms.

Recent studies demonstrated the use of environmental DNA (eDNA) from fishes to be appropriate as a non-invasive monitoring tool. Most of these studies ...

A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples

Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial communities, a relatively precise but effort-intensive technique to assay microbial community composition is phospholipid fatty acid (PLFA) analysis. PLFA was developed to analyze phospholipid biomarkers, which can be used as indicators of microbial biomass and the composition of broad functional groups of fungi and bacteria. It has commonly been used to compare soils under alternative plant communities, ecology, and management regimes. The PLFA method has been shown to be sensitive to detecting shifts in microbial community composition.
An alternative method, fatty acid methyl ester extraction and analysis (MIDI-FA) was developed for rapid extraction of total lipids, without separation of the phospholipid fraction, from pure cultures as a microbial identification technique. This method is rapid but is less suited for soil samples because it lacks an initial step separating soil particles and begins instead with a saponification reaction that likely produces artifacts from the background organic matter in the soil. 
This article describes a method that increases throughput while balancing effort and accuracy for extraction of lipids from the cell membranes of microorganisms for use in characterizing both total lipids and the relative abundance of indicator lipids to determine soil microbial community structure in studies with many samples. The method combines the accuracy achieved through PLFA profiling by extracting and concentrating soil lipids as a first step, and a reduction in effort by saponifying the organic material extracted and processing with the MIDI-FA method as a second step.

The article describes a method that increases throughput while balancing effort and accuracy for extraction of lipids from the cell membranes of microorganisms for use in characterizing both total lipids and the relative abundance of indicator lipids to determine soil microbial community structure in studies with many samples.

Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial ...

Extraction of Organochlorine Pesticides from Plastic Pellets and Plastic Type Analysis

Plastic resin pellets, categorized as microplastics (&#8804;5 mm in diameter), are small granules that can be unintentionally released to the environment during manufacturing and transport. Because of their environmental persistence, they are widely distributed in the oceans and on beaches all over the world. They can act as a vector of potentially toxic organic compounds (e.g., polychlorinated biphenyls) and might consequently negatively affect marine organisms. Their possible impacts along the food chain are not yet well understood. In order to assess the hazards associated with the occurrence of plastic pellets in the marine environment, it is necessary to develop methodologies that allow for rapid determination of associated organic contaminant levels. The present protocol describes the different steps required for sampling resin pellets, analyzing adsorbed organochlorine pesticides (OCPs) and identifying the plastic type. The focus is on the extraction of OCPs from plastic pellets by means of a pressurized fluid extractor (PFE) and on the polymer chemical analysis applying Fourier Transform-InfraRed (FT-IR) spectroscopy. The developed methodology focuses on 11 OCPs and related compounds, including dichlorodiphenyltrichloroethane (DDT) and its two main metabolites, lindane and two production isomers, as well as the two biologically active isomers of technical endosulfan. This protocol constitutes a simple and rapid alternative to existing methodology for evaluating the concentration of organic contaminants adsorbed on plastic pieces.

Microplastics act as vector of potentially toxic organic contaminants with unpredictable effects. This protocol describes an alternative methodology for assessing the levels of organochlorine pesticides adsorbed on plastic pellets and identifying the polymer chemical structure. The focus is on pressurized fluid extraction and attenuated total reflectance Fourier transform infrared spectroscopy.

Plastic resin pellets, categorized as microplastics (&#8804;5 mm in diameter), are small granules that can be unintentionally released to the environment ...