Name: modeling the size spectrum for macroinvertebrates and fishes in stream ecosystems
Uploaded: 2019-07-30T14:00:00
Description: Watch this Scientific Journal Video about Modeling the Size Spectrum for Macroinvertebrates and Fishes in Stream Ecosystems at JoVE.com

Funding for this work was provided by the National Science Foundation (grant DEB-1553111) and the Eppley Foundation for Scientific Research. This manuscript is VCU Rice Rivers Center contribution #89.

All methods described here have been approved by the Institutional Animal Care and Use Committee (IACUC) of Virginia Commonwealth University.
1. Collection and processing of fish samples
<ol>
	<li>Isolating fishes within the study reach to create a closed fish assemblage
	<ol>
		<li>Identify the upstream and downstream (direction is relative to a surveyor facing &#8216;upstream&#8217; and against the water current) ends of the study reach then mark the ends ...

This ataxic size spectra protocol can be used to quantify and model size structure within communities of stream fishes and invertebrates. Previous size spectra studies in stream ecosystems have ranged from basic descriptive research39,40 to comparisons along a longitudinal river profile41 and among distinct biogeographic regions42. Seasonal comparisons have been performed43,<sup cl...

Body size scaling relationships, such as the positive association between body mass and metabolic rate, are well-known at the individual organism level and are now being studied at higher levels of organization1,2,3. These allometric relationships are most often power-law functions of the form Y = aMb, where Y is the variable of interest (e.g., metabolism, abundance, or home range size), M is the body mass of a single or average individual, b is a scaling coefficient, and a is a constant. For statistical convenience, Y and M data are often log-transformed prior to analysis then modeled with linear equations of the form log (Y) = log (a) + b log (M), where b and log (a) become the linear model slope and intercept, respectively.
The size spectrum is a type of allometric relationship that predicts density (D, the number of individuals per unit area) or biomass (B, the summed mass of individuals per unit area) as a function of M (See Section 4 for additional information on the use of &#8216;normalized&#8217; D or B estimates.) Like other scaling relationships between M and D or between M and B, the size spectrum plays a central role in basic and applied ecology. At the population-level, biologists often interpret negative D <img alt="Image 1" src="/files/ftp_upload/59945/59945img01.jpg" />&#160;M relationships as evidence of density-dependent survival or as models of ecosystem carrying capacity (i.e., the &#8216;self-thinning rule&#8217;)4,5. At the community-level, B <img alt="Image 1" src="/files/ftp_upload/59945/59945img01.jpg" />&#160;M relationships can be used to study system-level effects of anthropogenic perturbations, such as size-selective fishing6,7. Allometric scaling of D and B with M are also central to recent efforts to unite population, community, and ecosystem ecology2,8,9.
One particularly important characteristic of the size spectrum is the fact that it is entirely ataxic9,10. This point is easy to miss when comparing scatterplots of D <img alt="Image 1" src="/files/ftp_upload/59945/59945img01.jpg" />&#160;M or B <img alt="Image 1" src="/files/ftp_upload/59945/59945img01.jpg" /> M data but the distinction between taxic and ataxic models is a critical one. In taxic models, a single M value is used to represent the average body mass of every individual of a given species or taxa11. In ataxic models, all individuals within a data set are partitioned among a series of body size intervals or M bins, regardless of their taxonomic identity12. The latter, ataxic approach is advantageous in aquatic ecosystems where many taxa exhibit indeterminate growth and experience one or more ontogenetic shifts in feeding behavior; in these instances, a single species-level M average will obscure the fact that a species can fill different functional roles throughout its life history9,13,14.
Here, we present a complete protocol to quantify the size spectrum within wadable streams and rivers. The protocol begins with field sampling methods to collect the necessary fish and benthic macroinvertebrate data. Fish will be collected through a &#8216;three-pass depletion&#8217; sampling process. Abundance will then be estimated from the depletion data with the Zippin method15. In depletion sampling, individual fishes within a closed study reach (i.e., individuals can neither enter nor leave the enclosed reach) are removed from the reach through three successive samples. Thus, the number of remaining fishes will be progressively depleted. From this depletion trend, total abundance within the study reach can be estimated then converted to D (in fish per m2), using the known surface area of the study reach. Benthic macroinvertebrates will be collected with standard fixed-area samplers, then identified and measured in the laboratory.
Next, the combined fish and macroinvertebrate data will be partitioned among size bins. Traditionally, the octave or log2 scale (i.e., doubling intervals) has been used to set size bin boundaries16. Once a list of size bins has been established, partitioning of individual benthic macroinvertebrates among their respective size bins is straightforward because invertebrates are directly enumerated as numbers of individuals per unit area. However, estimating fish abundances within size bins is more abstract because these estimates are inferred from the depletion data. Detailed instructions are therefore provided to estimate fish abundance within size bins, irrespective of taxonomic identity, from depletion sample data.
Finally, linear regression will be used to model the size spectrum. This protocol is fully compatible with the original, general method of Kerr and Dickie16 and identical to the methods used by McGarvey and Kirk, 201817 in a study of fish and invertebrate size spectra in West Virginia streams. By using this protocol, investigators can insure that their results are directly comparable with other studies that build upon Kerr and Dickie16, thereby accelerating a broad and robust understanding of body size scaling relationships in freshwater ecosystems and the mechanisms that drive them.

<table>
	<tbody>
		<tr>
			<td>Chest waders</td>
			<td>Multiple options</td>
			<td>n/a</td>
			<td>Personal protective equipment for use during electrofishing. Do NOT use &#39;breatheable&#39; waders as electrical current will pass through them.</td>
		</tr>
		<tr>
			<td>Rubber lineman&#39;s gloves</td>
			<td>Multiple options</td>
			<td>n/a</td>
			<td>Personal protective equipment for use during electrofishing.</td>
		</tr>
		<tr>
			<td>Dip nets with fiberglass poles</td>
			<td>Multiple options</td>
			<td>n/a</td>
			<td>Used to capture stunned fishes during electrofishing.</td>
		</tr>
		<tr>
			<td>Backpack electrofishing unit</td>
			<td>Smith-Root; Halltech; Midwest Lake Management; Aqua Shock Solutions</td>
			<td>www.smith-root.com; www.halltechaquatic.com; https://midwestlake.com; https://aquashocksolutions.com/</td>
			<td>Backpack electrofishers are currently manufactured and distributed by four independent companies in North America. Prices and warranty/technical support are the most important factors in choosing a vendor.</td>
		</tr>
		<tr>
			<td>Block nets/seines (&#215;2)</td>
			<td>Duluth Nets</td>
			<td>https://duluthfishnets.com/</td>
			<td>Necessary length will depend on stream width. 3/8 inch mesh is recommended.</td>
		</tr>
		<tr>
			<td>Cam-action utility straps with 1 inch nylon webbing (&#215;4)</td>
			<td>Multiple options</td>
			<td>n/a</td>
			<td>Used to secure/anchor block nets. Available at auto supply, hardware, and department stores.</td>
		</tr>
		<tr>
			<td>Large tent stakes (&#215;4)</td>
			<td>Multiple options</td>
			<td>n/a</td>
			<td>Used to secure/anchor block nets. Available at camping and department stores.</td>
		</tr>
		<tr>
			<td>5 gallon plastic buckets (&#215;5)</td>
			<td>Multiple options</td>
			<td>n/a</td>
			<td>Used to hold and transport fish during electrofishing. Available at hardware and paint supply stores.</td>
		</tr>
		<tr>
			<td>10-20 gallon totes (&#215;3)</td>
			<td>Multiple options</td>
			<td>n/a</td>
			<td>Used as livewells, sedation tanks, and recovery bins for captured fishes. Available at hardware and department stores.</td>
		</tr>
		<tr>
			<td>Battery powered &#39;bait bucket&#39; aeration pumps</td>
			<td>Cabelas</td>
			<td>IK-019008</td>
			<td>Used to aerate fish holding bins during field processing.</td>
		</tr>
		<tr>
			<td>Fish anesthesia (Tricaine-S)</td>
			<td>Syndel</td>
			<td>www.syndel.com</td>
			<td>Used to sedate fishes for field processing. Tricaine-S is regulated by the U.S. Food and Drug Administration.</td>
		</tr>
		<tr>
			<td>Folding camp table and chairs</td>
			<td>Cabelas</td>
			<td>IK-518976; IK-552777</td>
			<td>Used to process fish samples.</td>
		</tr>
		<tr>
			<td>Pop-up canopy</td>
			<td>Multiple options</td>
			<td>n/a</td>
			<td>Used as necessary for sun and rain protection.</td>
		</tr>
		<tr>
			<td>Fish measuring board</td>
			<td>Wildco</td>
			<td>3-118-E40</td>
			<td>Used to measure fish lengths.</td>
		</tr>
		<tr>
			<td>Battery powered field scale with weighing dish</td>
			<td>Multiple options</td>
			<td>n/a</td>
			<td>Used to weigh fishes. Must weigh be accurate to 0.1 or 0.01 grams.</td>
		</tr>
		<tr>
			<td>Clear plastic wind/rain baffle</td>
			<td>Multiple options</td>
			<td>n/a</td>
			<td>Used to shield scale in rainy or windy conditions. Must be large enough to cover the scale and a weighing dish.</td>
		</tr>
		<tr>
			<td>White plastic or enamel examination trays</td>
			<td>Multiple options</td>
			<td>n/a</td>
			<td>Trays are essential for examining fishes in the field.</td>
		</tr>
		<tr>
			<td>Stainless steel forceps</td>
			<td>Multiple options</td>
			<td>n/a</td>
			<td>Forceps are helpful when examining small fishes and in transfering invertebrates to specimen jars.</td>
		</tr>
		<tr>
			<td>Hand magnifiers</td>
			<td>Multiple options</td>
			<td>n/a</td>
			<td>Magnification is often helpful when identifying fish specimens in the field.</td>
		</tr>
		<tr>
			<td>Fish identification keys</td>
			<td>n/a</td>
			<td>n/a</td>
			<td>Laminated keys that are custom prepared for specific locations are most effective.</td>
		</tr>
		<tr>
			<td>Datasheets printed on waterproof paper</td>
			<td>Rite in the Rain</td>
			<td>n/a</td>
			<td>Waterproof paper is essential when working with aquatic specimens.</td>
		</tr>
		<tr>
			<td>Retractable fiberglass field tapes</td>
			<td>Lufkin</td>
			<td>n/a</td>
			<td>Used to measure stream channel dimensions.</td>
		</tr>
		<tr>
			<td>Surber sampler or Hess sampler</td>
			<td>Wildco</td>
			<td>3-12-D56; 3-16-C52</td>
			<td>Either of these fixed-area benthic samplers will work well in shallow streams with gravel or pebble substrate.</td>
		</tr>
		<tr>
			<td>70% ethanol or isopropyl alcohol</td>
			<td>Multiple options</td>
			<td>n/a</td>
			<td>Used as invertebrate preservative.</td>
		</tr>
		<tr>
			<td>Widemouth invertebrate specimen jars (20-32 oz.)</td>
			<td>U.S. Plastic Corp.</td>
			<td>67712</td>
			<td>Any widemouth plastic jars will work but these particular jars are durable and inexpensive.</td>
		</tr>
	</tbody>
</table>

modeling the size spectrum for macroinvertebrates and fishes in stream ecosystems

The size spectrum is an inverse, allometric scaling relationship between average body mass (M) and the density (D) of individuals within an ecological community or food web. Importantly, the size spectrum assumes that individual size, rather than species&#8217; behavioral or life history characteristics, is the primary determinant of abundance within an ecosystem. Thus, unlike traditional allometric relationships that focus on species-level data (e.g., mean species&#8217; body size vs. population density), size spectra analyses are &#8216;ataxic&#8217; &#8211; individual specimens are identified only by their size, without consideration of taxonomic identity. Size spectra models are efficient representations of traditional, complex food webs and can be used in descriptive as well as predictive contexts (e.g., predicting responses of large consumers to changes in basal resources). Empirical studies from diverse aquatic ecosystems have also reported moderate to high levels of similarity in size spectra slopes, suggesting that common processes may regulate the abundances of small and large organisms in very different settings. This is a protocol to model the community-level size spectrum in wadable streams. The protocol consists of three main steps. First, collect quantitative benthic fish and invertebrate samples that can be used to estimate local densities. Second, standardize the fish and invertebrate data by converting all individuals to ataxic units (i.e., individuals identified by size, irrespective of taxonomic identity), and summing individuals within log2 size bins. Third, use linear regression to model the relationship between ataxic M and D estimates. Detailed instructions are provided herein to complete each of these steps, including custom software to facilitate D estimation and size spectra modeling.

Exemplar results, including original field data, are presented for Slaunch Fork, West Virginia, a small stream in southern West Virginia. Additional size spectra model results are also presented for two other streams in the same region: Camp Creek and Cabin Creek, West Virginia. These are the three study sites included in McGarvey and Kirk17, but data presented here are from new samples collected in May 2015. A fully worked, manual example of the size spectra modeling process is included for the S...

Watch this Scientific Journal Video about Modeling the Size Spectrum for Macroinvertebrates and Fishes in Stream Ecosystems at JoVE.com

Modeling the Size Spectrum for Macroinvertebrates and Fishes in Stream Ecosystems

This is a protocol to model the size spectrum (scaling relationship between individual mass and population density) for combined fish and invertebrate data from wadable streams and rivers. Methods include: field techniques to collect quantitative fish and invertebrate samples; lab methods to standardize the field data; and statistical data analysis.

The size spectrum is an inverse, allometric scaling relationship between average body mass (M) and the density (D) of individuals within an ecological ...

The size spectrum predicts abundance as a function of individual size. Size spectra research suggests strong similarity in the abundances of relatively small and large organisms from diverse ecosystems. Unlike traditional size abundance scaling relationships that use species level average sizes, size spectrum models are ataxic and can account for the size of every individual within the sample.Demonstrating the procedure will be Brandon Gravett, Sarah Headley, and Giancarlo Racanelli, field technicians. After identifying the upstream and downstream ends of the study reach, mark the ends with removable flagging tape. Measure the width of the wetted stream channel at five to 10 transects distributed evenly along the length of the study reach, and estimate the total surface area of the study reach as the average wetted channel width multiplied by the total length of the reach.Make a loose bowline knot in each end of a piece of polypropylene rope and wrap the rope around a tree, root, large rock, or other solid object at the up and downstream ends of the study reach as an anchor. Feed one loop through the other to create an anchor point and shorten or lengthen the rope anchor by adding or removing wraps around the anchor object as necessary. Establish a second anchor point on the opposite side of the stream as just demonstrated, and use a bowline knot to create a loop in the lines at each of the four corners of a medium to coarse mesh block net.Using Cam Action tie-down straps, connect both sides of the top line in the block net to the anchor points, and insert the hooks at either end of the tie-down strap into the loops at the corners of the block net and the anchor points. Pull the free tether of the tie-down strap through the Cam buckle to tighten each point of contact, and pin the bottom line of the block net to the stream bank with tent stakes. Place large rocks on the side of the net facing upstream to pin the block net down to establish a seal with the bottom of the stream, taking care that the top of the net remains above water level.Then set a second block net at the downstream end of the study reach in the same manner. To perform a fish sampling depletion pass, beginning at the downstream end of the enclosed study reach, turn on the backpack electrofisher and move through the stream in the upstream direction. Progress slowly, moving side to side throughout the study reach to ensure that all of the in-stream habitats are sampled, and have supporting crew members follow to collect stunned fish with dip nets as they are spotted.Transfer the fish into temporary buckets, then to aerated holding tubs. Use small battery-powered bait bucket pumps with aeration stones to ensure that the captured fishes remain healthy. Pay particular attention to various small, young-of-year fishes as they are difficult to spot and capture.The first depletion pass is complete when the upstream net is reached. For processing of the first depletion pass fish, use small dip nets to retrieve the sampled fishes from the holding tank individually or in small batches for identification, and place the specimens in white trays. Using forceps and a magnifying glass, identify each fish, then measure its total length from the tip of the snout to the end of the caudal fin on a measuring board, and weigh it on a field balance with a 0.1 or 0.01-gram precision.Then record the species'identity and total length and weight for each specimen on waterproof data sheets. Once processed, return the fishes to a separate aerated recovery bin before releasing all of the fish downstream of the downstream block net. Select benthic macroinvertebrate sample sites within the boundaries of the fish sampling reach that are representative of the major types of physical habitats observed in the study reach.Place an appropriate fixed area sampling device firmly against the stream bottom with the sample collection net oriented downstream and move large cobbles as necessary to establish a firm seal with the substrate. Use a brush to vigorously scrub the substrate within the sampling area for two minutes, allowing dislodged benthic macroinvertebrates to drift into the sample net. Transfer the sample contents from the net to a plastic jar and preserve the specimens in 70%isopropyl alcohol.Then label the jar and store it in a safe location for later transfer to the lab. When all benthic macroinvertebrate and fish data have been properly formatted and plotted, a clear negative relationship between individual body mass and normalized density is often apparent. This size spectrum reflects a predictable transition from the smallest and most abundant invertebrates such as midges and small mayflies to larger caddisflies and stoneflies to fishes as shown here for samples from Slaunch Fork, West Virginia.Similar size spectra relationships were detected for benthic macroinvertebrates in fishes in Camp Creek and Cabin Creek, two other West Virginia streams, and linear regression was used to model the relationship. The size spectra slopes were all between 1.7 and 1.8 with overlapping 95%confidence intervals. This similarity indicates that the abundance decreases as the body size increases at approximately equal rates in all three streams.However, the differing size spectra intercepts reveal that differences in the overall density are variable among streams, but the highest densities observed in Camp Creek and much lower densities measured in Cabin Creek. As the number of size spectra studies grows, critical tests of the effects of different environmental influences on the size spectrum will become possible. It is important to remember that all fieldwork entails some risk and that electrofishing, in particular, can be dangerous.It is therefore essential that all crew members are properly trained.

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We present a protocol related to a video-tracking technique based on the background subtraction and image thresholding that makes it possible to ...

Combined Size and Density Fractionation of Soils for Investigations of Organo-Mineral Interactions

Combined size and density fractionation (CSDF) is a method used to physically separate soil into fractions differing in particle size and mineralogy. CSDF relies on sequential density separation and sedimentation steps to isolate (1) the free light fraction (uncomplexed organic matter), (2) the occluded light fraction (uncomplexed organic matter trapped in soil aggregates) and (3) a variable number of heavy fractions (soil minerals and their associated organic matter) differing in composition. Provided that the parameters of the CSDF (dispersion energy, density cut-offs, sedimentation time) are properly selected, the method yields heavy fractions of relatively homogeneous mineral composition. Each of these fractions is expected to have a different complexing ability towards organic matter, rendering this a useful method to isolate and study the nature of organo-mineral interactions. Combining density and particle size separation brings an improved resolution compared to simple size or density fractionation methods, allowing the separation of heavy components according to both mineralogy and size (related to surface area) criteria. As is the case for all physical fractionation methods, it may be considered as less disruptive or aggressive than chemically-based extraction methods. However, CSDF is a time-consuming method and furthermore, the quantity of material obtained in some fractions can be limiting for subsequent analysis. Following CSDF, the fractions may be analyzed for mineralogical composition, soil organic carbon concentration and organic matter chemistry. The method provides quantitative information about organic carbon distribution within a soil sample and brings light to the sorptive capacity of the different, naturally-occurring mineral phases, thus providing mechanistic information about the preferential nature of organo-mineral interactions in soils (i.e., which minerals, what type of organic matter).

Combined size and density fractionation (CSDF) is a method to physically separate soil into fractions differing in texture (particle size) and mineralogy (density). The purpose is to isolate fractions with different reactivities towards soil organic matter (SOM), in order to better understand organo-mineral interactions and SOM dynamics.

Combined size and density fractionation (CSDF) is a method used to physically separate soil into fractions differing in particle size and mineralogy. CSDF ...

Measuring the Shape and Size of Activated Sludge Particles Immobilized in Agar with an Open Source Software Pipeline

Experimental bioreactors, such as those treating wastewater, contain particles whose size and shape are important parameters. For example, the size and shape of activated sludge flocs can indicate the conditions at the microscale, and also directly affect how well the sludge settles in a clarifier.
Particle size and shape are both misleadingly &#39;simple&#39; measurements. Many subtle issues, often unaddressed in informal protocols, can arise when sampling, imaging, and analyzing particles. Sampling methods may be biased or not provide enough statistical power. The samples themselves may be poorly preserved or undergo alteration during immobilization. Images may not be of sufficient quality; overlapping particles, depth of field, magnification level, and various noise can all produce poor results. Poorly specified analysis can introduce bias, such as that produced by manual image thresholding and segmentation.
Affordability and throughput are desirable alongside reproducibility. An affordable, high throughput method can enable more frequent particle measurement, producing many images containing thousands of particles. A method that uses inexpensive reagents, a common dissecting microscope, and freely-available open source analysis software allows repeatable, accessible, reproducible, and partially-automated experimental results. Further, the product of such a method can be well-formatted, well-defined, and easily understood by data analysis software, easing both within-lab analyses and data sharing between labs.
We present a protocol that details the steps needed to produce such a product, including: sampling, sample preparation and immobilization in agar, digital image acquisition, digital image analysis, and examples of experiment-specific figure generation from the analysis results. We have also included an open-source data analysis pipeline to support this protocol.

The size and shape of particles in activated sludge are important parameters that are measured using varying methods. Inaccuracies arise from non-representative sampling, suboptimal images, and subjective analysis parameters. To minimize these errors and ease measurement, we present a protocol specifying every step, including an open source software pipeline.

Experimental bioreactors, such as those treating wastewater, contain particles whose size and shape are important parameters. For example, the size and ...

Combining Fluidic Devices with Microscopy and Flow Cytometry to Study Microbial Transport in Porous Media Across Spatial Scales

Understanding the transport, dispersion and deposition of microorganisms in porous media is a complex scientific task comprising topics as diverse as hydrodynamics, ecology and environmental engineering. Modeling bacterial transport in porous environments at different spatial scales is critical to better predict the consequences of bacterial transport, yet current models often fail to up-scale from laboratory to field conditions. Here, we introduce experimental tools to study bacterial transport in porous media at two spatial scales. The aim of these tools is to obtain macroscopic observables (such as breakthrough curves or deposition profiles) of bacteria injected into transparent porous matrices. At the small scale (10-1000 &#181;m), microfluidic devices are combined with optical video-microscopy and image processing to obtain breakthrough curves and, at the same time, to track individual bacterial cells at the pore scale. At larger scale, flow cytometry is combined with a self-made robotic dispenser to obtain breakthrough curves. We illustrate the utility of these tools to better understand how bacteria are transported in complex porous media such as the hyporheic zone of streams. As these tools provide simultaneous measurements across scales, they pave the way for mechanism-based models, critically important for upscaling. Application of these tools may not only contribute to the development of novel bioremediation applications but also shed new light on the ecological strategies of microorganisms colonizing porous substrates.

Breakthrough curves (BTCs) are efficient tools to study the transport of bacteria in porous media. Here we introduce tools based on fluidic devices in combination with microscopy and flow cytometric counting to obtain BTCs.

Understanding the transport, dispersion and deposition of microorganisms in porous media is a complex scientific task comprising topics as diverse as ...