The authors gratefully acknowledge Instituto de Qu&#237;mica de San Luis &#34;Dr. Roberto Olsina&#34;- Consejo Nacional de Investigaciones Cient&#237;ficas y Tecnol&#243;gicas (INQUISAL-CONICET), Universidad Nacional de San Luis (Project PROICO 2-1914), Laborat&#243;rio de Patologia Experimental (LAPEx) - Instituto de Bioci&#234;ncias (INBIO) - Universidade Federal de Mato Grosso do Sul (UFMS), C&#225;tedra de Citolog&#237;a - Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoci&#243;n Cient&#237;fica (FONCYT; PICT-2018-02570 and PICT-2018-01067) for financial support. We would also like to thank native speaker Lidia Unger and GAECI-UNSL (scientific writing assistance center) from the National University of San Luis for the proofreading of the manuscript.

The authors declare no competing interests.

The biomarkers at the individual level are very simple to determine and very low-cost, as examining these biomarkers requires only a few pieces of equipment that are usually available in any research laboratory. In addition, these biomarkers provide general information on the health and fitness of the animals. The number of animals employed in each protocol is critical for obtaining reliable results. Due to the variability of data, a minimum of five animals (N = 5) is necessary for each treatment. In detail, a critical s...

The input of environmental stressors into natural water bodies can affect the health of the aquatic ecosystem1. Exposure to these environmental stressors can affect the survival or fitness of aquatic organisms through different toxicity mechanisms, including direct exposure (both short- and long-term)2. Hence, standardized laboratory bioassays to assess toxicological endpoints related to fitness and survival may be an unreliable estimate of the many indirect effects of stress in the field. Furthermore, alterations in normal physiological levels and effects on individuals, such as in terms of prey capture, may be better long-term indicators of the impact on survival and reproductive fitness in organisms and, ultimately, on the health of the ecosystem1,3. Predicting changes in ecosystem composition and function, as well as organism health, based on a known set of environmental parameters and contaminant concentrations, is important for improving pollution management1.
Biomarkers are defined as biochemical, physiological, or histological changes due to either exposure to or the effects of xenobiotic chemicals4,5. Biomarkers have proven to be very useful as early warning signals4,5. An important question that biomarkers help answer is whether certain stressors are present in high enough concentrations in the environment to cause adverse effects. This information contributes to the assessment of whether it is worth investigating the nature and extent of the damage and the causative agents or whether no more resources should be invested in that case6,7,8. Moreover, since the concept of evaluating a single biomarker as a bioindicator may not be adequate5,7,8,9,10, there is a growing trend toward performing a comprehensive evaluation of multiple biomarkers in order to detect early warning signs and, thus, prevent irreversible effects on ecosystems.
It is very important to note that all toxic effects begin with the interaction of a stressor with biomolecules. In this sense, effects can cascade through the biochemical, subcellular, cellular, tissue, organ, individual, population, community, ecosystem, landscape, and biospheric levels of organization. Cells are the primary site of interaction between environmental stressors and biological systems. Thus, understanding molecular and genetic effects allows researchers to associate low and high levels of ecological organization and helps them to predict the effect of environmental pollutants, for example, on human health, that have not yet been tested5. Moreover, due to the high specificity of cells, they are not only useful for evaluating environmental pollutants but also human health5,11. Therefore, understanding the effects of stressors at the biochemical level may provide insights into the causes of the observed effects and allow them to be connected with those at the next higher level5. In addition, by understanding the biochemical mechanisms of stressors, the effects of new stressors that have not yet been toxicologically evaluated may be predicted with respect to other well-known contaminants based on their similarities in function. In the presence of various environmental stressors, genetic and biochemical biomarkers may provide valuable information on the specific effects observed. In addition to this, histochemical evaluations related to biochemical changes can provide information on toxicodynamics5. In short, a comprehensive analysis of cellular, biochemical, and histological biomarkers is necessary10,12, and this type of analysis, in turn, should be included in biomonitoring programs for local species5,13,14.
The study of biomarkers under laboratory conditions may, nonetheless, present some difficulties, including difficulties in the detection of sublethal effects and chronic impacts after exposure to pollutants and in the validation and standardization of the methods employed, as well as the complex time- or dose-dependent responses, the unclear or undetermined links to fitness, and the lack of integrated mechanistic models1,4. To solve these problems, the solution is not to increase the number of biomarkers measured but to carefully design studies and testable hypotheses that contribute to explaining the mechanistic bases of chemical effects on whole organisms4.
The new questions in ecotoxicology highlight the importance of applying a battery of biomarkers to generate ecotoxicological predictions that improve the interpretation of the effects of environmental stressors on organisms, as well as decision-making about their possible impact. Moreover, the importance of combining both concepts-biomarkers and bioindicators-in environmental risk assessments and biomonitoring is that this will allow researchers to determine whether organisms in a specific environment of interest are physiologically normal or stressed. The approach taken in this study resembles that of the biochemical analysis that is carried out in humans. In this sense, a battery of biomarkers may be analyzed to see if an organism is healthy both in the field and in the laboratory6. Finally, biomarkers will contribute to ecological risk assessments in two ways: (1) assessing the exposure of rare and/or long-lived species, and (2) testing hypotheses about the mechanisms of chemical impacts at different levels of biological organization4.
In the last decade, biomarkers have been used in anurans for biomonitoring the exposure to cytotoxic and genotoxic contaminants. Among these, the techniques that have been used most frequently are the micronucleus (MN) assay and the comet assay or the induction of single-stranded DNA breaks by single-cell gel electrophoresis (SCGE) assay. In addition, those techniques have been successfully used to estimate the DNA damage induced by various environmental stressors in several neotropical anurans14,15,16,17,18,19. Other biomarkers can used to examine changes in the oxidative status in organisms exposed to environmental pollutants16,17,18,19. Oxidative stress is a response to exposure to different xenobiotics, leading to several detrimental effects, including on the antioxidant capacity of the exposed individuals5,6,7,19,20.
In ecotoxicological studies, bioindicator species are used because they are organisms that identify the long-term interactions and adverse effects of environmental stressors at higher organizational levels (e.g., organism, population, community, and ecosystem levels)10,20,21. By integrating the two concepts-biomarkers and bioindicators-species can be screened to broadly define biochemical, physiological, or ecological structures or processes that are correlated or linked with measured biological effects at one or more levels of biological organization. Finally, the great challenge of utilizing both concepts to improve the estimates of the toxicity of a stressor relates to analyzing biomarkers and bioindicators that have high utility in the evaluation of ecological risks20. In this sense, there is consensus on the relevance of employing biomarkers and bioindicators as early warning signs, as they offer relevant information about the response of a test organism to environmental stressors12,20,21.
Amphibians are one of the most threatened and rapidly declining groups of organisms worldwide. One of the main reasons for this decline is pollutants that enter their habitat, such as pesticides, metals, and emerging pollutants22,23,24,25. Anurans have several characteristics that make them useful as bioindicator species, such as their permeable skin, close relationship with water, and sensitivity to environmental pollution2,23,24. These characteristics make amphibians effective bioindicators of environmental health7,8,22,23,24,26.
Nevertheless, it is necessary not only to consider the optimization of basic procedures and the generation of historical data in control groups but also to employ specific bioassays to evaluate responses in organs and tissues to elucidate the nature and variation of effects observed in bioindicators. In this sense, the present work aims to describe several ecotoxicological methodologies to be employed in all stages of neotropical anurans at different ecological levels and validate them as useful biomarkers to be employed both in wildlife and laboratory conditions. This work presents a battery of biomarkers that may be integrated and that have been proven for laboratory and wildlife biomonitoring in anurans exposed to environmental stressors.

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			<td>Analytical scale</td>
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			<td></td>
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			<td>Electrophoresis power supply</td>
			<td>&#160;Enduro</td>
			<td>&#160;E0203-250V&#160;</td>
			<td></td>
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			<td>Eosin&#160;</td>
			<td>Merck</td>
			<td></td>
			<td></td>
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			<td>Fluorescence photomicroscope</td>
			<td>&#160;Olympus</td>
			<td>&#160;BX50</td>
			<td>Equipped with an appropriate filter combination</td>
		</tr>
		<tr>
			<td>Hematoxylin of Harris</td>
			<td>Merck</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>High resolution photo camera&#160;</td>
			<td></td>
			<td></td>
			<td>&#160;&#62;16 megapixels</td>
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		<tr>
			<td>Homogenizer</td>
			<td></td>
			<td></td>
			<td></td>
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		<tr>
			<td>Horizontal electrophoresis chamber</td>
			<td>&#160;Sigma</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Microcentrifuge</td>
			<td>Denver Instrument</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Microscope</td>
			<td>Leica</td>
			<td>DM4000 B</td>
			<td>Equipped with image capture system Leica DFC 280</td>
		</tr>
		<tr>
			<td>Microtome</td>
			<td>Leica</td>
			<td>2265</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraplast</td>
			<td>Sigma</td>
			<td>P3558</td>
			<td></td>
		</tr>
		<tr>
			<td>Personal Computer</td>
			<td></td>
			<td></td>
			<td>&#160;Eqquiped with Mac OS X, Lynux or Windows</td>
		</tr>
		<tr>
			<td>Refrigerated centrifuge</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>UV&#8211;Vis spectrophotometer</td>
			<td>Rayleigh</td>
			<td>723G</td>
			<td>With UV-lamp</td>
		</tr>
	</tbody>
</table>

ecotoxicological methodologies to evaluate biomarkers at different scales in neotropical anurans

The new questions in ecotoxicology highlight the importance of applying a battery of biomarkers, as this results in ecotoxicological predictions that improve not only the interpretation of the effects of environmental stressors on organisms but also the determination of their possible impact. It is well known that the use of ecotoxicological biomarkers at different levels of organization allows for the prediction of the biological responses of organisms to environmental stressors, which is useful in environmental risk assessment. 
Nevertheless, it is necessary to consider the optimization of basic procedures, to generate historical data in control groups, and to employ specific bioassays to evaluate responses in organs and tissues in order to elucidate the nature and variation of the effects observed. Therefore, the present work aims to describe several ecotoxicological methodologies employed in all stages of neotropical anurans at different ecological levels and to validate them as useful biomarkers to be used both in wildlife and in laboratory conditions. In this work, these biomarkers were applied at the individual/organismic level (body condition index), histological/physiological level (histopathology, histometric, and pigmentary analyses), biochemical level (oxidative stress enzymes), and genetic level (direct and oxidative damage in DNA by comet assay). 
Although these methodologies have small variations or modifications depending on the species, these techniques provide effective biomarkers for evaluating the effect of xenobiotics on anurans, which possess certain characteristics that make them useful indicator species of aquatic and terrestrial ecosystems. In conclusion, the battery of biomarkers employed in the present study has proven to be adequate for estimating toxic responses in Neotropical anurans and can be further recommended as bioindicators for identifying the impact of pollutants on the aquatic ecosystems of the region. Finally, it is recommended to achieve the standardization of these important biomarkers for anurans in specific regions as well as to possibly include them in risk assessments and decision-making.

All the biomarker techniques presented here are simple, rapid, convenient, sensitive, low cost, and accurate methods. For each biomarker, it is important to note the following.
Individual level 
Scaled mass index 
Taking photographs on the millimeter scale is of great importance since this value will be used to calibrate the software, and this results in better objectivity with respect to the caliper measurement when taking the SVL variable. In addit...

Read this Scientific Article Protocol about Ecotoxicological Methodologies to Evaluate Biomarkers at Different Scales in Neotropical Anurans at JoVE.com

Ecotoxicological Methodologies to Evaluate Biomarkers at Different Scales in Neotropical Anurans

In this paper, standardized ecotoxicological methods for the evaluation of biomarkers in neotropical anuran species are presented. Specifically, this paper details several methodologies at different scales of ecotoxicological evaluation, such as the genetic, cellular-histological, biochemical, morphological, and individual levels.

The new questions in ecotoxicology highlight the importance of applying a battery of biomarkers, as this results in ecotoxicological predictions that ...

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240 Views.  Universidad Nacional de San Luis (UNSL). In this paper, standardized ecotoxicological methods for the evaluation of biomarkers in neotropical anuran species are presented. Specifically, this paper details several methodologies at different scales of ecotoxicological evaluation, such as the genetic, cellular-histological, biochemical, morphological, and individual levels.

Video: Ecotoxicological Methodologies to Evaluate Biomarkers at Different Scales in Neotropical Anurans

Protocols for Robust Herbicide Resistance Testing in Different Weed Species

Robust protocols to test putative herbicide resistant weed populations at whole plant level are essential to confirm the resistance status. The presented protocols, based on whole-plant bioassays performed in a greenhouse, can be readily adapted to a wide range of weed species and herbicides through appropriate variants. Seed samples from plants that survived a field herbicide treatment are collected and stored dry at low temperature until used. Germination methods differ according to weed species and seed dormancy type. Seedlings at similar growth stage are transplanted and maintained in the greenhouse under appropriate conditions until plants have reached the right growth stage for herbicide treatment. Accuracy is required to prepare the herbicide solution to avoid unverifiable mistakes. Other critical steps such as the application volume and spray speed are also evaluated. The advantages of this protocol, compared to others based on whole plant bioassays using one herbicide dose, are related to the higher reliability and the possibility of inferring the resistance level. Quicker and less expensive in vivo or in vitro diagnostic screening tests have been proposed (Petri dish bioassays, spectrophotometric tests), but they provide only qualitative information and their widespread use is hindered by the laborious set-up that some species may require. For routine resistance testing, the proposed whole plant bioassay can be applied at only one herbicide dose, so reducing the costs.

A robust and flexible approach to confirm herbicide resistance in weed populations is presented. This protocol allows the herbicide resistance levels to be inferred and applied to a wide range of weed species and herbicides with minor adaptations.

Robust protocols to test putative herbicide resistant weed populations at whole plant level are essential to confirm the resistance status. The presented ...

Use of a Battery of Chemical and Ecotoxicological Methods for the Assessment of the Efficacy of Wastewater Treatment Processes to Remove Estrogenic Potency

Endocrine Disrupting Compounds pose a substantial risk to the aquatic environment. Ethinylestradiol (EE2) and estrone (E1) have recently been included in a watch list of environmental pollutants under the European Water Framework Directive. Municipal wastewater treatment plants are major contributors to the estrogenic potency of surface waters. Much of the estrogenic potency of wastewater treatment plant (WWTP) effluents can be attributed to the discharge of steroid estrogens including estradiol (E2), EE2 and E1 due to incomplete removal of these substances at the treatment plant. An evaluation of the efficacy of wastewater treatment processes requires the quantitative determination of individual substances most often undertaken using chemical analysis methods. Most frequently used methods include Gas Chromatography-Mass Spectrometry (GCMS/MS) or Liquid Chromatography-Mass Spectrometry (LCMS/MS) using multiple reaction monitoring (MRM). Although very useful for regulatory purposes, targeted chemical analysis can only provide data on the compounds (and specific metabolites) monitored. Ecotoxicology methods additionally ensure that any by-products produced or unknown estrogenic compounds present are also assessed via measurement of their biological activity. A number of in vitro bioassays including the Yeast Estrogen Screen (YES) are available to measure the estrogenic activity of wastewater samples. Chemical analysis in conjunction with in vivo and in vitro bioassays provides a useful toolbox for assessment of the efficacy and suitability of wastewater treatment processes with respect to estrogenic endocrine disrupting compounds. This paper utilizes a battery of chemical and ecotoxicology tests to assess conventional, advanced and emerging wastewater treatment processes in laboratory and field studies.

Endocrine Disrupting Compounds (EDC) pose a substantial risk to the aquatic environment. Municipal wastewater treatment plants are major contributors to the estrogenic potency of surface waters. The methodology provided in this paper allows for an assessment of the efficacy and suitability of wastewater treatment processes with respect to EDC removal.

Endocrine Disrupting Compounds pose a substantial risk to the aquatic environment. Ethinylestradiol (EE2) and estrone (E1) have recently been included in ...

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 ...

Adherence of Bacteria to Plant Surfaces Measured in the Laboratory

This manuscript describes a method to measure bacterial binding to axenic plant surfaces in the light microscope and through the use of viable cell counts. Plant materials used include roots, sprouts, leaves, and cut fruits. The methods described are inexpensive, easy, and suitable for small sample sizes. Binding is measured in the laboratory and a variety of incubation media and conditions can be used. The effect of inhibitors can be determined. Situations that promote and inhibit binding can also be assessed. In some cases it is possible to distinguish whether various conditions alter binding primarily due to their effects on the plant or on the bacteria.

An easy method for measuring and characterizing bacterial adhesion to plants, particularly roots and sprouts, is described in this article.

This manuscript describes a method to measure bacterial binding to axenic plant surfaces in the light microscope and through the use of viable cell ...

Protocol for Acute and Chronic Ecotoxicity Testing of the Turquoise Killifish Nothobranchius furzeri

The killifish Nothobranchius furzeri is an emerging model organism in the field of ecotoxicology and its applicability in acute and chronic ecotoxicity testing has been demonstrated. Overall, the sensitivity of the species to toxic compounds is in the range with, or higher than, that of other model species.
This work describes protocols for acute, chronic, and multigenerational bioassays of single and combined stressor effects on N. furzeri. Due to its short maturation time and life-cycle, this vertebrate model allows the study of endpoints such as maturation time and fecundity within four months. Transgenerational full life-cycle exposure trials can be performed in as little as 8 months. Since this species produces eggs that are drought-resistant and remain viable for years, the on-site culture of the species is not needed but individuals can be recruited when required. The protocols are designed to measure life-history traits (mortality, growth, fecundity, weight) and critical thermal maximum.

Protocol for Acute and Chronic Ecotoxicity Testing of the Turquoise Killifish Nothobranchius furzeri

In this work, we describe an acute, chronic and multigenerational bioassay to study the effects of single and combined stressors on the Turquoise killifish Nothobranchius furzeri. This protocol is designed to study life-history traits (mortality, growth, fecundity, weight) and critical thermal maximum.

The killifish Nothobranchius furzeri is an emerging model organism in the field of ecotoxicology and its applicability in acute and chronic ecotoxicity ...

Lab-Scale Model to Evaluate Odor and Gas Concentrations Emitted by Deep Bedded Pack Manure

A lab-scaled simulated bedded pack model was developed to study air quality and nutrient composition of deep-bedded packs used in cattle mono-slope facilities. This protocol has been used to effectively evaluate many different bedding materials, environmental variables (temperature, humidity), and potential mitigation treatments that can improve air quality in commercial deep-bedded mono-slope facilities. The model is dynamic and allows researchers to easily collect many chemical and physical measurements from the bedded pack. Weekly measurements, collected over the course of six to seven weeks, allows sufficient time to see changes in air quality measurements over time as the bedded pack matures. The data collected from the simulated bedded packs is within the range of concentrations previously measured in commercial deep-bedded mono-slope facilities. Past studies have demonstrated that 8 - 10 experimental units per treatment are sufficient to detect statistical differences among the simulated bedded packs. The bedded packs are easy to maintain, requiring less than 10 minutes of labor per bedded packs per week to add urine, feces, and bedding. Sample collection using the gas sampling system requires 20 - 30 minutes per bedded pack, depending on the measurements that are being collected. The use of lab-scaled bedded packs allows the researcher to control variables such as temperature, humidity, and bedding source that are difficult or impossible to control in a research or commercial facility. While not a perfect simulation of &#34;real-world&#34; conditions, the simulated bedded packs serve as a good model for researchers to use to examine treatment differences among bedded packs. Several lab-scale studies can be conducted to eliminate possible treatments before trying them in a research or commercial-sized facility.

A protocol has been developed to measure gases, odors, and nutrient composition in lab-scaled bedded manure packs, which can be used to study ways to improve air quality in commercial cattle facilities using deep-bedded manure packs.

A lab-scaled simulated bedded pack model was developed to study air quality and nutrient composition of deep-bedded packs used in cattle mono-slope ...

Composition and Distribution Analysis of Bioaerosols Under Different Environmental Conditions

Variable microorganisms in particulate matter (PM) under different environmental conditions may have significant impacts on human health. In this study, we described a protocol for multiple analyses of the biological compositions in environmental PM. Five experiments are presented: (1) PM number monitoring by using a laser particle counter; (2) PM collection by using a cyclonic aerosol sampler; (3) PM collection by using a high-volume air sampler with filters; (4) culturable microbes collection by the Andersen six-stage sampler; and (5) detection of biological composition of environmental PM by bacterial 16SrDNA and fungal ITS region sequencing. We selected hazy days and a livestock farm as two typical examples of the application in this protocol. In this study, these two sampling methods, cyclonic aerosol sampler and filter sampler, showed different sampling efficiency. The cyclonic aerosol sampler performed much better in terms of collecting bacteria, while these two methods showed the same efficiency in collecting fungi. Filter samplers can work under low temperature conditions while cyclonic aerosol samplers have a sampling limitation for temperature. A solid impacting sampler, such as an Andersen six-stage sampler, can be used to sample bioaerosols directly into the culture medium, which increases the survival rate of culturable microorganisms. However, this method mainly relies on culture while more than 99% of microbes cannot be cultured. DNA extracted from the culturable bacteria collected by the Andersen six-stage sampler and samples collected by cyclonic aerosol sampler and filter sampler were detected by bacterial 16S rDNA and fungal ITS region sequencing.All the methods above may have wide application in many fields of study, such as environmental monitoring and airborne pathogen detection. From these results, we can conclude that these methods can be used under different conditions and may help other researchers further explore the health impacts of environmental bioaerosols.

Understanding the biological composition of environmental particulate matter is important for the study of its significant impacts on human health and disease spread. Here, we used three types of bioaerosol sampling methods and a biological analysis of airborne microbes to better explore airborne microbial communities under different environmental conditions.

Variable microorganisms in particulate matter (PM) under different environmental conditions may have significant impacts on human health. In this study, ...

Automated 3D Optical Coherence Tomography to Elucidate Biofilm Morphogenesis Over Large Spatial Scales

Biofilms are a most successful microbial lifestyle and prevail in a multitude of environmental and engineered settings. Understanding biofilm morphogenesis, that is the structural diversification of biofilms during community assembly, represents a remarkable challenge across spatial and temporal scales. Here, we present an automated biofilm imaging system based on optical coherence tomography (OCT). OCT is an emerging imaging technique in biofilm research. However, the amount of data that currently can be acquired and processed hampers the statistical inference of large scale patterns in biofilm morphology. The automated OCT imaging system allows covering large spatial and extended temporal scales of biofilm growth. It combines a commercially available OCT system with a robotic positioning platform and a suite of software solutions to control the positioning of the OCT scanning probe, as well as the acquisition and processing of 3D biofilm imaging datasets. This setup allows the in situ and non-invasive automated&#160;monitoring of biofilm development and may be further developed to couple OCT imaging with macrophotography and microsensor profiling.

Microbial biofilms form complex architectures at interphases and develop into highly scale-dependent spatial patterns. Here, we introduce an experimental system (hard- and software) for the automated acquisition of 3D optical coherence tomography (OCT) datasets. This toolset allows the non-invasive and multi-scale characterization of biofilm morphogenesis in space and time.

Biofilms are a most successful microbial lifestyle and prevail in a multitude of environmental and engineered settings. Understanding biofilm ...

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 ...

Laser-Induced Fluorescence Emission (L.I.F.E.) as Novel Non-Invasive Tool for In-Situ Measurements of Biomarkers in Cryospheric Habitats

Global warming affects microbial communities in a variety of ecosystems, especially cryospheric habitats. However, little is known about microbial-mediated carbon fluxes in extreme environments. Hence, the methodology of sample acquisition described in the very few studies available implies two major problems: A) high resolution data require a large number of samples, which is difficult to obtain in remote areas; B) unavoidable sample manipulation such as cutting, sawing, and melting of ice cores that leads to a misunderstanding of in situ conditions. In this study, a prototype device that requires neither sample preparation nor sample destruction is presented. The device can be used for in situ measurements with a high spectral and spatial resolution in terrestrial and ice ecosystems and is based on the Laser-Induced Fluorescence Emission (L.I.F.E.) technique. Photoautotrophic supraglacial communities can be identified by the detection of L.I.F.E. signatures in photopigments. The L.I.F.E. instrument calibration for the porphyrin derivates chlorophylla (chla) (405 nm laser excitation) and B-phycoerythrin (B-PE) (532 nm laser excitation) is demonstrated. For the validation of this methodology, L.I.F.E. data were ratified by a conventional method for chla quantification that involved pigment extraction and subsequent absorption spectroscopy. The prototype applicability in the field was proven in extreme polar environments. Further testing on terrestrial habitats took place during Mars analog simulations in the Moroccan dessert and on an Austrian rock glacier. The L.I.F.E. instrument enables high resolution scans of large areas with acceptable operation logistics and contributes to a better understanding of the ecological potential of supraglacial communities in the context of global change.

Laser-Induced Fluorescence Emission L.I.F.E. as Novel Non-Invasive Tool for In-Situ Measurements of Biomarkers in Cryospheric Habitats

Carbon fluxes in the cryosphere are hardly assessed yet but are crucial regarding climate change. Here we show a novel prototype device that captures the phototrophic potential in supraglacial environments based on laser-induced fluorescence emission (L.I.F.E.) technology offering high spectral and spatial resolution data under in situ conditions.