This study was supported by the National Science Foundation (OIA-1655221, OCE-1655686) and Rhode Island Sea Grant (NA22-OAR4170123, RISG22-R/2223-95-5-U). We also would like to thank the Rhode Island School of Design for developing the Vis-A-Thon project and this visualization.

1. Applying the N-mass balance model
<ol>
	<li>Download the dissolved inorganic nitrogen (DIN) data from the US Environmental Protection Agency (USEPA) for 166 stations in Narragansett Bay from 1990 to 2015. 
	NOTE: In this study, the sum of ammonium (NH4+), nitrite (NO2-), and nitrate (NO3-) concentrations were considered as the DIN concentration.</li>
	<li>Split the Narragansett Bay into fifteen boxes along its axis modified from the previous study14 using Adobe Illustrator to divide the Bay in the map (Figure 1).</li>
	<li>Apply the N-mass balance model to calculate the mean concentration of DIN at each box. 
	NOTE: In this study, the N-mass balance model, consisting of DIN input and output terms, was modified from previous studies2,15 and applied to each box (1-15) of the Narragansett Bay as Equation 1. 
	<img alt="Equation 7" src="/files/ftp_upload/65728/65728eq07v2.jpg" style="margin: auto;" />&#160; Eq. (1) 
	Table 1 shows the definitions of each term and unit used in this model of Narragansett Bay. The model calculates the mean DIN concentration by determining the difference in each box of Narragansett Bay, representing the net DIN removal by biological production. Detailed information on the N-mass balance model is shown in the previous studies2,15. The detailed values used in the model of this study were derived from the previous studies14.</li>
	<li>Calculate the potential primary production (PPP) rate based on the N-mass balance model results by converting the net DIN removal to carbon units using the Redfield ratio (C: N = 106: 16, molar ratio) in a spreadsheet file.</li>
</ol>
2. Visualizing three zones in the map of Narragansett Bay
<ol>
	<li>Plot the identified three zones in the map of Narragansett Bay as a contour plot using the Ocean Data View software.
	<ol>
		<li>Save the PPP rate data of each box as a text file (.txt) from the spreadsheet file. 
		NOTE: The .txt file also includes the location of each box number as latitude and longitude. Put the longitude as a negative value. The PPP rate data is labeled as PPP [gC&#183;m-2&#183;day-1].</li>
		<li>Load the PPP rate data into the Ocean Data View software.
		<ol>
			<li>Go to open in the File menu.</li>
			<li>Click Associate Variables Box, Latitude, Longitude with Station, latitude [degrees_north], and Longitude [degrees_east], in the Metadata Variable Association window, then click the OK button.</li>
			<li>Click the OK button in the Import window.</li>
		</ol>
		</li>
		<li>Draw the contour plot to show the PPP ranges in the map of Narragansett Bay.
		<ol>
			<li>Right-click on the map, click Zoom, drag the red box to zoom into the data area of the map, and then click on Enter.</li>
			<li>Click the 1 SCATTER window of the Layout Templates in the View menu.</li>
			<li>Right-click in the Sample panel and select Derived Variables.</li>
			<li>Click the Add button after selecting Latitude under Metadata from the list of Choices panel. Do the same thing for Longitude and then click the OK button.</li>
			<li>Select drvd: Longitude [degrees_East] as X-Variable by right-clicking on the scatter window.</li>
			<li>Select drvd: Latitude [degrees_North] as Y-Variable by right-clicking on the scatter window.</li>
			<li>Select PPP [gC&#183;m-2&#183;day -1] as Z-Variable by right-clicking on the scatter window.</li>
			<li>Select Properties by right-clicking on the scatter window and go to the Display Style option.
			<ol>
				<li>Select the Gridded field.</li>
				<li>Go to the Contours option and click the &#60;&#60; button to make 0, 0.1, and 2 values only remain in the Already Defined Panes of the left.</li>
				<li>Click the OK button.</li>
			</ol>
			</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Based on the contour plot from the Ocean Data View Software, define the edge of the brown, green, and blue zones in Narraganset Bay, and visualize the zones using Adobe Illustrator to plot three zones in the map. 
	NOTE: Following the previous study15, the PPP rate of the brown zone was over 2 gC&#183;m-2&#183;day-1, the green zone was between 0.1-2 gC&#183;m-2&#183;day-1, and the blue zone was less than 0.1 gC&#183;m-2&#183;day-1, respectively.</li>
</ol>
3. Converting the contour plot of three zones into the three-dimensional (3D) frame with LED light
<ol>
	<li>Etch three acrylic panels as 5.5&#39;&#39; x 8&#39;&#39; with a laser cutter to show the boundary of each zone.</li>
	<li>Stack three acrylic panels in an illuminated frame.Overlap each acrylic panel showing the blue, green, and brown zones. Place a panel showing green zones on top of the blue zones panel and a brown zones panel on top of that.</li>
	<li>For the second physical model, etch four acrylic sheets as 5.5&#39;&#39; x 8&#39;&#39; with a laser cutter, with the UV printed three boundaries of zones and one panel to represent the entire Narragansett Bay (as per steps 3.1-3.2).</li>
	<li>Change the color of each zone into brown, green, and blue using the LEDs placed at the bottom of the frame.</li>
</ol>

Integrated Visualization of Biogeochemical Data for Nutrient Management

<ol>
	<li>Nixon, S. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coastal+marine+eutrophication:+A+definition,+social+causes,+and+future+concerns.">Coastal marine eutrophication: A definition, social causes, and future concerns.</a> Ophelia. 41, 199-219 (1995).</li><li>Kim, J. S., Brush, M. J., Song, B., Anderson, I. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reconstructing+primary+production+in+a+changing+estuary:+A+mass+balance+modeling+approach.">Reconstructing primary production in a changing estuary: A mass balance modeling approach.</a> Limnology and Oceanography. 66 (6), 2535-2546 (2021).</li><li>Kemp, W. M., 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=Eutrophication+of+Chesapeake+Bay:+historical+trends+and+ecological+interactions.">Eutrophication of Chesapeake Bay: historical trends and ecological interactions.</a> Marine Ecology Progress Series. 303, 1-29 (2005).</li><li>Brush, M. J., Malone, T. C., Malej, A., Faganeli, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Coastal Ecosystems in Transition: A Comparative Analysis of the Northern Adriatic and Chesapeake Bay. Chapter 5, (2021).</li><li>Howarth, R. W., Marino, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nitrogen+as+the+limiting+nutrient+for+eutrophication+in+coastal+marine+ecosystems:+Evolving+views+over+three+decades.">Nitrogen as the limiting nutrient for eutrophication in coastal marine ecosystems: Evolving views over three decades.</a> Limnology and Oceanography. 51 (1 part 2), 364-376 (2006).</li><li>Paerl, H. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Controlling+eutrophication+along+the+freshwater-marine+continuum:+Dual+nutrient+(N+and+P)+reductions+are+essential.">Controlling eutrophication along the freshwater-marine continuum: Dual nutrient (N and P) reductions are essential.</a> Estuaries and Coasts. 32, 593-601 (2009).</li><li>Kim, J. S., Chapman, P., Rowe, G., DiMarco, S. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Categorizing+zonal+productivity+on+the+continental+shelf+with+nutrient-salinity+ratios.">Categorizing zonal productivity on the continental shelf with nutrient-salinity ratios.</a> Journal of Marine Systems. 206, 103336 (2020).</li><li>Rowe, G. T., Chapman, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Continental+shelf+hypoxia:+Some+nagging+questions.">Continental shelf hypoxia: Some nagging questions.</a> Gulf of Mexico Science. 20 (2), 153-160 (2002).</li><li>Nixon, S. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Eutrophication+and+the+macroscope.">Eutrophication and the macroscope.</a> Hydrobiologia. 629, 5-19 (2009).</li><li>Barbier, E. B., 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=The+value+of+estuarine+and+coastal+ecosystem+services.">The value of estuarine and coastal ecosystem services.</a> Ecological Monographs. 81 (2), 169-193 (2011).</li><li>Cloern, J. E., Foster, S. Q., Kleckner, A. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phytoplankton+primary+production+in+the+world's+estuarinecoastal+ecosystem.">Phytoplankton primary production in the world's estuarinecoastal ecosystem.</a> Biogeosciences. 11 (9), 2477-2501 (2014).</li><li>Codiga, D. L., Stoffel, H. E., Oviatt, C. A., Schmidt, C. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Managed+nitrogen+load+decrease+reduces+chlorophyll+and+hypoxia+in+warming+temperate+urban+estuary.">Managed nitrogen load decrease reduces chlorophyll and hypoxia in warming temperate urban estuary.</a> Frontiers in Marine Science. 9, 930347 (2022).</li><li>Sigman, D. M., Hain, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+biological+productivity+of+the+ocean.">The biological productivity of the ocean.</a> Nature Education Knowledge. 3 (10), 21 (2012).</li><li>Kremer, J. N., 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=Simulating+property+exchange+in+estuarine+ecosystem+models+at+ecologically+appropriate+scales.">Simulating property exchange in estuarine ecosystem models at ecologically appropriate scales.</a> Ecological Modelling. 221 (7), 1080-1088 (2010).</li><li>Kim, J. S., Chapman, P., Rowe, G., DiMarco, S. F., Thornton, D. C. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Implications+of+different+nitrogen+input+sources+for+potential+production+and+carbon+flux+estimates+in+the+coastal+Gulf+of+Mexico+(GOM)+and+Korean+Peninsula+coastal+waters.">Implications of different nitrogen input sources for potential production and carbon flux estimates in the coastal Gulf of Mexico (GOM) and Korean Peninsula coastal waters.</a> Ocean Science. 16, 45-63 (2020).</li><li>Lake, S. J., Brush, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+contribution+of+microphytobenthos+to+total+productivity+in+upper+Narragansett+Bay,+Rhode+Island.">The contribution of microphytobenthos to total productivity in upper Narragansett Bay, Rhode Island.</a> Estuarine, Coastal and Shelf Science. 95 (2-3), 289-297 (2011).</li><li>Brush, M. J., Nixon, S. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modeling+the+role+of+macroalgae+in+a+shallow+sub-estuary+of+Narragansett+Bay,+RI+(USA).">Modeling the role of macroalgae in a shallow sub-estuary of Narragansett Bay, RI (USA).</a> Ecological Modelling. 221 (7), 1065-1079 (2010).</li><li>Deacutis, C. F., Murray, D., Prell, W., Saarman, E., Korhun, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hypoxia+in+the+upper+half+of+Narragansett+Bay,+RI,+during+August+2001+and+2002.">Hypoxia in the upper half of Narragansett Bay, RI, during August 2001 and 2002.</a> Northeastern Naturalist. 13 (Special Issue 4), 173-198 (2006).</li><li>Oviatt, C., 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=Managed+nutrient+reduction+impacts+on+nutrient+concentrations,+water+clarity,+primary+production,+and+hypoxia+in+a+north+temperate+estuary.">Managed nutrient reduction impacts on nutrient concentrations, water clarity, primary production, and hypoxia in a north temperate estuary.</a> Estuarine, Coastal and Shelf Science. 199, 25-34 (2017).</li><li>Boesch, D. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Barriers+and+bridges+in+abating+coastal+eutrophication.">Barriers and bridges in abating coastal eutrophication.</a> Frontiers in Marine Science. 6, 123 (2019).</li><li>Oviatt, C. A., Keller, A. A., Reed, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Annual+primary+production+in+Narragansett+Bay+with+no+bay-wide+winter-spring+phytoplankton+bloom.">Annual primary production in Narragansett Bay with no bay-wide winter-spring phytoplankton bloom.</a> Estuarine, Coastal and Shelf Science. 54, 1013-1026 (2002).</li></ol>

The authors have no conflicts of interest to declare.

This study estimated the extent of nutrient impacts from riverine inputs in Narraganset Bay (NB) based on the N-mass balance model by defining the three theoretical zones. Historically, hypoxic zones appeared near the Providence River, the western side of Greenwich Bay, and Mount Hope Bay during the summer period18, which were defined as brown zones in this study. Moreover, the zonation of NB is comparable to the results of a previous study19, which examined nutrient concen...

Primary productivity, the production of organic compounds by phytoplankton, fuels ecosystem food webs, and is important for understanding the system&#39;s function in response to environmental changes1,2. Estuarine primary productivity is also closely linked to eutrophication which is defined as excessive nutrients in the ecosystem1, causing several harmful consequences in the coastal regions, such as an overgrowth of phytoplankton leading to large algal blooms and subsequent hypoxia3,4. Importantly, primary productivity in estuaries is highly dependent on the riverine nutrient loading, particularly nitrogen concentrations, which are the typical limiting nutrient in most temperate ocean ecosystems5,6. However, an estimation of the extent of riverine nitrogen impacts in coastal areas remains challenging.
To estimate the estuarine primary productivity, a nitrogen (N) mass balance model is a useful tool to calculate nitrogen fluxes2. The N-mass balance model also provides an understanding of biological mechanisms beyond data observations, revealing information at the edges of different primary productivity zones7. Three different zones8, defined as brown, green, and blue zones, are particularly useful for predicting the impact of nutrient loading in hypoxic regions. The brown zone, defined as the nearest region of a river mouth, represents a high physical process, the green zone has high biological productivity, and the blue zone represents low biological process. The boundary of each zone depends on river flow, nutrient concentrations, and mixing rates8.
Narragansett Bay (NB) is a coastal, temperate estuary in Rhode Island, USA, supporting economic and ecological services and goods9,10,11, in which hypoxia has been consistently occurring. These hypoxic events, defined as the period of low dissolved oxygen (i.e., less than 2-3 mg of oxygen per liter), are particularly prevalent in July and August and are heavily impacted by riverine nitrogen loading during these months12. With an increase in primary production and hypoxia due to anthropogenic emissions of nutrients13, understanding the nitrogen inputs into NB is critical to managing and addressing coastal issues such as eutrophication and hypoxia. Thus, in this study, the rate of primary production in NB is calculated from the N-mass balance model using historically observed nutrient data, especially dissolved inorganic nitrogen (DIN). Based on the results of the N-mass balance model by converting to carbon units using the Redfield ratio, three different primary productivity zones were identified to visualize the extent of nitrogen influence from the river in NB. The model was then recreated into a 3D representation to better visualize the different zones. The products produced from this study can better inform nutrient management in NB in response to hypoxia and eutrophication. Further, results from this study are applicable to other coastal regions to visualize the effects of riverine transport on nutrients and primary productivity.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Adobe Illustrator&#160;</td>
			<td>Adobe</td>
			<td>version 27.6.1</td>
			<td>https://www.adobe.com/products/illustrator.html</td>
		</tr>
		<tr>
			<td>Ampersand Gessobord Uncradled 1/8&#34; Profile 8&#34; x 8&#34;</td>
			<td>Risdstore</td>
			<td>70731053088</td>
			<td>https://www.risdstore.com/ampersand-gessobord-8x8-flat-1-8-profile.html</td>
		</tr>
		<tr>
			<td>Ocean Data View software</td>
			<td></td>
			<td></td>
			<td>https://odv.awi.de/en/software/download/</td>
		</tr>
		<tr>
			<td>W-Series (Wide) Flexible LED Strip Light - Ultra Bright (18 LEDs/foot)</td>
			<td>aspectLED</td>
			<td>SKU AL-SL-W-U</td>
			<td>https://www.aspectled.com/products/w-wide-5050-ultra-bright?gclid=CjwKCAjwm4ukBhAuEiwA0z 
			QxkyqisRPqBcHvXEW8KcJE-bK0d2cvGtqlOxXWJI_ 
			E2rd6DzttPR0FLRoCgfkQAvD_BwE</td>
		</tr>
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</table>

visualization of productivity zones based on nitrogen mass balance model in narragansett bay, rhode island

Primary productivity in the coastal regions, linked to eutrophication and hypoxia, provides a critical understanding of ecosystem function. Although primary productivity largely depends on riverine nutrient inputs, estimation of the extent of riverine nutrient influences in the coastal regions is challenging. A nitrogen mass balance model is a practical tool to evaluate coastal ocean productivity to understand biological mechanisms beyond data observations. This study visualizes the biological production zones in Narragansett Bay, Rhode Island, USA, where hypoxia frequently occurs, by applying a nitrogen mass balance model. The Bay is divided into three zones - brown, green, and blue zones - based on primary productivity, which are defined by the mass balance model results. Brown, green, and blue zones represent a high physical process, a high biological process, and a low biological process zone, depending on river flow, nutrient concentrations, and mixing rates. The results of this study can better inform nutrient management in the coastal ocean in response to hypoxia and eutrophication.

Three theoretical zones of Narragansett Bay based on the N-mass balance model 
The three theoretical zones in Narragansett Bay (NB) were defined based on the N-mass balance model results, in which the DIN data were applied to fifteen boxes of NB, and then the mean DIN in each box was converted to the PPP rates for the summer period. As shown in Figure 2, based on the mean summer (June to September) PPP rates of each box, three (brown, green, and blue) zones in NB were i...

Watch this Scientific Journal Video about Visualization of Productivity Zones Based on Nitrogen Mass Balance Model in Narragansett Bay, Rhode Island at JoVE.com

Author Spotlight: Understanding Riverine Nitrogen Impacts and Primary Productivity for Effective Nutrient Management

Here, we aim to visualize the zonation of biological productivity in Narragansett Bay, Rhode Island, based on the nitrogen mass balance model. The results will inform nutrient management in the coastal regions to reduce hypoxia and eutrophication.

Visualization of Productivity Zones Based on Nitrogen Mass Balance Model in Narragansett Bay, Rhode Island

Primary productivity in the coastal regions, linked to eutrophication and hypoxia, provides a critical understanding of ecosystem function. Although ...

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314 Views.  University of Texas - Rio Grande Valley. Here, we aim to visualize the zonation of biological productivity in Narragansett Bay, Rhode Island, based on the nitrogen mass balance model. The results will inform nutrient management in the coastal regions to reduce hypoxia and eutrophication.

Video: Author Spotlight: Understanding Riverine Nitrogen Impacts and Primary Productivity for Effective Nutrient Management

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

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

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

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

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

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis

Meta-omic technologies such as metagenomics, metatranscriptomics and metaproteomics can aid in the understanding of microbial community structure and metabolism. Although powerful, metagenomics alone can only elucidate functional potential. On the other hand, metaproteomics enables the description of the expressed in situ metabolism and function of a community. Here we describe a protocol for cell lysis, protein and DNA isolation, as well as peptide digestion and extraction from marine microbial cells collected on a cartridge filter unit (such as the Sterivex filter unit) and preserved in an RNA stabilization solution (like RNAlater). In mass spectrometry-based proteomics studies, the identification of peptides and proteins is performed by comparing peptide tandem mass spectra to a database of translated nucleotide sequences. Including the metagenome of a sample in the search database increases the number of peptides and proteins that can be identified from the mass spectra. Hence, in this protocol DNA is isolated from the same filter, which can be used subsequently for metagenomic analysis.

This protocol is for the extraction and concentration of protein and DNA from microbial biomass collected from seawater, followed by the generation of tryptic peptides suitable for tandem mass spectrometry-based proteomic analysis.

Meta-omic technologies such as metagenomics, metatranscriptomics and metaproteomics can aid in the understanding of microbial community structure and ...

Quantification of Heavy Metals and Other Inorganic Contaminants on the Productivity of Microalgae

Increasing demand for renewable fuels has researchers investigating the feasibility of alternative feedstocks, such as microalgae. Inherent advantages include high potential yield, use of non-arable land and integration with waste streams. The nutrient requirements of a large-scale microalgae production system will require the coupling of cultivation systems with industrial waste resources, such as carbon dioxide from flue gas and nutrients from wastewater. Inorganic contaminants present in these wastes can potentially lead to bioaccumulation in microalgal biomass negatively impact productivity and limiting end use. This study focuses on the experimental evaluation of the impact and the fate of 14 inorganic contaminants (As, Cd, Co, Cr, Cu, Hg, Mn, Ni, Pb, Sb, Se, Sn, V and Zn) on Nannochloropsis salina growth. Microalgae were cultivated in photobioreactors illuminated at 984 &#181;mol m-2 sec-1 and maintained at pH 7 in a growth media polluted with inorganic contaminants at levels expected based on the composition found in commercial coal flue gas systems. Contaminants present in the biomass and the medium at the end of a 7 day growth period were analytically quantified through cold vapor atomic absorption spectrometry for Hg and through inductively coupled plasma mass spectrometry for As, Cd, Co, Cr, Cu, Mn, Ni, Pb, Sb, Se, Sn, V and Zn. Results show N. salina is a sensitive strain to the multi-metal environment with a statistical decrease in biomass yieldwith the introduction of these contaminants. The techniques presented here are adequate for quantifying algal growth and determining the fate of inorganic contaminants.

Integration of microalgal cultivation with industrial flue gas will ultimately introduce heavy metals and other inorganic compounds into the growth media. This study presents a procedure used to determine the end fate and impact of heavy metals and inorganic contaminants on the growth of Nannochloropsis salina grown in photobioreactors.

Increasing demand for renewable fuels has researchers investigating the feasibility of alternative feedstocks, such as microalgae. Inherent advantages ...

Biofilm Removal Using Carbon Dioxide Aerosols without Nitrogen Purge

Biofilms can cause serious concerns in many applications. Not only can they cause economic losses, but they can also present a public health hazard. Therefore, it is highly desirable to remove biofilms from surfaces. Many studies on CO2 aerosol cleaning have employed nitrogen purges to increase biofilm removal efficiency by reducing the moisture condensation generated during the cleaning. However, in this study, periodic jets of CO2 aerosols without nitrogen purges were used to remove Pseudomonas putida biofilms from polished stainless steel surfaces. CO2 aerosols are mixtures of solid and gaseous CO2 and are generated when high-pressure CO2 gas is adiabatically expanded through a nozzle. These high-speed aerosols were applied to a biofilm that had been grown for 24 hr. The removal efficiency ranged from 90.36% to 98.29% and was evaluated by measuring the fluorescence intensity of the biofilm as the treatment time was varied from 16 sec to 88 sec. We also performed experiments to compare the removal efficiencies with and without nitrogen purges; the measured biofilm removal efficiencies were not significantly different from each other (t-test, p &gt; 0.55). Therefore, this technique can be used to clean various bio-contaminated surfaces within one minute.

Biofilms on surfaces can be effectively and rapidly removed by using a periodic jet of carbon dioxide aerosols without a nitrogen purge.

Biofilms can cause serious concerns in many applications. Not only can they cause economic losses, but they can also present a public health hazard. ...

Automated, High-resolution Mobile Collection System for the Nitrogen Isotopic Analysis of NOx

Nitrogen oxides (NOx = NO + NO2) are a family of atmospheric trace gases that have great impact on the environment. NOx concentrations directly influence the oxidizing capacity of the atmosphere through interactions with ozone and hydroxyl radicals. The main sink of NOx is the formation and deposition of nitric acid, a component of acid rain and a bioavailable nutrient. NOx is emitted from a mixture of natural and anthropogenic sources, which vary in space and time. The collocation of multiple sources and the short lifetime of NOx make it challenging to quantitatively constrain the influence of different emission sources and their impacts on the environment. Nitrogen isotopes of NOx have been suggested to vary amongst different sources, representing a potentially powerful tool to understand the sources and transport of NOx. However, previous methods of collecting atmospheric NOx integrate over long (week to month) time spans and are not validated for the efficient collection of NOx in relevant, diverse field conditions. We report on a new, highly efficient field-based system that collects atmospheric NOx for isotope analysis at a time resolution between 30 min and 2 hr. This method collects gaseous NOx in solution as nitrate with 100% efficiency under a variety of conditions. Protocols are presented for collecting air in urban settings under both stationary and mobile conditions. We detail the advantages and limitations of the method and demonstrate its application in the field. Data from several deployments are shown to 1) evaluate field-based collection efficiency by comparisons with in situ NOx concentration measurements, 2) test the stability of stored solutions before processing, 3) quantify in situ reproducibility in a variety of urban settings, and 4) demonstrate the range of N isotopes of NOx detected in ambient urban air and on heavily traveled roadways.

Automated, High-resolution Mobile Collection System for the Nitrogen Isotopic Analysis of NOx

Previous work suggests that the nitrogen isotopic composition of atmospheric nitrogen oxides might distinguish the influence of different sources in the environment. We report on an automated, mobile, field-based method for the high collection efficiency of atmospheric NOx for N isotopic analysis at an hourly time resolution.

Nitrogen oxides (NOx = NO + NO2) are a family of atmospheric trace gases that have great impact on the environment. NOx concentrations directly influence ...

A Video Surveillance System to Monitor Breeding Colonies of Common Terns (Sterna Hirundo)

Many waterbird populations have faced declines over the last century, including the common tern (Sterna hirundo), a waterbird species with a widespread breeding distribution, that has been recently listed as endangered in some habitats of its range. Waterbird monitoring programs exist to track populations through time; however, some of the more intensive approaches require entering colonies and can be disruptive to nesting populations. This paper describes a protocol that utilizes a minimally invasive surveillance system to continuously monitor common tern nesting behavior in typical ground-nesting colonies. The video monitoring system utilizes wireless cameras focused on individual nests as well as over the colony as a whole, and allows for observation without entering the colony. The video system is powered with several 12 V car batteries that are continuously recharged using solar panels. Footage is recorded using a digital video recorder (DVR) connected to a hard drive, which can be replaced when full. The DVR may be placed outside of the colony to reduce disturbance. In this study, 3,624 h of footage recorded over 63 days in weather conditions ranging from 12.8 &#176;C to 35.0 &#176;C produced 3,006 h (83%) of usable behavioral data. The types of data retrieved from the recorded video can vary; we used it to detect external disturbances and measure nesting behavior during incubation. Although the protocol detailed here was designed for ground-nesting waterbirds, the principal system could easily be modified to accommodate alternative scenarios, such as colonial arboreal nesting species, making it widely applicable to a variety of research needs.

A Video Surveillance System to Monitor Breeding Colonies of Common Terns Sterna Hirundo

This paper describes a protocol that uses a remote video monitoring surveillance system to continuously monitor breeding colonies of ground-nesting waterbirds. The system includes five cameras monitoring individual nests and one camera monitoring the colony as a whole, and is powered by car batteries that are recharged via solar panels.

Many waterbird populations have faced declines over the last century, including the common tern (Sterna hirundo), a waterbird species with a widespread ...

Preparation of Biomass-based Mesoporous Carbon with Higher Nitrogen-/Oxygen-chelating Adsorption for Cu(II) Through Microwave Pre-Pyrolysis

An environment-friendly technique for synthesizing biomass-based mesoporous activated carbon with high nitrogen-/oxygen-chelating adsorption for Cu(II) is proposed. Bagasse impregnated with phosphoric acid is utilized as the precursor. To pyrolyze the precursor, two separate heating modes are used: microwave pyrolysis and conventional electric-heating pyrolysis. The resulting bagasse-derived carbon samples are modified with nitrification and reduction modification. Nitrogen (N)/oxygen (O) functional groups are simultaneously introduced to the surface of activated carbon, enhancing its adsorption of Cu(II) by complexing and ion-exchange. Characterization and copper adsorption experiments are performed to investigate the physicochemical properties of four prepared carbon samples and determine which heating method favors the subsequent modification for doping of N/O functional groups. In this technique, based on analyzing data of nitrogen adsorption, Fourier transform infrared spectroscopy, and batch adsorption experiments, it is proven that microwave-pyrolyzed carbon has more defect sites and, therefore, time-saving effective microwave pyrolysis contributes more N/O species to the carbon, although it leads to a lower specific surface area. This technique offers a promising route to synthesis adsorbents with higher nitrogen and oxygen content and a higher adsorption capacity of heavy-metal ions in wastewater remediation applications.

Preparation of Biomass-based Mesoporous Carbon with Higher Nitrogen-/Oxygen-chelating Adsorption for CuII Through Microwave Pre-Pyrolysis

Here, we present a protocol to synthesize nitrogen/oxygen dual-doped mesoporous carbon from biomass by chemical activation in different pyrolysis modes followed by modification. We demonstrate that the microwave pyrolysis benefits the subsequent modification process to simultaneously introduce more nitrogen and oxygen functional groups on the carbon.

An environment-friendly technique for synthesizing biomass-based mesoporous activated carbon with high nitrogen-/oxygen-chelating adsorption for Cu(II) is ...

Evaluation of the Productivity of Social Wasp Colonies (Vespinae) and an Introduction to the Traditional Japanese Vespula Wasp Hunting Technique

For vespine wasps, colony productivity is typically estimated by counting the number of larval cells. This paper presents an improved method that enables researchers to estimate more accurately the number of adults produced, counting the number of meconia (the stools left in the cells by wasp larvae when pupating into adults, per 100 cells) in each comb. This method can be applied before or after colony collapse (i.e., in active or inactive nests). The paper also describes how to locate wild Vespula wasp colonies by &#34;flagging&#34; wasp baits and chasing the wasp collecting them, using a method traditionally performed by local people in central Japan (as illustrated in the associated video). The Vespula chasing method described has several advantages: it is easy to reinitiate the chase from a point where the forager flying back to the nest was lost, and it is easy to pinpoint the nest location as marked wasps often lose their flag at the nest entrance. These methods for estimating colony productivity and collecting nests can be valuable for researchers studying social wasps.

Evaluation of the Productivity of Social Wasp Colonies Vespinae and an Introduction to the Traditional Japanese Vespula Wasp Hunting Technique

This methodological paper evaluates the productivity of a social wasp colony by examining the number of meconia per 100 cells of comb, to estimate the total number of adults the wasps produced. The associated video describes how to search for Vespula wasp nests, a method developed by amateur wasp chasers.

For vespine wasps, colony productivity is typically estimated by counting the number of larval cells. This paper presents an improved method that enables ...

Investigation of Xenobiotics Metabolism In Salix alba Leaves via Mass Spectrometry Imaging

The method presented uses mass spectrometry imaging (MSI) to establish the metabolic profile of S. alba leaves when exposed to xenobiotics. Using a non-targeted approach, plant metabolites and xenobiotics of interest are identified and localized in plant tissues to uncover&#160;specific distribution patterns. Then, in silico prediction of potential metabolites (i.e., catabolites and conjugates) from the identified xenobiotics is performed. When a xenobiotic metabolite is located in the tissue, the type of enzyme involved in its alteration by the plant is recorded. These results were used to describe different types of biological reactions occurring in S. alba leaves in response to xenobiotic accumulation in the leaves. The metabolites were predicted in two generations, allowing the documentation of successive biological reactions to transform xenobiotics in the leaf tissues.

Investigation of Xenobiotics Metabolism In Salix alba Leaves via Mass Spectrometry Imaging

This method uses mass spectrometry imaging (MSI) to understand metabolic processes in S. alba leaves when exposed to xenobiotics. The method allows the spatial localization of compounds of interest and their predicted metabolites within specific, intact tissues.

The method presented uses mass spectrometry imaging (MSI) to establish the metabolic profile of S. alba leaves when exposed to xenobiotics. Using a ...

Quantification of the Potential Impact of Glyphosate-Based Products on Microbiomes

Glyphosate-based products (GBP) are the most common broad-spectrum herbicides worldwide. The target of glyphosate is the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in the shikimate pathway, which is virtually universal in plants. The inhibition of the enzyme stops the production of three essential amino acids: phenylalanine, tyrosine, and tryptophan. EPSPS is also present in fungi and prokaryotes, such as archaea and bacteria; thus, the use of GBP may have an impact on the microbiome composition of soils, plants, herbivores, and secondary consumers. This article aims to present general guidelines to assess the effect of GBP on microbiomes from field experiments to bioinformatics analyses and provide a few testable hypotheses. Two field experiments are presented to test the GBP on non-target organisms. First, plant-associated microbes from 10 replicated control and GBP treatment plots simulating no-till cropping are sampled and analyzed. In the second experiment, samples from experimental plots fertilized by either poultry manure containing glyphosate residues or non-treated control manure were obtained. Bioinformatics analysis of EPSPS protein sequences is utilized to determine the potential sensitivity of microbes to glyphosate. The first step in estimating the effect of GBP on microbiomes is to determine their potential sensitivity to the target enzyme (EPSPS). Microbial sequences can be obtained either from public repositories or by means of PCR amplification. However, in the majority of field studies, microbiome composition has been determined based on universal DNA markers such as the 16S rRNA and the internal transcribed spacer (ITS). In these cases, sensitivity to glyphosate can only be estimated through a probabilistic analysis of EPSPS sequences using closely related species. The quantification of the potential sensitivity of organisms to glyphosate, based on the EPSPS enzyme, provides a robust approach for further experiments to study target and non-target resistant mechanisms.

Glyphosate-based products (GBP) are the most common broad-spectrum herbicides worldwide. In this article, we introduce general guidelines to quantify the effect of GBP on microbiomes, from field experiments to bioinformatics analyses.