Name: evolution of staircase structures in diffusive convection
Uploaded: 2018-09-05T15:30:00
Description: Watch this Scientific Journal Video about Evolution of Staircase Structures in Diffusive Convection at JoVE.com

This work was supported by the Chinese NSF grants (41706033, 91752108 and 41476167), Grangdong NSF grants (2017A030313242 and 2016A030311042) and LTO grant (LTOZZ1801).

1. Working Tank
Note: The experiment is carried out in a rectangular tank. The tank includes top and bottom plates and a side wall. The top and bottom plates are made of copper with electroplated surfaces. There is a water chamber within the top plate. An electric heating pad is inserted in the bottom plate. The side wall is made of transparent Plexiglas. The tank size is Lx = 257 mm (length), Ly = 65 mm (width) and Lz = 257 mm (height). The thickness of the side...

<ol>
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E., Tanny, J., Ozsoy, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+diffusive+regime+of+double+diffusive+convection.">The diffusive regime of double diffusive convection.</a> Progress in Oceanography. 56, 461-481 (2003).</li><li>Timmermans, M. L., Toole, J., Krishfield, R., Winsor, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ice-Tethered+Profiler+observations+of+the+double-diffusive+staircase+in+the+Canada+Basin+thermocline.">Ice-Tethered Profiler observations of the double-diffusive staircase in the Canada Basin thermocline.</a> Journal of Geophysical Research: Oceans. 113, 1-10 (2008).</li><li>Zhou, S. Q., Lu, Y. 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T., Neshyba, S., Denner, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermal+stratification+in+the+Arctic+Ocean.">Thermal stratification in the Arctic Ocean.</a> Science. 166 (3903), 373-374 (1969).</li><li>Padman, L., Dillon, T. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Vertical+heat+fluxes+through+the+Beaufort+Sea+thermohaline+staircase.">Vertical heat fluxes through the Beaufort Sea thermohaline staircase.</a> Journal of Geophysical Research: Oceans. 92 (C10), 10799-10806 (1987).</li><li>Sirevaag, A., Fer, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Vertical+heat+transfer+in+the+Arctic+Ocean:+The+role+of+double-diffusive+mixing.">Vertical heat transfer in the Arctic Ocean: The role of double-diffusive mixing.</a> Journal of Geophysical Research: Oceans. 117 (C7), (2012).</li><li>Guthrie, J. 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M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spatial+variability+of+the+Arctic+Ocean's+double-diffusive+staircase.">Spatial variability of the Arctic Ocean's double-diffusive staircase.</a> Journal of Geophysical Research: Oceans. 122 (2), 980-994 (2017).</li><li>Schmid, M., Busbridge, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Double-diffusive+convection+in+Lake+Kivu.">Double-diffusive convection in Lake Kivu.</a> Limnology and Oceanography. 55 (1), 225-238 (2010).</li><li>Sommer, T., 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=Interface+structure+and+flux+laws+in+a+natural+double-diffusive+layering.">Interface structure and flux laws in a natural double-diffusive layering.</a> Journal of Geophysical Research: Oceans. 118 (11), 6092-6106 (2013).</li><li>Carpenter, J. 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In this paper a detailed experimental protocol is described to simulate the thermohaline DC staircase structures in a rectangular tank. An initial linear density stratification of working fluid is constructed using the two-tank method. The top plate is kept at a constant temperature and the bottom one at constant heat flux. The whole evolution process of the DC staircase, including its generation, development, mergence, and disappearance, are visualized with the shadowgraph technique, and the variances of the temperature...

Double diffusive convection (DDC) is one of the most important vertical mixing processes. It occurs when the vertical density distribution of the stratified water column is controlled by two or more scalar components gradients of opposite directions, where the components have distinctly different molecular diffusivities1. It widely occurs in oceanography2, the atmosphere3, geology4, astrophysics5, material science6, metallurgy7, and architectural engineering8. DDC is present in almost half of the global ocean, and it has important effects on oceanic multi-scale processes and even climatic changes9.
There are two primary modes for DDC: salt finger (SF) and diffusive convection (DC). SF occurs when a warm, salty water mass overlies cooler, fresher water in the stratified environment. When the warm and salty water lies below the cold and fresh water, the DC will form. The remarkable feature of the DC is that the vertical profiles of temperature, salinity and density are staircase-like, composed by alternant homogenous convecting layers and thin, strongly stratified interfaces. DC mainly occurs in high latitude oceans and some interior salt lakes, such as the Arctic and Antarctic Oceans, the Okhotsk Sea, the Red Sea and African Kivu Lake10. In the Arctic Ocean, there exist basin-wide and persistent DC staircases in the upper and deep oceans11,12. It has an important effect on diapycnal mixing in the upper ocean and may significantly influence the ice-melting, which recently arouses more and more interests in the oceanography community13.
The DC staircase structure was first discovered in the Arctic Ocean in 196914. After that, Padman &#38; Dillon15, Timmermans et al.11, Sirevaag &#38; Fer16, Zhou &#38; Lu12, Guthrie et al.17, Bebieva &#38; Timmermans18, and Shibley et al.19 measured the DC staircases in different basins of the Arctic Ocean, including the vertical and horizontal scales of the convecting layer and interface, the depth and total thickness of the staircase, the vertical heat transfer, the DC processes in mesoscale eddy and the temporal and spatial changes of the staircase structures. Schmid et al.20 and Sommer et al.21 observed the DC staircases by using a microstructure profiler in Kivu Lake. They reported the main structure features and heat fluxes of DC and compared the measured heat fluxes with the existing parametric formula. With computer processing speeds improving, the numerical simulations of DC have recently been done, for example, to examine the interface structure and instability, heat transfer through interface, layer merging event, and so on22,23,24.
Field observation has greatly enhanced the understanding of ocean DC for oceanographers, but the measurement is strongly limited by indeterminate oceanic flow environments and instruments. For example, the DC interface has an extremely small vertical scale, thinner than 0.1 m in some lakes and oceans25, and some special high-resolution instruments are needed. The laboratory experiment shows its unique advantages in exploring the fundamental dynamic and thermodynamic laws of DC. With a laboratory experiment, one can observe the evolution of the DC staircase, measure the temperature and salinity, and propose some parameterizations for the oceanic applications26,27. Furthermore, in a laboratory experiment, the controlled parameters and conditions are readily adjusted as required. For example, Turner first simulated the DC staircase in the laboratory in 1965 and proposed a heat transfer parameterization across the diffusive interface, which was frequently updated and extensively used in the in situ oceanic observations28.
In this paper, a detailed experimental protocol is described to simulate the evolution process of the DC staircase, including the generation, development and disappearance, in stratified saline water heated from below. The temperature and salinity are measured by a micro-scale instrument as well as the DC staircases being monitored with the shadowgraph technique. The experimental setup, evolution process, data analysis, and discussion of results are described in detail. By altering the initial and boundary conditions, the present experimental setup and method can be used to simulate other oceanic phenomena, such as the oceanic horizontal convection, deep-sea hydrothermal eruptions, surface mixed layer deepening, the effect of submarine geothermal on ocean circulation, and so on.

<table border="0" cellpadding="0" cellspacing="0" width="623">
	<tbody>
		<tr height="28">
			<td height="28" style="height:28px;width:185px;">Rectangular tank</td>
			<td style="width:152px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">Custom made part</td>
		</tr>
		<tr height="28">
			<td height="28" style="height:28px;width:185px;">Plexiglas</td>
			<td style="width:152px;"></td>
			<td style="width:119px;"></td>
			<td>Custom made part</td>
		</tr>
		<tr height="26">
			<td height="26" style="height:27px;width:185px;">Electric heating pad</td>
			<td style="width:152px;"></td>
			<td style="width:119px;"></td>
			<td>Custom made part</td>
		</tr>
		<tr height="26">
			<td height="26" style="height:27px;width:185px;">Distilled water</td>
			<td style="width:152px;"></td>
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			<td style="width:167px;">Multiple suppliers</td>
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			<td height="26" style="height:27px;width:185px;">Optical table</td>
			<td style="width:152px;">Liansheng Inc.</td>
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			<td height="29" style="height:29px;width:185px;">Thermiostors</td>
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			<td style="width:119px;"></td>
			<td>Custom made part</td>
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			<td height="29" style="height:29px;width:185px;">Digital multimeter</td>
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			<td height="63" style="height:63px;width:185px;">Micro-scale conductivity and temperature instrument (MSCTI)</td>
			<td style="width:152px;">PME. Inc.</td>
			<td style="width:119px;">Model 125</td>
			<td></td>
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			<td height="42" style="height:42px;width:185px;">Multifunction data acquisition (MDA)</td>
			<td style="width:152px;">MCC. Inc.</td>
			<td style="width:119px;">USB-2048</td>
			<td></td>
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			<td height="42" style="height:42px;width:185px;">Motorized precision translation stage (MPTS)</td>
			<td style="width:152px;">Thorlabs Inc.</td>
			<td style="width:119px;">LTS300</td>
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		<tr height="29">
			<td height="29" style="height:29px;width:185px;">Tracing paper</td>
			<td style="width:152px;"></td>
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			<td style="width:167px;">Multiple suppliers</td>
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			<td height="28" style="height:28px;width:185px;">LED lamp</td>
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			<td height="28" style="height:28px;width:185px;">Camcorder</td>
			<td style="width:152px;">Sony Inc.</td>
			<td style="width:119px;">XDR-XR550</td>
			<td></td>
		</tr>
		<tr height="28">
			<td height="28" style="height:28px;width:185px;">De-gassed fresh water</td>
			<td style="width:152px;"></td>
			<td style="width:119px;"></td>
			<td>Custom made part</td>
		</tr>
		<tr height="28">
			<td height="28" style="height:28px;width:185px;">Saline water</td>
			<td style="width:152px;"></td>
			<td style="width:119px;"></td>
			<td>Custom made part</td>
		</tr>
		<tr height="30">
			<td height="30" style="height:31px;width:185px;">Flexible tube</td>
			<td style="width:152px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">Multiple suppliers</td>
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			<td height="30" style="height:31px;width:185px;">Electric magnetic stirrer&#160;</td>
			<td style="width:152px;">Meiyingpu Inc.</td>
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			<td height="28" style="height:28px;width:185px;">Plastic soft tube</td>
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			<td height="42" style="height:42px;width:185px;">Direct-current power supply</td>
			<td style="width:152px;">GE Inc.</td>
			<td style="width:119px;">GPS-3030</td>
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			<td height="32" style="height:32px;width:185px;">Matlab</td>
			<td style="width:152px;">MathWorks Inc.</td>
			<td style="width:119px;">R2012a</td>
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	</tbody>
</table>

evolution of staircase structures in diffusive convection

Diffusive convection (DC) occurs when the vertical stratified density is controlled by two opposing scalar gradients that have distinctly different molecular diffusivities, and the larger- and smaller- diffusivity scalar gradients have negative and positive contributions for the density distribution, respectively. The DC occurs in many natural processes and engineering applications, for example, oceanography, astrophysics and metallurgy. In oceans, one of the most remarkable features of DC is that the vertical temperature and salinity profiles are staircase-like structure, composed of consecutive steps with thick homogeneous convecting layers and relatively thin and high-gradient interfaces. The DC staircases have been observed in many oceans, especially in the Arctic and Antarctic Oceans, and play an important role on the ocean circulation and climatic change. In the Arctic Ocean, there exist basin-wide and persistent DC staircases in the upper and deep oceans. The DC process has an important effect on diapycnal mixing in the upper ocean and may significantly influence the surface ice-melting. Compared to the limitations of field observations, laboratory experiment shows its unique advantage to effectively examine the dynamic and thermodynamic processes in DC, because the boundary conditions and the controlled parameters can be strictly adjusted. Here, a detailed protocol is described to simulate the evolution process of DC staircase structure, including its generation, development and disappearance, in a rectangular tank filled with stratified saline water. The experimental setup, evolution process, data analysis, and discussion of results are described in detail.

Figure 1 shows the schematic of the experimental setup. Its components are described in the protocol. The main parts are shown in Figure 1a and the detailed working tank is shown in Figure 1b. Figure 2 shows the temperature changes at the bottom (Tb, the red curve) and top (Tt, the black curve) plates. It is indicated that the temperature of the two plates are almost the same as th...

Watch this Scientific Journal Video about Evolution of Staircase Structures in Diffusive Convection at JoVE.com

Evolution of Staircase Structures in Diffusive Convection

Diffusive convection (DC) widely occurs in natural processes and engineering applications, characterized by a series of staircases with homogeneous convecting layers and stratified interfaces. An experimental procedure is described to simulate the evolution process of the DC staircase structure, including the generation, development and disappearance, in a rectangular tank.

Diffusive convection (DC) occurs when the vertical stratified density is controlled by two opposing scalar gradients that have distinctly different ...

This method can be used to explore the key issues in the dynamic processes of diffusive convection staircase structures, such as their generation, development, and disappearance. With the present experimental setup, we can clearly see the evolution of diffusive convection, which is very difficult, if it is not impossible, to observe directly in the ocean. Gather the components of the working tank.These include copper top and bottom plates and an acrylic sidewall assembly. The top plate is electroplated and encloses a water chamber accessible by tubes. It also has places for thermistors.The bottom plate is also electroplated and has slots for thermistors. It contains a heating pad. Use distilled water to carefully clean the copper plates and the acrylic sidewalls.When done, assemble the tank using screws to ensure it is water-tight. This completed tank is 257 millimeters in length and height and 65 millimeters wide. At an optical table, set up a stainless-steel supporting frame.On top of the frame, place an insulating slab. With everything in place, place the assembled tank on the slab. Insert thermistors into the top and bottom plates, and connect them to the data acquisition system.A thermistor monitors the temperature of the plate into which it is placed. Next, move a precision vertical translation stage into place for mounting a probe. Through the top plate, place a micro scale conductivity and temperature instrument sensor into the tank.Fix the instrument to the precision translation stage. Now, set up software for sensor data acquisition and thermistor readings. Return to the tank to adjust the position of the conductivity and temperature sensor.Set the initial position of the sensor at its lowest point, here, 20 millimeters above the bottom of the tank. Then, set the parameters of the motion for the translation stage for the experiment. Use the shadowgraph technique to monitor the experiment.For this, attach a piece of tracing paper on the outside of one side of the tank. On the opposite side of the tank, about five meters away, place a light source. To produce a nearly collimated beam, use a narrow beam LED as a light source.Place a high-speed camcorder about a meter in front of the tracing paper in the beam path. With the lamp and camcorder on, adjust their positions for a clear image. Obtain two identical rectangular tanks for the working fluid.The tanks are the same size as the working tank. Join them at their base with a clamped flexible tube, 10 centimeters in length. Place the two tanks at the same height.Arrange for one tank to have an electric stirrer in it. Next, clamp a flexible 50-centimeter tube into a peristaltic pump. Use the tube to join the tank with the stirrer to the working tank.Fill the tank that has no stirrer with saline solution of 60 grams per kilogram concentration. Fill the other tank with an equal volume of degassed fresh water. Once the tanks are filled, unclamp the connecting tube.Continuously homogenize the mixing water with the electric stirrer. Control the flow rate in the working tank with the peristaltic pump. The working tank takes approximately three hours to fill and be ready for the experiment.For an experiment, use a refrigerated circulator to set the top plate boundary conditions. At the top plate, connect the water chamber to the refrigerated circulator using eight soft plastic tubes. At the circulator, set the temperature for the top plate to the room temperature.Now, connect the bottom plate's heating pad to a DC power supply, and set its power level. Turn on the camcorder to record the flow pattern. Begin monitoring temperature and salinity data.Then, start vertical motion of the sensor. Finally, turn on the refrigerated circulator and the DC power supply to achieve the working fluid boundary conditions. This is an example of a shadowgraph image taken when the top plate is at the room temperature and the bottom plate is being heated.There are three convecting layers in the image, where the fluid density is homogeneous. There are also three interface layers, where large density gradients exist. This intensity fluctuation profile has three peaks that correspond to the interfaces.Here is the evolution of the intensity fluctuation profile in time, which reveals layer generation, development, and disappearance associated with the diffusive convection staircase. The temperature profile and the salinity profile provide other views of the evolution in time of the system. In these profiles, each continuous line represents data collected over 404 seconds.The data sets in the temperature profile are each offset by 1.5 degrees Celsius from the one before. For the salinity profile, each data set is offset by three grams per kilogram from the previous set. This method can also be applied to simulate other phenomenon in oceans, such as global oceanic circulation, mixed layer deepening, and hydrothermal plume eruption.If you want to try this procedure, please do remember to initially adjust the conductivity and temperature sensors to the lowest position of the translation stage to prevent the sensor for crashing on the bottom plate. With the presented results, we can further develop new parameterization of layer thickness, heat flux, and add diffusivity in diffusive convection, which would pave the way for the community of physical oceanography to study the phenomena in the oceanic application.

evolution-of-staircase-structures-in-diffusive-convection

Research

JoVE Journal

Environment

Optimize Flue Gas Settings to Promote Microalgae Growth in Photobioreactors via Computer Simulations

Flue gas from power plants can promote algal cultivation and reduce greenhouse gas emissions1. Microalgae not only capture solar energy more efficiently than plants3, but also synthesize advanced biofuels2-4. Generally, atmospheric CO2 is not a sufficient source for supporting maximal algal growth5. On the other hand, the high concentrations of CO2 in industrial exhaust gases have adverse effects on algal physiology. Consequently, both cultivation conditions (such as nutrients and light) and the control of the flue gas flow into the photo-bioreactors are important to develop an efficient &ldquo;flue gas to algae&rdquo; system. Researchers have proposed different photobioreactor configurations4,6 and cultivation strategies7,8 with flue gas. Here, we present a protocol that demonstrates how to use models to predict the microalgal growth in response to flue gas settings. We perform both experimental illustration and model simulations to determine the favorable conditions for algal growth with flue gas. We develop a Monod-based model coupled with mass transfer and light intensity equations to simulate the microalgal growth in a homogenous photo-bioreactor. The model simulation compares algal growth and flue gas consumptions under different flue-gas settings. The model illustrates: 1) how algal growth is influenced by different volumetric mass transfer coefficients of CO2; 2) how we can find optimal CO2 concentration for algal growth via the dynamic optimization approach (DOA); 3) how we can design a rectangular on-off flue gas pulse to promote algal biomass growth and to reduce the usage of flue gas. On the experimental side, we present a protocol for growing Chlorella under the flue gas (generated by natural gas combustion). The experimental results qualitatively validate the model predictions that the high frequency flue gas pulses can significantly improve algal cultivation.

Flue gas from power plants is a cheap CO2 source for algal growth. We have built prototype &#34;flue gas to algal cultivation&#34; systems and described how to scale up the algal cultivation process. We have demonstrated the use of a mass-transfer bio-reaction model to simulate and to design the optimal operation of flue gas for the growth of Chlorella sp. in algal photo-bioreactors.

Flue gas from power plants can promote algal cultivation and reduce greenhouse gas emissions1. Microalgae not only capture solar energy more efficiently ...

Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health

Growers often use fungicide sprays during bloom to protect crops against disease, which exposes bees to fungicide residues. Although considered &#34;bee-safe,&#34; there is mounting evidence that fungicide residues in pollen are associated with bee declines (for both honey and bumble bee species). While the mechanisms remain relatively unknown, researchers have speculated that bee-microbe symbioses are involved. Microbes play a pivotal role in the preservation and/or processing of pollen, which serves as nutrition for larval bees. By altering the microbial community, it is likely that fungicides disrupt these microbe-mediated services, and thereby compromise bee health. This manuscript describes the protocols used to investigate the indirect mechanism(s) by which fungicides may be causing colony decline. Cage experiments exposing bees to fungicide-treated flowers have already provided the first evidence that fungicides cause profound colony losses in a native bumble bee (Bombus impatiens). Using field-relevant doses of fungicides, a series of experiments have been developed to provide a finer description of microbial community dynamics of fungicide-exposed pollen. Shifts in the structural composition of fungal and bacterial assemblages within the pollen microbiome are investigated by next-generation sequencing and metagenomic analysis. Experiments developed herein have been designed to provide a mechanistic understanding of how fungicides affect the microbiome of pollen-provisions. Ultimately, these findings should shed light on the indirect pathway through which fungicides may be causing colony declines.

Microbial consortia within bumble bee hives enrich and preserve pollen for bee larvae. Using next generation sequencing, along with laboratory and field-based experiments, this manuscript describes protocols used to test the hypothesis that fungicide residues alter the pollen microbiome, and colony demographics, ultimately leading to colony loss.

Growers often use fungicide sprays during bloom to protect crops against disease, which exposes bees to fungicide residues. Although considered ...

Experimental Protocol for Detecting Cyanobacteria in Liquid and Solid Samples with an Antibody Microarray Chip

Global warming and eutrophication make some aquatic ecosystems behave as true bioreactors that trigger rapid and massive cyanobacterial growth; this has relevant health and economic consequences. Many cyanobacterial strains are toxin producers, and only a few cells are necessary to induce irreparable damage to the environment. Therefore, water-body authorities and administrations require rapid and efficient early-warning systems providing reliable data to support their preventive or curative decisions. This manuscript reports an experimental protocol for the in-field detection of toxin-producing cyanobacterial strains by using an antibody microarray chip with 17 antibodies (Abs) with taxonomic resolution (CYANOCHIP). Here, a multiplex fluorescent sandwich microarray immunoassay (FSMI) for the simultaneous monitoring of 17 cyanobacterial strains frequently found blooming in freshwater ecosystems, some of them toxin producers, is described. A microarray with multiple identical replicates (up to 24) of the CYANOCHIP was printed onto a single microscope slide to simultaneously test a similar number of samples. Liquid samples can be tested either by direct incubation with the antibodies (Abs) or after cell concentration by filtration through a 1- to 3-&#956;m filter. Solid samples, such as sediments and ground rocks, are first homogenized and dispersed by a hand-held ultrasonicator in an incubation buffer. They are then filtered (5 - 20 &#956;m) to remove the coarse material, and the filtrate is incubated with Abs. Immunoreactions are revealed by a final incubation with a mixture of the 17 fluorescence-labeled Abs and are read by a portable fluorescence detector. The whole process takes around 3 h, most of it corresponding to two 1-h periods of incubation. The output is an image, where bright spots correspond to the positive detection of cyanobacterial markers.

Experimental Protocol for Detecting Cyanobacteria in Liquid and Solid Samples with an Antibody Microarray Chip

The presence of cyanobacterial toxins in fresh water reservoirs for human consumption is a major concern for water management authorities. To evaluate the risk of water contamination, this article describes an protocol for the in-field detection of cyanobacterial strains in liquid and solid samples by using an antibody microarray chip.

Global warming and eutrophication make some aquatic ecosystems behave as true bioreactors that trigger rapid and massive cyanobacterial growth; this has ...

Ecotoxicological Method with Marine Bacteria Vibrio anguillarum to Evaluate the Acute Toxicity of Environmental Contaminants

Bacteria are an important component of the ecosystem, and microbial community alterations can have a significant effect on biogeochemical cycling and food webs. Toxicity testing based on microorganisms are widely used because they are relatively quick, reproducible, cheap, and are not associated with ethical issues. Here, we describe an ecotoxicological method to evaluate the biological response of the marine bacterium Vibrio anguillarum. This method assesses the acute toxicity of chemical compounds, including new contaminants such as nanoparticles, as well as environmental samples. The endpoint is the reduction of bacterial culturability (i.e., the capability to replicate and form colonies) due to exposure to a toxicant. This reduction can be generally referred to as mortality. The test allows for the determination of the LC50, the concentration that causes a 50% decrease of bacteria actively replicating and forming colonies, after a 6 h exposure. The culturable bacteria are counted in terms of colony forming units (CFU), and the &#34;mortality&#34; is evaluated and compared to the control. In this work, the toxicity of copper sulphate (CuSO4) was evaluated. A clear dose-response relationship was observed, with a mean LC50 of 1.13 mg/L, after three independent tests. This protocol, compared to existing methods with microorganisms, is applicable in a wider range of salinity and has no limitations for colored/turbid samples. It uses saline solution as the exposure medium, avoiding any possible interferences of growth medium with the investigated contaminants. The LC50 calculation facilitates comparisons with other bioassays commonly applied to ecotoxicological assessments of the marine environment.

Ecotoxicological Method with Marine Bacteria Vibrio anguillarum to Evaluate the Acute Toxicity of Environmental Contaminants

This work describes a new protocol to assess the ecotoxicity of pollutants, including emerging contaminants such as nanomaterials, using the marine bacterium Vibrio anguillarum. This method allows for the determination of the LC50, or mortality, the concentration that causes a 50% decrease in bacteria culturability, after a 6 h exposure.

Bacteria are an important component of the ecosystem, and microbial community alterations can have a significant effect on biogeochemical cycling and food ...

BtM, a Low-cost Open-source Datalogger to Estimate the Water Content of Nonvascular Cryptogams

Communities of nonvascular cryptogams, such as mosses or lichens, are an important part of the Earth's biodiversity, contributing to the regulation of the carbon and nitrogen cycles in many ecosystems. Being poikilohydric organisms, they do not actively control their internal water content and need a humid environment to activate their metabolism. Therefore, studying water relationships of nonvascular cryptogams is crucial to understand both their diversity patterns and their functions in the ecosystems. We present the BtM datalogger, a low-cost open-source platform for the study of the water content of nonvascular cryptogams. The datalogger is designed to measure ambient temperature, humidity, and conductance from up to eight samples simultaneously. We provide a design for a printed circuit board (PCB), a detailed protocol to assemble the components, and the required source code. All this makes the assembly of the BtM datalogger accessible to any research group, even to those without previous specialized knowledge. Therefore, the design presented here has the potential to help popularize the use of this type of device among ecologists and field biologists.

We present a simple and cost-effective method to build an open-source datalogger that measures the conductance of nonvascular cryptogams together with the environmental temperature and humidity. We describe the hardware design of the datalogger and provide step-by-step assembly instructions, the list of required open-source logging software, the code to run the datalogger, and a calibration protocol.

Communities of nonvascular cryptogams, such as mosses or lichens, are an important part of the Earth's biodiversity, contributing to the regulation of the ...

Leaf Area Index Estimation Using Three Distinct Methods in Pure Deciduous Stands

Accurate estimations of leaf area index (LAI), defined as half of the total leaf surface area per unit of horizontal ground surface area, are crucial for describing the vegetation structure in the fields of ecology, forestry, and agriculture. Therefore, procedures of three commercially used methods (litter traps, needle technique, and a plant canopy analyzer) for performing LAI estimation were presented step-by-step. Specific methodological approaches were compared, and their current advantages, controversies, challenges, and future perspectives were discussed in this protocol. Litter traps are usually deemed as the reference level. Both the needle technique and the plant canopy analyzer (e.g., LAI-2000) frequently underestimate LAI values in comparison with the reference. The needle technique is easy to use in deciduous stands where the litter completely decomposes each year (e.g., oak and beech stands). However, calibration based on litter traps or direct destructive methods is necessary. The plant canopy analyzer is a commonly used device for performing LAI estimation in ecology, forestry, and agriculture, but is subject to potential error due to foliage clumping and the contribution of woody elements in the field of view (FOV) of the sensor. Eliminating these potential error sources was discussed. The plant canopy analyzer is a very suitable device for performing LAI estimations at the high spatial level, observing a seasonal LAI dynamic, and for long-term monitoring of LAI.

An accurate estimation of leaf area index (LAI) is crucial for many models of material and energy fluxes within plant ecosystems and between an ecosystem and the atmospheric boundary layer. Therefore, three methods (litter traps, needle technique, and PCA) for taking precise LAI measurements were in the presented protocol.

Accurate estimations of leaf area index (LAI), defined as half of the total leaf surface area per unit of horizontal ground surface area, are crucial for ...

Streamlined Sampling and Cultivation of the Pelagic Cosmopolitan Larvacean, Oikopleura dioica

Oikopleura dioica is a planktonic chordate with exceptional filter-feeding ability, rapid generation time, conserved early development, and a compact genome. For these reasons, it is considered a useful model organism for marine ecological studies, evolutionary developmental biology, and genomics. As research often requires a steady supply of animal resources, it is useful to establish a reliable, low-maintenance culture system. Here we describe a step-by-step method for establishing an O. dioica culture. We describe how to select potential sampling sites, collection methods, target animal identification, and the set-up of the culturing system. We provide troubleshooting advice based on our own experiences. We also highlight critical factors that help sustain a robust culture system. Although the culture protocol provided here is optimized for O. dioica, we hope our sampling technique and culture setup will inspire new ideas for maintaining other fragile pelagic invertebrates.

Streamlined Sampling and Cultivation of the Pelagic Cosmopolitan Larvacean, Oikopleura dioica

Oikopleura dioica is a tunicate model organism in various fields of biology. We describe sampling methods, species identification, culturing setup, and culturing protocols for the animals and algal feed. We highlight key factors that helped strengthen the culture system and discuss the possible problems and resolutions.

Oikopleura dioica is a planktonic chordate with exceptional filter-feeding ability, rapid generation time, conserved early development, and a compact ...

A Telemetric, Gravimetric Platform for Real-Time Physiological Phenotyping of Plant&ndash;Environment Interactions

Food security for the growing global population is a major concern. The data provided by genomic tools far exceeds the supply of phenotypic data, creating a knowledge gap. To meet the challenge of improving crops to feed the growing global population, this gap must be bridged.
Physiological traits are considered key functional traits in the context of responsiveness or sensitivity to environmental conditions. Many recently introduced high-throughput (HTP) phenotyping techniques are based on remote sensing or imaging and are capable of directly measuring morphological traits, but measure physiological parameters mainly indirectly.
This paper describes a method for direct physiological phenotyping that has several advantages for the functional phenotyping of plant&#8211;environment interactions. It helps users overcome the many challenges encountered in the use of load-cell gravimetric systems and pot experiments. The suggested techniques will enable users to distinguish between soil weight, plant weight and soil water content, providing a method for the continuous and simultaneous measurement of dynamic soil, plant and atmosphere conditions, alongside the measurement of key physiological traits. This method allows researchers to closely mimic field stress scenarios while taking into consideration the environment&#8217;s effects on the plants&#8217; physiology. This method also minimizes pot effects, which are one of the major problems in pre-field phenotyping. It includes a feed-back fertigation system that enables a truly randomized experimental design at a field-like plant density. This system detects the soil-water-content limiting threshold (&#952;) and allows for the translation of data into knowledge through the use of a real-time analytic tool and an online statistical resource. This method for the rapid and direct measurement of the physiological responses of multiple plants to a dynamic environment has great potential for use in screening for beneficial traits associated with responses to abiotic stress, in the context of pre-field breeding and crop improvement.

A Telemetric, Gravimetric Platform for Real-Time Physiological Phenotyping of Plant&#8211;Environment Interactions

This high-throughput, telemetric, whole-plant water relations gravimetric phenotyping method enables direct and simultaneous real-time measurements, as well as the analysis of multiple yield-related physiological traits involved in dynamic plant&#8211;environment interactions.

Food security for the growing global population is a major concern. The data provided by genomic tools far exceeds the supply of phenotypic data, creating ...

Field Measurement of Effective Leaf Area Index using Optical Device in Vegetation Canopy

Leaf area index (LAI) is an essential canopy variable describing the amount of foliage in an ecosystem. The parameter serves as the interface between green components of plants and the atmosphere, and many physiological processes occur there, primarily photosynthetic uptake, respiration, and transpiration. LAI is also an input parameter for many models involving carbon, water, and the energy cycle. Moreover, ground-based in situ measurements serve as the calibration method for LAI obtained from remote sensing products. Therefore, straightforward indirect optical methods are necessary for making precise and rapid LAI estimates. The methodological approach, advantages, controversies, and future perspectives of the newly developed LP 110 optical device based on the relation between radiation transmitted through the vegetation canopy and canopy gaps were discussed in the protocol. Furthermore, the instrument was compared to the world standard LAI-2200 Plant Canopy Analyzer. The LP 110 enables more rapid and more straightforward processing of data acquired in the field, and it is more affordable than the Plant Canopy Analyzer. The new instrument is characterized by its ease of use for both above- and below-canopy readings due to its greater sensor sensitivity, in-built digital inclinometer, and automatic logging of readings at the correct position. Therefore, the hand-held LP 110 device is a suitable gadget for performing LAI estimation in forestry, ecology, horticulture, and agriculture based on the representative results. Moreover, the same device also enables the user to take accurate measurements of incident photosynthetically active radiation (PAR) intensity.

Fast and precise leaf area index (LAI) estimation in terrestrial ecosystems is crucial for a wide range of ecological studies and calibrating remote sensing products. Presented here is the protocol for using the new LP 110 optical device for taking ground-based in situ LAI measurements.

Leaf area index (LAI) is an essential canopy variable describing the amount of foliage in an ecosystem. The parameter serves as the interface between ...

Low-Cost Automated Flight Intercept Trap for the Temporal Sub-Sampling of Flying Insects Attracted to Artificial Light at Night

Sampling methods are selected depending on the targeted species or the spatial and temporal requirements of the study. However, most methods for passive sampling of flying insects have a poor temporal resolution because it is time-consuming, costly and/or logistically difficult to perform. Effective sampling of flying insects attracted to artificial light at night (ALAN) requires sampling at user-defined time points (nighttime only) across well-replicated sites resulting in major time and labor-intensive survey effort or expensive automated technologies. Described here is a low-cost automated intercept trap that requires no specialist equipment or skills to construct and operate, making it a viable option for studies that require temporal sub-sampling across multiple sites. The trap can be used to address a wide range of other ecological questions that require a greater temporal and spatial scale than is feasible with previous trap technology.

To study the impacts of artificial light at night (ALAN) on nocturnal flying insects, sampling needs to be confined to nighttime. The protocol describes a low-cost automated flight intercept trap that allows researchers to sample at user-defined periods with increased replication.

Sampling methods are selected depending on the targeted species or the spatial and temporal requirements of the study. However, most methods for passive ...