Name: vacusip, an improved inex method for in situ measurement of particulate and dissolved compounds processed by active suspension feeders
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Description: Watch this Scientific Journal Video about VacuSIP, an Improved InEx Method for In Situ Measurement of Particulate and Dissolved Compounds Processed by Active Suspension Feeders at JoVE.com

We thank Manel Bolivar for his assistance in the fieldwork. We are grateful to the &#34;Parc Natural del Montgr&#236;, les Illes Medes i el Baix Ter&#34; for their support to our research and sampling permissions. The underwater manipulator was designed by Ayelet Dadon-Pilosof and fabricated by Mr. Pilosof. This work was supported by the Spanish Government project CSI-Coral [grant number CGL2013-43106-R to RC and MR] and by a F.P.U fellowship from &#34;Ministerio de Educaci&#242;n, Cultura y Deporte (MECD)&#34; to TM. This is a contribution from the Marine Biogeochemistry and Global Change research group funded by the Catalan Government [grant number 2014SGR1029] and ISF grant 1280/13 and BSF grant 2012089&#160;to G. Yahel.

1. Preparatory Steps and Cleaning Procedures
<ol>
	<li>Cleaning solution
	<ol>
		<li>Wear protective gear, a lab coat, and gloves at all times. Carry out these preparatory steps in a clean space free of dust and smoke.</li>
		<li>Prepare a 5-10% hydrochloric acid (HCl) solution with fresh, high quality, double distilled water.</li>
		<li>Prepare a 5% highly soluble basic mix of anionic and non-ionic surfactant solution (See Materials List) with fresh, high quality, double distilled water.</li>
...

<ol>
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Preparatory steps
Collector vials for DOM and nutrient analysis
Since collector vessels may interact with dissolved micro-constituents and the sampler walls may be a substrate for bacteria growth 30-34, different vials for DOM and nutrient collection were tested. Borosilicate is not recommended for silica quantification 33,35, since glass bottles can increase the initial concentration of silica by up t...

Benthic suspension feeders play essential roles in the functioning of marine ecosystems 1. By filtering large volumes of water 2,3, they remove and excrete particulate (plankton and detritus) and dissolved compounds 1 (and references therein) and are an important agent of benthic-pelagic coupling 4,5 and nutrient cycling 6,7. Accurately measuring the particulate and dissolved compounds removed and excreted by benthic suspension feeders (such as sponges, ascidians, polychaetes, and bivalves) is fundamental to understand their physiology, metabolism, and feeding ecology. Together with pumping rate measurements, it also enables a quantification of the nutrient fluxes mediated by these organisms and their ecological impact on water quality as well as on ecosystem scale processes.
Choosing the appropriate method of measuring removal and production rates of particulate and dissolved compounds by&#160;suspension filter feeders is crucial for obtaining reliable data concerning their feeding activity 8. As pointed out by Riisg&#229;rd and others, inappropriate methodologies bias results, distort experimental conditions, produce incorrect estimations of ingestion and excretion of certain substances, and can lead to erroneous quantification of the nutrient fluxes processed by these organisms.
The two most frequently employed methods to measure particulate and dissolved nutrient fluxes in filter feeders involve either incubation (indirect techniques) or simultaneous collection of ambient and exhaled water (direct techniques). Incubation techniques are based on measuring the rate of change in the concentration of particulate and dissolved nutrients in the incubated water, and estimating rates of production or removal compared to adequate controls 8. However, enclosing an organism in an incubation chamber can alter its feeding and pumping behavior due to changes in the natural flow regime, due to a decline in oxygen and/or in food concentration, or due to accumulation of excretion compounds in the incubation water 7,9 (and references therein). In addition to the effects of confinement and modified water supply, a major bias of incubation techniques stems from re-filtration effects (see for example 10). Although some of these methodological problems have been overcome by using the right volume and shape of the incubation vessel 11 or with the introduction of a recirculating bell-jar system in situ12, this technique often underestimates removal and production rates. Quantifying the metabolism of dissolved compounds such as dissolved organic nitrogen (DON) and carbon (DOC) or inorganic nutrients, has proven to be especially prone to biases caused by incubation techniques 13.
In the late 60s and early 70s, Henry Reiswig 9,14,15 pioneered the application of direct techniques to quantify particle removal by giant Caribbean sponges, by separately sampling the water inhaled and exhaled by the organisms in situ. Due to the difficulty to apply Reiswig&#39;s technique on smaller suspension feeders and in more challenging underwater conditions, the bulk of research in this field was restricted to the laboratory (in vitro) employing mostly indirect incubation techniques 16. Yahel and colleagues refitted Reiswig&#39;s direct in situ technique to work in smaller-scale conditions. Their method, termed InEx 16, is based on simultaneous underwater sampling of the water inhaled (In) and exhaled (Ex) by undisturbed organisms. The different concentration of a substance (e.g., bacteria) between a pair of samples (InEx) provides a measure of the retention (or production) of that substance by the animal. The InEx technique employs open-ended tubes and relies on the excurrent jet produced by the pumping activity of the studied organism to passively replace the ambient water in the collecting tube. While Yahel and colleagues have successfully applied this technique in the study of over 15 different suspension feeders taxa (e.g., 17), the method is constrained by the high level of practice and experience required, by the minuscule size of&#160;some excurrent orifices, and by sea conditions.
To overcome these obstacles, we developed an alternative technique based on controlled suction of the sampled water through minute tubes (external diameter &#60; 1.6 mm). Our goal was to create a simple, reliable, and inexpensive device that would allow clean and controlled in situ water sampling from a very specific point, such as the excurrent orifice of benthic suspension feeders. To be effective, the method has to be non-intrusive so as not to affect the ambient flow regime or modify the behavior of the studied organisms. The device presented here is termed VacuSIP. It is a simplification of the SIP system developed by Yahel et al. (2007) 18 for ROV-based point sampling in the deep sea. The VacuSIP is considerably cheaper than the original SIP and it has been adapted for SCUBA-based work. The system was designed according to principles presented and tested by Wright and Stephens (1978) 19 and M&#248;hlenberg and Riisg&#229;rd (1978) 20 for laboratory settings.
Although the VacuSIP system was designed for in situ studies of the metabolism of benthic suspension feeders, it can also be used for laboratory studies and wherever a controlled and clean, point-source water sample is required. The system is especially useful when integration over prolonged periods (min-hours) or in situ filtrations are required. The VacuSIP has been used successfully at the Yahel lab since 2011, and has also been employed in two recent studies of nutrient fluxes mediated by Caribbean and Mediterranean sponge species 21 (Morganti et al. submitted).
The use of specific samplers, the prolonged sampling duration, and the field conditions, in which VacuSIP is applied, entail some deviations from standard oceanographic protocols for collecting, filtering, and storing samples for sensitive analytes. To reduce the risk of contamination by the VacuSIP system or the risk of modification of the sampled water by bacterial activity after collection, we tested various in situ filtration and storage procedures. Different filtering devices, collection vessels, and storing procedures were examined in order to achieve the most suitable technique for the analysis of dissolved inorganic (PO43-, NOx-, NH4+, SiO4) and organic (DOC + DON) compounds, and ultra-plankton (&#60;10 &#181;m) and particulate organic (POC + PON) sampling. To further reduce the risk of contamination, especially under field conditions, the number of handling steps was reduced to the bare minimum. The visual format in which the method is presented is oriented to facilitate reproducibility and to reduce the time required to efficiently apply the technique.
System overview 
To sample in situ&#160;pumped water from suspension feeders with exhalant orifices as small as 2 mm, the pumping activity of each specimen is first visualized by releasing filtered fluorescein dyed seawater next to the inhalant orifice(s) and observing its flow from the excurrent aperture 16 (see also Figure 2B in 18). The water inhaled and exhaled by the study specimen (incurrent and excurrent) are then simultaneously sampled with the use of a pair of minute tubes installed on custom-built manipulator or on two of the &#34;arms&#34; of an upside-down flexible portable tripod (Figure 1 and Supplementary Video 1). The water inhaled by the study organism is collected by carefully positioning the proximal end of one tube inside or near the inhalant aperture of the study organism. An identical tube is then positioned inside the excurrent orifice. This operation requires good care to avoid contact or disturbance of the animal, e.g., by sediment resuspension. To begin the sampling, a diver pierces a septum in the collecting vessel with a syringe needle attached to the distal end of each tube, allowing the external water pressure to force the sampled water into the vessel through the sampling tube. The suction is initiated by the vacuum previously created in the vials and by the pressure difference between the external water and the evacuated sample container.
To ensure a clean collection of exhaled water and to avoid accidental suction of ambient water 16, the water sampling rate needs to be kept at a significantly lower rate (&#60;10%) than the excurrent flow rate. The suction rate is controlled by the length of the tube and its internal diameter (ID). The small internal diameter also ensures a negligible dead volume (&#60; 200&#160;&#181;l per meter of tubing). Sampling over prolonged periods (minutes to hours) makes it possible to integrate the inherent patchiness of most substances of interest. To ensure that samples are adequately preserved in prolonged underwater sampling sessions as well as for transportation to the lab, an in situ filtration is recommended for sensitive analytes. The selection of sampling vessels, filtration assembly, and tubing are dictated by the study organisms and the specific research question. The protocol described below assumes that a full metabolic profile is of interest (for an overview see Figure 2). However, the modular nature of the protocol allows for easy modification to accommodate simpler or even very different sampling schemes. For a full metabolic profile, the sampling protocol should include the following steps: (1) Flow visualization; (2) Sampling ultra-plankton feeding (plankton &#60; 10 &#181;m); (3) Sampling inorganic nutrients uptake and excretion (using in-line filters); (4) Sampling dissolved organic uptake and excretion (using in-line filters); (5) Particulate feeding and excretion (using in-line filters); (6) Repeat step 2 (ultra-plankton feeding as quality check); (7) Flow visualization.
When logistically feasible, it is recommended that the metabolic profile measurements are combined with pumping rate (e.g., the dye front speed method, in 16) as well as with respiration measurements. These measurements are best taken at the beginning and end of the sampling session. For respiration measurement, underwater optodes or micro-electrodes are preferable.

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			<td style="width:459px;">flexible portable tripod&#160;</td>
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			<td height="21" style="height:21px;">Flangeless Ferrule</td>
			<td>IDEX Health &#38; Science&#160;</td>
			<td>P-200X</td>
			<td>1/16&#34; in Blue/pk</td>
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			<td height="21" style="height:21px;">Male Nut</td>
			<td>IDEX Health &#38; Science&#160;</td>
			<td>P-205X&#160;</td>
			<td>1/16&#34; in Green/10pk</td>
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			<td height="21" style="height:21px;">Female to Female Luer</td>
			<td>IDEX Health &#38; Science&#160;</td>
			<td>P-658</td>
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			<td height="21" style="height:21px;">Female-Male Luer</td>
			<td>IDEX Health &#38; Science&#160;</td>
			<td>P-655</td>
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			<td height="21" style="height:21px;">Peek Tubing (250&#181;m ID)</td>
			<td>IDEX Health &#38; Science&#160;</td>
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			<td>Mix well the two component resin before use</td>
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			<td>Cole -Parmer&#160;</td>
			<td>03756-20</td>
			<td>40 ml glass vials. Manifactured also by Thomas Scientific (ref. number 9711F09)&#160;</td>
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			<td>Wheaton</td>
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			<td>pre-vacuum by the manufacturer&#160;</td>
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			<td>Thomas Scientific</td>
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			<td>250 ml glass bottles&#160;</td>
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			<td height="21" style="height:21px;">Septum Cap 1</td>
			<td>Wheaton</td>
			<td>W240844SP (E7865R)</td>
			<td>22-400 for HDPE vials&#160;</td>
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			<td height="21" style="height:21px;">Septum Cap 2&#160;</td>
			<td>Wheaton</td>
			<td>W240846 (1078-5553)</td>
			<td>24-400 for glass vials and bottles. Also manufactured by Thermo Scientific National (ref. 03-377-42)</td>
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			<td>Pall&#160;</td>
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			<td>Pall&#160;</td>
			<td>516-8064</td>
			<td>ring for stainless steel filter holders</td>
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			<td height="21" style="height:21px;">TCLP Glass Filters</td>
			<td>Pall&#160;</td>
			<td>516-9126</td>
			<td>binder-free glass fiber filters, 13mm of diameter,&#160; pore size 0.7&#181;m</td>
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			<td height="21" style="height:21px;">Polycarbonate Filter Holders&#160;</td>
			<td>Cole -Parmer&#160;</td>
			<td>17295</td>
			<td>13mm of diameter</td>
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			<td height="21" style="height:21px;">Isopore Membrane Filters</td>
			<td>Millipore</td>
			<td>GTTP01300</td>
			<td>13mm of diameter, pore size 0.2 &#181;m&#160;</td>
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			<td height="21" style="height:21px;">Contrad 2000 Solution&#160;</td>
			<td>Decon Labs</td>
			<td>E123FH</td>
			<td>highly soluble basic mix of anionic and non-ionic surfactant solution&#160;</td>
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			<td height="21" style="height:21px;">Sterile Syringe Filters</td>
			<td>VWR International Eurolab S.L.</td>
			<td>514-0061P</td>
			<td>25mm of diameter , pore size 0.2 &#181;m&#160;</td>
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			<td height="21" style="height:21px;">Fluorescein</td>
			<td>Sigma-Aldrich</td>
			<td>(old ref.28802) 46955-100G&#160;</td>
			<td>100g&#160;</td>
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			<td height="21" style="height:21px;">Holdex, disposable,sterile</td>
			<td>Greiner bio-one</td>
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			<td>sterile, single-use tube holder with off-center luer for Vacuette</td>
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			<td>IcoGammaPlus</td>
			<td>5160</td>
			<td>0.7mm x 30mm</td>
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			<td height="21" style="height:21px;">Cryovials Nalgene</td>
			<td>Nalgene</td>
			<td>V5007(Cat. No.5000-0020)</td>
			<td>2ml&#160;</td>
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			<td height="21" style="height:21px;">Cryobox carton&#160;</td>
			<td>Rubilabor</td>
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			<td height="21" style="height:21px;">Orthophosphoric Acid</td>
			<td>Sigma</td>
			<td>79617</td>
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			<td height="21" style="height:21px;">Paraformaldehyde</td>
			<td>Sigma</td>
			<td>P6148</td>
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			<td height="21" style="height:21px;">Glutaraldehyde</td>
			<td>Merck</td>
			<td>8,206,031,000</td>
			<td>25%, 1 L</td>
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			<td height="21" style="height:21px;">Hand Vacuum Pump&#160;</td>
			<td>B&#252;rkle&#160;</td>
			<td>5620-2181</td>
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vacusip, an improved inex method for in situ measurement of particulate and dissolved compounds processed by active suspension feeders

Benthic suspension feeders play essential roles in the functioning of marine ecosystems. By filtering large volumes of water, removing plankton and detritus, and excreting particulate and dissolved compounds, they serve as important agents for benthic-pelagic coupling. Accurately measuring the compounds removed and excreted by suspension feeders (such as sponges, ascidians, polychaetes, bivalves) is crucial for the study of their physiology, metabolism, and feeding ecology, and is fundamental to determine the ecological relevance of the nutrient fluxes mediated by these organisms. However, the assessment of the rate by which suspension feeders process particulate and dissolved compounds in nature is restricted by the limitations of the currently available methodologies. Our goal was to develop a simple, reliable, and non-intrusive method that would allow clean and controlled water sampling from a specific point, such as the excurrent aperture of benthic suspension feeders, in situ. Our method allows simultaneous sampling of inhaled and exhaled water of the studied organism by using minute tubes installed on a custom-built manipulator device and carefully positioned inside the exhalant orifice of the sampled organism. Piercing a septum on the collecting vessel with a syringe needle attached to the distal end of each tube allows the external pressure to slowly force the sampled water into the vessel through the sampling tube. The slow and controlled sampling rate allows integrating the inherent patchiness in the water while ensuring contamination free sampling. We provide recommendations for the most suitable filtering devices, collection vessel, and storing procedures for the analyses of different particulate and dissolved compounds. The VacuSIP system offers a reliable method for the quantification of undisturbed suspension feeder metabolism in natural conditions that is cheap and easy to learn and apply to assess the physiology and functional role of filter feeders in different ecosystems.

Optimization of seawater collection methods
Selection of collector vials and cleaning procedure
VacuSIP-compatible collecting vessels should have a septum that allows sampling to be initiated by piercing with a syringe needle. They should withstand the elevated underwater pressure (2-3 bars at typical scuba working depths), an...

Watch this Scientific Journal Video about VacuSIP, an Improved InEx Method for In Situ Measurement of Particulate and Dissolved Compounds Processed by Active Suspension Feeders at JoVE.com

VacuSIP, an Improved InEx Method for In Situ Measurement of Particulate and Dissolved Compounds Processed by Active Suspension Feeders

We introduce the VacuSIP, a simple, non-intrusive, and reliable method for clean and accurate point sampling of water. The system was developed and evaluated for the simultaneous collection of the water inhaled and exhaled by benthic suspension feeders in situ, to cleanly measure removal and excretion of particulate and dissolved compounds.

VacuSIP, an Improved InEx Method for In Situ Measurement of Particulate and Dissolved Compounds Processed by Active Suspension Feeders

Benthic suspension feeders play essential roles in the functioning of marine ecosystems. By filtering large volumes of water, removing plankton and ...

The overall goal of this method is to clean the collector of water inhaled and exhaled by Benthic suspension feeders under natural conditions so that the particulate and dissolved compounds they removed and excreted can be quantified. When preparing collection vessels for dissolved organics and ammonia analysis, use new pre-cleaned EPA vials. For sampling other nutrients, use EPA glass vials.Use HDPE vials for silicate. Rinse the vials and caps with high quality double distilled water. Then replace punctured silicon septum with new ones and soak the vials and caps in 10%hydrochloric acid for at least three days followed by three rinses with high quality double distilled water.To further prepare the glass vials for nutrients, combust them at 450 degrees Celsius for four hours and allow them to cool in the furnace. Then attach the caps and wrap the vials in aluminum foil. Next mix DDW with 0.2 micron filtered surfactant to prepare the five percent solution.Now place a combusted binder free glass fiber filter inside the cleaned inline stainless steel swinnex filter holder. Then use an acid-cleaned syringe to run 100 milliliters of the filtered surfactant solution through the entire assembly. Rinse the assembly clean using 100 milliliters of high quality double distilled water.If the filter assembly is for sampling silica, then prepare it with a polycarbonate filter and run 30 milliliters of five percent hydrochloric acid through it followed by 30 milliliters of high quality double distilled water. Assemble the system for underwater work using PEEK tubing. Use a sharp knife or PEEK cutter to prepare the required lengths.Fit each tube with a male luer connector attached to a syringe needle. Make sure that the flat side of the blue flangeless ferrule is aligned with the end of the tube, then tighten the green nut by hand. Then, using insulating tape, secure the PEEK tubing to the tripod arms for a custom built manipulator.Next, attach capped disposable syringe needles to the male luer connectors. Clearly label the sampling gear and color code the inhale and exhale sampling components such as with blue tape for in and yellow for out. Similarly, color code the sampling vessels to better identify pairs of vessels that are sequentially numbered.Now evacuate the sampling vessels before the dive, ideally with a good vacuum pump. A standard Lyophilizer provides a high vacuum and works as well. Finally line up all the sampling vessels as needed for the dive.Plan all sampling steps out in advance and pack accordingly. First confirm whether the specimen is pumping by releasing filtered fluorescing dye next to the inhalant orifice and confirm that the dye is emerging through the exhale end orifice. Next install the VacuSIP device and make sure it is stable.Then place the inhalant sampling tube within the inhalant orifice or very close to it, making certain that the inhalant tube is not in the proximity of any other exhalant orifices. Next carefully direct the exhalant sampling tube towards the exhalant syphon and very gently insert it one to five millimeters into the syphon. Take great care not to make contact with or otherwise disturb the sampled organism.Then secure the sampling assembly in close working proximity. If you use the customized manipulator, take the same care in positioning the inhalant and exhalant tube. Ultra-plankton sampling requires no filter.To sample ultra-plankton use the needle to pierce the inhaled and exhaled evacuated tube's septum. Check that the water is dripping and collect two to six milliliters of water from each tube. For silicates, install the inline stainless polycarbonate filter holders with the polycarbonate membranes between the needle and the luer male connector at the distill end of the tube.Then pierce the septum cap of the prepared HDPE vials to start sampling. To sample dissolved organics and inorganics, have three pairs of vials ready. One for nitrates and phosphates, one for ammonia, and a third pair for dissolved organics.To sample dissolved organics or nutrients, replace the polycarbonate filter assembly with a pre-cleaned inline stainless steel filter holder that contains a pre-combusted glass filter. Then pierce the septum cap of an EPA glass vial to start sampling. Dissolved inorganics were collected in new EPA glass vials cleaned by the manufacturer or re-used EPA vials cleaned according to the described protocol.The recycled vials reported higher ammonia concentrations but other values were similar. Stainless steel filter holders and polycarbonate inline Swinnex filter holders were compared by filtering pure water and testing for dissolved organic and inorganic nutrients. Polycarbonate membrane and pre-combusted glass fiber filter were tested with each holder.The combination of stainless steel filter holder and combusted glass fiber filter worked best. Cell counts were made with the flow cytometer to test the sample quality. When in-ex sample pairs are properly collected, most cells were removed from the exhaled water.In contrast, improper collection did not garner the same result. When the VacuSIP is properly employed, patterns of removal or excretion were evident for most analysed compounds. The measurements seen here were taken from a mediterranean sponge.

vacusip-an-improved-inex-method-for-situ-measurement-particulate

Research

JoVE Journal

Environment

A Noninvasive Method For In situ Determination of Mating Success in Female American Lobsters (Homarus americanus)

Despite being one of the most productive fisheries in the Northwest Atlantic, much remains unknown about the natural reproductive dynamics of American lobsters. Recent work in exploited crustacean populations (crabs and lobsters) suggests that there are circumstances where mature females are unable to achieve their full reproductive potential due to sperm limitation. To examine this possibility in different regions of the American lobster fishery, a reliable and noninvasive method was developed for sampling large numbers of female lobsters at sea. This method involves inserting a blunt-tipped needle into the female&#39;s seminal receptacle to determine the presence or absence of a sperm plug and to withdraw a sample that can be examined for the presence of sperm. A series of control studies were conducted at the dock and in the laboratory to test the reliability of this technique. These efforts entailed sampling 294 female lobsters to confirm that the presence of a sperm plug was a reliable indicator of sperm within the receptacle and thus, mating. This paper details the methodology and the results obtained from a subset of the total females sampled. Of the 230 female lobsters sampled from George&#39;s Bank and Cape Ann, MA (size range = 71-145 mm in carapace length), 90.3% were positive for sperm. Potential explanations for the absence of sperm in some females include: immaturity (lack of physiological maturity), breakdown of the sperm plug after being used to fertilize a clutch of eggs, and lack of mating activity. The surveys indicate that this technique for examining the mating success of female lobsters is a reliable proxy that can be used in the field to document reproductive activity in natural populations.

A Noninvasive Method For In situ Determination of Mating Success in Female American Lobsters Homarus americanus

Fishery-induced changes to exploited crustacean fisheries, such as the American lobster fishery, could potentially influence their reproductive dynamics, leading to a reduction in mating success. This study&#39;s goal was to develop a noninvasive method for ascertaining the mating success of female lobsters that may be physiologically or functionally mature.

Despite being one of the most productive fisheries in the Northwest Atlantic, much remains unknown about the natural reproductive dynamics of American ...

EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. I. Collection of Virus Samples

EPA Method 1615 was developed with a goal of providing a standard method for measuring enteroviruses and noroviruses in environmental and drinking waters. The standardized sampling component of the method concentrates viruses that may be present in water by passage of a minimum specified volume of water through an electropositive cartridge filter. The minimum specified volumes for surface and finished/ground water are 300 L and 1,500 L, respectively. A major method limitation is the tendency for the filters to clog before meeting the sample volume requirement. Studies using two different, but equivalent, cartridge filter options showed that filter clogging was a problem with 10% of the samples with one of the filter types compared to 6% with the other filter type. Clogging tends to increase with turbidity, but cannot be predicted based on turbidity measurements only. From a cost standpoint one of the filter options is preferable over the other, but the water quality and experience with the water system to be sampled should be taken into consideration in making filter selections.

EPA Method 1615 uses an electropositive filter to concentrate enteroviruses and noroviruses in environmental and drinking waters. This manuscript describes the procedure for collecting samples for Method 1615 analyses.

EPA Method 1615 was developed with a goal of providing a standard method for measuring enteroviruses and noroviruses in environmental and drinking waters. ...

EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. II. Total Culturable Virus Assay

A standardized method is required when national studies on virus occurrence in environmental and drinking waters utilize multiple analytical laboratories. The U.S Environmental Protection Agency&#8217;s (USEPA) Method 1615 was developed with the goal of providing such a standard for measuring Enterovirus and Norovirus in these waters. Virus is concentrated from water using an electropositive filter, eluted from the filter surface with beef extract, and then concentrated further using organic flocculation. Herein we present the protocol from Method 1615 for filter elution, secondary concentration, and measurement of total culturable viruses. A portion of the concentrated eluate from each sample is inoculated onto ten replicate flasks of Buffalo Green Monkey kidney cells. The number of flasks demonstrating cytopathic effects is used to quantify the most probable number (MPN) of infectious units per liter. The method uses a number of quality controls to increase data quality and to reduce interlaboratory and intralaboratory variation. Laboratories must meet defined performance standards. Method 1615 was evaluated by examining virus recovery from reagent-grade and ground waters seeded with Sabin poliovirus type 3. Mean poliovirus recoveries with the total culturable assay were 111% in reagent grade water and 58% in groundwaters.

Here we present a procedure to measure total culturable viruses using the Buffalo Green Monkey kidney cell line. The procedure provides a standardized tool for measuring the occurrence of infectious viruses in environmental and drinking waters.

A standardized method is required when national studies on virus occurrence in environmental and drinking waters utilize multiple analytical laboratories. ...

EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. Part III. Virus Detection by RT-qPCR

EPA Method 1615 measures enteroviruses and noroviruses present in environmental and drinking waters. This method was developed with the goal of having a standardized method for use in multiple analytical laboratories during monitoring period 3 of the Unregulated Contaminant Monitoring Rule. Herein we present the protocol for extraction of viral ribonucleic acid (RNA) from water sample concentrates and for quantitatively measuring enterovirus and norovirus concentrations using reverse transcription-quantitative PCR (RT-qPCR). Virus concentrations for the molecular assay are calculated in terms of genomic copies of viral RNA per liter based upon a standard curve. The method uses a number of quality controls to increase data quality and to reduce interlaboratory and intralaboratory variation. The method has been evaluated by examining virus recovery from ground and reagent grade waters seeded with poliovirus type 3 and murine norovirus as a surrogate for human noroviruses. Mean poliovirus recoveries were 20% in groundwaters and 44% in reagent grade water. Mean murine norovirus recoveries with the RT-qPCR assay were 30% in groundwaters and 4% in reagent grade water.

Here we present a procedure to quantify enterovirus and norovirus in environmental and drinking waters using reverse transcription-quantitative PCR. Mean virus recovery from groundwater with this standardized procedure from EPA Method 1615 was 20% for poliovirus and 30% for murine norovirus.

EPA Method 1615 measures enteroviruses and noroviruses present in environmental and drinking waters. This method was developed with the goal of having a ...

Spotting Cheetahs: Identifying Individuals by Their Footprints

The cheetah (Acinonyx jubatus) is Africa's most endangered large felid and listed as Vulnerable with a declining population trend by the IUCN1. It ranges widely over sub-Saharan Africa and in parts of the Middle East. Cheetah conservationists face two major challenges, conflict with landowners over the killing of domestic livestock, and concern over range contraction. Understanding of the latter remains particularly poor2. Namibia is believed to support the largest number of cheetahs of any range country, around 30%, but estimates range from 2,9053 to 13,5204. The disparity is likely a result of the different techniques used in monitoring.
Current techniques, including invasive tagging with VHF or satellite/GPS collars, can be costly and unreliable. The footprint identification technique5 is a new tool accessible to both field scientists and also citizens with smartphones, who could potentially augment data collection. The footprint identification technique analyzes digital images of footprints captured according to a standardized protocol. Images are optimized and measured in data visualization software. Measurements of distances, angles, and areas of the footprint images are analyzed using a robust cross-validated pairwise discriminant analysis based on a customized model. The final output is in the form of a Ward's cluster dendrogram. A user-friendly graphic user interface (GUI) allows the user immediate access and clear interpretation of classification results.
The footprint identification technique algorithms are species specific because each species has a unique anatomy. The technique runs in a data visualization software, using its own scripting language (jsl) that can be customized for the footprint anatomy of any species. An initial classification algorithm is built from a training database of footprints from that species, collected from individuals of known identity. An algorithm derived from a cheetah of known identity is then able to classify free-ranging cheetahs of unknown identity. The footprint identification technique predicts individual cheetah identity with an accuracy of &gt;90%.

The cheetah (Acinonyx jubatus) is an iconic, endangered species, but conservation efforts are challenged by habitat shrinkage and conflict with commercial farmers. The footprint identification technique, a robust, accurate and cost-effective image classification system, is a new approach to monitoring cheetahs.

The cheetah (Acinonyx jubatus) is Africa's most endangered large felid and listed as Vulnerable with a declining population trend by the IUCN1. It ranges ...

The Benthic Exchange of O2, N2 and Dissolved Nutrients Using Small Core Incubations

The measurement of sediment-water exchange of gases and solutes in aquatic sediments provides data valuable for understanding the role of sediments in nutrient and gas cycles. After cores with intact sediment-water interfaces are collected, they are submerged in incubation tanks and kept under aerobic conditions at in situ temperatures. To initiate a time course of overlying water chemistry, cores are sealed without bubbles using a top cap with a suspended stirrer. Time courses of 4-7 sample points are used to determine the rate of sediment water exchange. Artificial illumination simulates day-time conditions for shallow photosynthetic sediments, and in conjunction with dark incubations can provide net exchanges on a daily basis. The net measurement of N2 is made possible by sampling a time course of dissolved gas concentrations, with high precision mass spectrometric analysis of N2:Ar ratios providing a means to measure N2 concentrations. We have successfully applied this approach to lakes, reservoirs, estuaries, wetlands and storm water ponds, and with care, this approach provides valuable information on biogeochemical balances in aquatic ecosystems.

The Benthic Exchange of O2, N2 and Dissolved Nutrients Using Small Core Incubations

Here, we present small core incubations for the measurement of sediment-water gas and solute exchange. These will provide reliable measurements of sediment-water exchange that assess the role of sediment in influencing biological and biogeochemical processes in aquatic ecosystems.

The measurement of sediment-water exchange of gases and solutes in aquatic sediments provides data valuable for understanding the role of sediments in ...

A Simple Approach to Manipulate Dissolved Oxygen for Animal Behavior Observations

The ability to manipulate dissolved oxygen (DO) in a laboratory setting has significant application to investigate a number of ecological and organismal behavior questions. The protocol described here provides a simple, reproducible, and controlled method to manipulate DO to study behavioral response in aquatic organisms resulting from hypoxic and anoxic conditions. While performing degasification of water with nitrogen is commonly used in laboratory settings, no explicit method for ecological (aquatic) application exists in the literature, and this protocol is the first to describe a protocol to degasify water to observe organismal response. This technique and protocol were developed for direct application for aquatic macroinvertebrates; however, small fish, amphibians, and other aquatic vertebrates could be easily substituted. It allows for easy manipulation of DO levels ranging from 2 mg/L to 11 mg/L with stability for up to a 5 min animal-observation period. Beyond a 5 min observation period water temperatures began to rise, and at 10 min DO levels became too unstable to maintain. The protocol is scalable to the study organism, reproducible, and reliable, allowing for rapid implementation into introductory teaching labs and high-level research applications. The expected results of this technique should relate dissolved oxygen changes to behavioral responses of organisms.

This article describes a simple and reproducible protocol to manipulate dissolved oxygen conditions in a laboratory setting for animal behavior studies. This protocol may be used in both teaching and research laboratory settings to evaluate organismal response of macroinvertebrates, fishes, or amphibians to changes in dissolved oxygen concentration.

The ability to manipulate dissolved oxygen (DO) in a laboratory setting has significant application to investigate a number of ecological and organismal ...

Understanding Dissolved Organic Matter Biogeochemistry Through In Situ Nutrient Manipulations in Stream Ecosystems

Dissolved organic matter (DOM) is a highly diverse mixture of molecules providing one of the largest sources of energy and nutrients to stream ecosystems. Yet the in situ study of DOM is difficult as the molecular complexity of the DOM pool cannot be easily reproduced for experimental purposes. Nutrient additions to streams however, have been shown to repeatedly alter the in situ and ambient DOM pool. Here we demonstrate an easily replicable field-based method for manipulating the ambient pool of DOM at the ecosystem scale. During nutrient pulse experiments changes in the concentration of both dissolved organic carbon and dissolved organic nitrogen can be examined across a wide-range of nutrient concentrations. This method allows researchers to examine the controls on the DOM pool and make inferences regarding the role and function that certain fractions of the DOM pool play within ecosystems. We advocate the use of this method as a technique to help develop a deeper understanding of DOM biogeochemistry and how it interacts with nutrients. With further development this method may help elucidate the dynamics of DOM in other ecosystems.

Understanding Dissolved Organic Matter Biogeochemistry Through In Situ Nutrient Manipulations in Stream Ecosystems

Dissolved organic matter provides an important source of energy and nutrients to stream ecosystems. Here we demonstrate a field-based method to manipulate the ambient pool of dissolved organic matter in situ through easily replicable nutrient pulses.

Dissolved organic matter (DOM) is a highly diverse mixture of molecules providing one of the largest sources of energy and nutrients to stream ecosystems. ...

Production and Measurement of Organic Particulate Matter in a Flow Tube Reactor

Organic particulate matter (PM) is increasingly recognized as important to the Earth's climate system as well as public health in urban regions, and the production of synthetic PM for laboratory studies have become a widespread necessity. Herein, experimental protocols demonstrate approaches to produce aerosolized organic PM by &#945;-pinene ozonolysis in a flow tube reactor. Methods are described for measuring the size distributions and morphology of the aerosol particles. The video demonstrates basic operations of the flow tube reactor and related instrumentation. The first part of the video shows the procedure for preparing gas-phase reactants, ozonolysis, and production of organic PM. The second part of the video shows the procedures for determining the properties of the produced particle population. The particle number-diameter distributions show different stages of particle growth, namely condensation, coagulation, or a combination of both, depending on reaction conditions. The particle morphology is characterized by an aerosol particle mass analyzer (APM) and a scanning electron microscope (SEM). The results confirm the existence of non-spherical particles that have grown from coagulation for specific reaction conditions. The experimental results also indicate that the flow tube reactor can be used to study the physical and chemical properties of organic PM for relatively high concentrations and short time frames.

This paper describes the operation procedure for the flow tube reactor and related data collection. It shows the protocols for setting the experiments, recording data and generating the number-diameter distribution as well as the particle mass information, which gives useful information about chemical and physical properties of the organic aerosols.

Organic particulate matter (PM) is increasingly recognized as important to the Earth's climate system as well as public health in urban regions, and the ...

Production and Measurement of Organic Particulate Matter in the Harvard Environmental Chamber

The production and the evolution of atmospheric organic particulate matter (PM) are insufficiently understood for accurate simulations of atmospheric chemistry and climate. The complex production mechanisms and reaction pathways make this a challenging research topic. To address these issues, an environmental chamber, providing enough residence time and close-to-ambient concentrations of precursors for secondary organic materials, is needed. The Harvard Environmental Chamber (HEC) was built to serve this need, simulating the production of gas and particle phase species from volatile organic compounds (VOCs). The HEC has a volume of 4.7 m3 and a mean residence time of 3.4 h under typical operating conditions. It is operated as a completely mixed flow reactor (CMFR), providing the possibility of indefinite steady-state operation across days for sample collection and data analysis. The operation procedures are described in detail in this article. Several types of instrumentation are used to characterize the produced gas and particles. A High-Resolution Time-of-Fight Aerosol Mass Spectrometer (HR-ToF-AMS) is used to characterize particles. A Proton-Transfer-Reaction Mass Spectrometer (PTR-MS) is used for gaseous analysis. Example results are presented to show the use of the environmental chamber in a wide variety of applications related to the physicochemical properties and reaction mechanisms of organic atmospheric particulate matter.

This paper describes operation procedures for the Harvard Environmental Chamber (HEC) and related instrumentation for measuring gaseous and particle species. The environmental chamber is used to produce and study secondary organic species produced from the organic precursors, especially related to atmospheric organic particulate matter.

The production and the evolution of atmospheric organic particulate matter (PM) are insufficiently understood for accurate simulations of atmospheric ...