Category: News

Cahaba River Project

  • April 4th, 2019
  • in News
graduate students
Graduate student researchers Elise Chapman, Julie Jarnigan, and Corianne Tatariw (pictured left to right) at the shoals found within the Fall Line of the Cahaba River. Shoals contain abundant Justicia americana plant beds, interspersed among which are the rare Spider Lily plants.

Understanding variation in the relative importance of nitrogen (N) retention mechanisms from Ridge and Valley headwaters to the Mobile Bay

Drs. Jennifer Edmonds and Behzad Mortazavi, Department of Biological Sciences.  This work is currently funded by the USGS through the Alabama Water Resource Research Institute in Auburn, AL.

Widespread nutrient enrichment within the Mobile River Basin of the southeastern US has the potential to increase the delivery of nitrogen (N) and phosphorus (P) to the Gulf Coast. The extent to which nutrient enrichment and associated anoxic conditions persist in the Mobile Bay is largely unknown; however, reducing N transport to Alabama’s coastal waterways will likely ameliorate possible loss of commercial and recreational value due to hypoxic events similar to the Dead Zones widely observed in the Gulf of Mexico.

Through our collaboration between researchers in Tuscaloosa and DISL, we are evaluating the patterns and controls on two important mechanisms for nitrogen retention (denitrification and plant uptake) within the Cahaba River, a key drainage system within the Mobile basin in central Alabama that receives large inputs of anthropogenic N from activity in Birmingham, AL.

Our project includes both laboratory and field activities designed to assess the competition between plant uptake of N and utilization of nitrate by sediment microorganisms. In organic matter-rich sediments experiencing low oxygen conditions, microorganisms will convert nitrate to N2 (g) as they respire, permanently removing N from the ecosystem and preventing it from reaching coastal waters.

Field research for this project has focused on six sites along the river starting above Birmingham in the Ridge and Valley physiographic province and ending downstream ~275 km in the Coastal Plain. Evidence from lab experiments suggests carbon limitation of sediment denitrification at all sites, with the exception of our samples taken from the shoal habitat (see photo). In contrast to the two other physiographic types, the shoals site on the Fall Line had only a small response to C additions, but responded strongly to N addition. This suggests that C limitation of denitrifying bacteria was alleviated by the presence of organic matter rich sediments associated with shoal macrophytes, something we are exploring further in 2010-11. Denitrification potentials measured at coastal sites by the Mortazavi lab as part of this same project also showed evidence of strong N limitation, but no effects of adding C, most likely due to high primary production (i.e., organic matter production) coupled with low water nitrate concentrations.

Future work will relate the patterns in N retention in the Cahaba River to the larger river network and its receiving ecosystem, the Mobile Bay.

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Effects of Agricultural Land Use on the Molecular Composition of Streamwater Dissolved Organic Matter and Microbial Community Structure

  • April 4th, 2019
  • in News

Research Team: Yuehan Lu, Department of Geological Sciences; Robert Findlay, Department of Biological Sciences; Natasha Dimova, Department of Geological Sciences Amount Requested: $32,000
Project Duration: two years (02/15/14-02/15/16)

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1. Motivation and Significance

Dissolved organic matter/organic carbon (DOM/DOC) plays a pivotal role in a variety of environmental and ecosystem processes within aquatic systems (DOC and DOM are often used interchangeably because DOC is the primary component of DOM). DOM protects aquatic biota by attenuating ultraviolet-B penetration [Williamson and Zagarese 1994], affects the physical states and transport of ecotoxins and trace metal pollutants [Driscoll et al. 1988; Worrall et al. 1997; Yamashita and Jaffé2008], and serves as the basal substrate and energy sources for heterotrophic food webs [Benner 2003; Kirchman 2003].

Agricultural land use has been recognized as a global change that has fundamentally altered terrestrial landscapes and soil environments [Foley et al. 2005]. Land use may directly alter the quantity and characteristics of allochthonous DOM, i.e., DOM exported from watersheds to receiving waters. By changing physical landscapes and through the effects of nutrients and organics transferred from land to water, agricultural land use can also indirectly modify autochthonous DOM, i.e., DOM from the algae and bacteria living in water. Recent studies have shown that agricultural land use in watersheds may change the quantity, sources, ages, composition and reactivity of DOM in receiving waters [e.g., Warner et al. 2009; Wilson and Xenopoulos 2009; Aitkenhead-Peterson et al. 2009; Sickman et al. 2010; Williams et al. 2010], which may have substantial environmental and ecological ramifications for downstream rivers and coastal oceans. (see figure in PDF)

An example of the potential downstream ramifications is that agricultural land use may favor hypoxia (Fig.1). Hypoxia, defined as dissolved oxygen concentrations less than 2mg/L and also referred to as ‘dead zones’, has plagued coastal ecosystems worldwide despite many costly management practices and restoration efforts [Bianchi et al. 2010]. Although the conventional understanding of the underlying mechanisms primarily identifies the importance of elevated nutrients in creating hypoxic events, organic matter exported from the land to coastal waters has gained much attention for its significant role in oxygen consumption [e.g., Eldridge and Morse 2008; Bianchi et al. 2010]. This role may be further enhanced by the possibility of agricultural land use increasing the proportions of bioreactive DOM (i.e., DOM can be readily remineralized or assimilated by heterotrophic bacteria) [Williams et al. 2010]. Bioreactive DOM has a greater potential than biorefractory DOM to contribute to hypoxia, either directly through bacterial respiration—the consumption of oxygen to convert DOM to CO2—or indirectly through supplying organic and inorganic nutrients, which stimulates algal blooms that eventually decompose and consume oxygen (Fig. 1).

Compared with coastal oceans, riverine metabolism may be more susceptible to land useinduced changes in the properties of DOM [Aufdenkampe et al. 2011]. Allochthonous OM acts as a substrate source for riverine food webs [Roach 2013] and heavily subsidizes riverine respiration, as shown by the prevalence of net heterotrophic rivers (i.e., respiration > autochthonous primary productivity) [Raymond et al. 1997; Jassby and Cloern 2000; Griffith and Raymond 2011]. The changes in DOM due to agricultural land use can alter how DOM is processed, and therefore, the relative importance of allochthonous vs. autochthonous OM in supporting riverine metabolism. For example, agricultural land use may reduce the structural complexity and molecular weights of DOM [Wilson and Xenopoulos 2009], providing easier access to bacterial remineralization and thereby increasing the subsidies of allochthonous OM to riverine respiration (Fig. 1). Using high-resolution molecular analysis, Lu and students found a similar pattern demonstrating that agricultural watershed exported DOM with lower amounts of condensed and aromatic structures [Li et al., in prep]

It is thus clear that agricultural land use may change the bioreactivity and molecules of DOM and that these changes could have far-reaching impacts on downstream environments and ecosystems. However, our understanding of how agricultural land use alters the molecular composition and reactivity of DOM remains incoherent and thus not well integrated in modeling and management efforts [Stanley et al., 2013]. In this proposal, we request funding to conduct a focused investigation on variation in DOM and associated microbial responses from streams draining a gradient of agricultural land use. This project will yield preliminary data and demonstrate the effectiveness of our research strategy in order to lead to a successful large-scale proposal.

2. Work Plan and Hypotheses

Study Area

Five streams along a gradient of watershed land use within the Bear Creek Watershed (BCW), Northwestern Alabama are be chosen for this study. The BCW watershed was selected for the following reasons.

  1. Contrasting co-existance of both agricultural and forest land use: based on the 2006 NLCD BCW comprises ~16% agricultural land, 57% forestland, 5.5% urban land, and 22% of other land use (open water, wetland, shrub, grassland, and barren land). The delineated subwatersheds show a gradient of % agricultural land use ranging between ~2% and 32%.
  2. Availability of of data on sediment and water quality from long-term monitoring: sediment/water qualities and organism health are monitored by the Geological Survey of Alabama (GSA) and the Tennessee Valley Authority (TVA) and the USGS monitors the stream discharges.
  3. Easy access and availability of laboratory facilities: the site is close to the University of Alabama (UA) campus (ca. 80miles away). Sampling efforts may be coordinated with the GSA sediment survey trips of the; thus, the sampling cost and resolution may be further improved.

Plan 1: Quantitatively assessing the importance of agricultural land use in determining streamwater DOM molecular composition, reactivity and associated microbial responses (microbial abundance and community composition) at base flow The five streams will be sampled three times at base flow. In addition to the characterization of DOM and microbes, a series of watershed, hydrology and inorganic water chemistry variables DOM properties will be determined (Table 1). We hypothesize that watershed land use is the primary factor determining DOM properties during baseflow conditions.

Variables Method PI
Land use (e.g., % forest; %cropland; % urban land)1 ArcGIS watershed delineation Lu
Watershed physical parameters (e.g., stream length, width,
depth, drainage area, topography)
ArcGIS analysis and field
Water chemistry parameters (inorganic nutrients,
Chlorophyll-a, in situ parameters)
Field sampling and laboratory
%Groundwater input to streamflow Radon222 in streamwater Dimova
Stream/river Discharge evaluations Flow rate measurements Dimova
DOM biodegradability Laboratory incubations Lu
DOM sources C:N ratios; δ13C-DOC; DOM
optical properties
DOM molecular composition FT-ICRMS analysis Lu
Microbial community Phospholipid fatty acids (PLFA) Findlay

Plan 2: Quantitatively assessing the importance of agricultural land use vs. hydrological variation in determining streamwater DOM reactivity, molecular composition and associated microbial responses. The five streams will be sampled twice after storm events. Hydrological variations may change the sources, ages and compositions of DOM by shifting hydrologic flowpaths and altering in-stream production and processing of DOM [Taylor et al. 2003;Vidon et al. 2008; Fellman et al. 2009b; Wiegner et al. 2009; Hong et al. 2012]. Differentiating the influences of hydrological variation vs. land use on DOM will be achieved through comparing the DOM in streams during baseflow conditions vs. storm events. We hypothesize that high discharges/storm events will reduce the relative importance of watershed land use in determining DOM properties and associated microbial responses.

Summer 2014 Summer 2014 Fall 2014 Spring 2015 Summer 2015 Fall 2015
Watershed characterization x
Objective 1 data collection x x x x
Objective 2 data collection x x x x
Proposal submission x x
Manuscript preparation x x x

4. Budget and Budget Justification

$6,000 for a Radon instrument; $6,000 for the high-resolution molecular analysis of DOM at the COSMIC lab at Old Dominion University; $3,750 for the PLFA analysis; $ 3,000 for additional DOM and water chemistry parameters such as C:N ratios, optical properties and nutrients; $1,200 for the field sampling ($100/trip *12 trips=$1200); $12,050 for supporting a MS student for spring 2014 (tuition $4750+ stipend $6700+ health insurance $600).

5. External Funding Opportunities Strengthened

a. A proposal to understand the influences of flow paths on DOM and heterotrophic bacteria will be submitted to Hydrological Sciences for co-review by NSF DEB program in December, 2014. Full proposal will be submitted in July, 2015.

b. Lu recently submitted her CAREER proposal to NSF DEB ($~750K) in July 2013. She expects the proposal will be criticized primarily on the lack of the preliminary data to demonstrate the potency of the proposed research strategy. This CFS fund will allow her to collect preliminary data that lead to a more compelling CAREER proposal.

Geo-Ecological Modeling of Riverine Habitat Occurrence and Nutrient Retention

  • April 4th, 2019
  • in News

Research Team: Jennifer Edmonds and Behzad Mortazavi, Department of Biological Sciences Sagy Cohen and Lisa Davis, Department of Geography
Amount Requested: $32,000
Project Duration: two years (6/15/13-6/14/15)

Download proposal as a printable PDF

1. Introduction

The U.S. EPA has identified accelerated nutrient (phosphate and nitrogen) loading and loss of aquatic habitat as the two primary causes of river impairment in the United States, with 55% of U.S. rivers and streams incapable of supporting healthy aquatic life due to the presence of excess nutrients and/or excess sediment (EPA, 2013). Because the number of rivers affected by non-point source nutrient contamination is so large, improving the biological integrity of American waterways requires research that can be applied at regional and continental scales, which coupled geospatial-ecological models are uniquely able to achieve. Due to this pressing need for regional to continental-scale models to address water quality issues, modeling has become an increasingly requested component of many of the current grant competitions in Biological and Geosciences NSF directorates. Thus, this proposal requests funds for the development of a model that addresses nutrient retention in rivers, and highlights the importance of habitat frequently lost to river regulation. The funds we request here are critical to successfully competing for larger, external competitions in the future. Our ideas progressed from several synergistic activities amongst team members:

  • The awarding of a UA research stimulation 2-year postdoctoral grant to our team in January, 2013, for the explicit purpose of addressing the objectives listed below. The post-doc fellow will arrive at UA this fall, 2013. The award only covers the cost of the post-doc salary.
  • A manuscript in press in Ecology that was co-authored by Jennifer Edmonds (Dept. of Biology) and Behzad Mortazavi (Dept. of Biology) measuring microbial N retention in the Cahaba River.
  • Work by two Davis graduate students (Edmonds and Cohen serving as committee members) exploring geologic constraints on Cahaba River shoal formation, and fine sediment transport and storage associated with plant growth.
  • 2. Statement of Research Objectives

The proposed research has two objectives to be completed initially in the Cahaba River, AL: (1) developing a geomorphic numerical model using geospatial technology to understand and predict bedrock shoal formation and occurrence (Fig. 1) and, (2) integrating the geomorphic numerical model with inchannel measurements of nitrogen (N) retention both within the shoals and Coastal Plain river portions.

3. Summary of Research Design and Respective Facutly Contributions

Objective 1

Within this objective we will first develop a geo-spatial model that predicts the occurrence of shoal habitat in the Cahaba River (Fig. 1). Bedrock shoals are renowned for their biodiversity (Argentina et al 2010, Davenport 1996, Lydeard et al 2004), but despite being such biologically rich areas worthy of conservation, existing research, of which there is very little, has been limited to the formation of alluvial shoals (Duncan et al., 2009). To date, no one has ever completed work on bedrock shoal formation or the ecosystem services (such as excess nutrient removal) they provide. Davis and her student recently developed a statistical model capable of correctly predicting the location of bedrock outcroppings that form shoals in the Cahaba River with 96% accuracy based on rock strike and its orientation relative to streamflow direction and rock integrity (Bishop, 2013). Davis is currently working with her students to measure sub-meter scale geologic and geomorphic factors including (a) the influence of rock void space available for root development on macrophyte patch density and (b) sediment trapping by shoal macrophytes. Davis and students are also currently making system-wide measurements of rock dip to examine its effect (if any) on shoal width, which could influence patch density. Summer graduate student support is requested to help complete this portion of the research, which will not only support the geophysical portion of the model but will also aid in the biogeochemical characterization of the shoals. Edmonds’ lab found a direct correlation between the ability of shoal plants to encourage N retention and the density of the rooting zone of a plant patch, therefore relationships found between rock void space, sediment trapping, and macrophypte density will be directly linked to N retention in the shoals through our computer modeling.

Dr. Cohen will work with Davis and the post-doc to build a computer model predicting bedrock shoal occurrence for the Cahaba River, eventually applying it in other watersheds to identify shoal habitat, both current and former, in rivers across the eastern U.S. Modeling shoal distribution would broaden our appreciation of the habitat loss due to damming, as well as suggest possible habitat and ecosystem services that could be gained from dismantling old dams on rivers with geomorphologic and geologic conditions favoring shoal formation. This modeling effort would also include quantifying the distribution of Coastal Plain river habitat, as previous work by Edmonds and Mortazavi (Tatariw et al 2013) found fine benthic sediments in these rivers were “hot spots” of nitrogen (N) retention via denitrification (conversion of nitrate to N2 (g) by microbes), and therefore important for evaluating linkages between geomorphic structure and excess nutrient removal in large river ecosystems (Obj. 2). Funds are requested for a mid-range computer for the new post-doc and geospatial software packages essential for completing this goal.

Objective 2

Objective 2 will focus on the biological implications of variation in geomorphic structure in the Cahaba River, to link N retention to changes in geomorphology as rivers move from the Valley and Ridge physiographic province onto the Coastal Plain. Drs. Mortazavi and Edmonds will guide the design and implementation of this work, comparing several important N retention processes mediated by microorganisms in both shoal and Coastal Plain river sediments using stable isotope (15N) tracers added to intact sediment cores to determine rates of N removal. The movement of 15N between inorganic, organic, and gaseous forms would be determined within the intact sediment cores using a mass inlet mass spectrometer (MIMS) housed in Dr. Mortazavi’s laboratory at Dauphin Island Sea Lab (DISL). The goal is to develop empirical relationships (i.e., Fig. 2) that would inform our modeling efforts, linking geomorphic structure and N removal in rivers. Funds are requested for lab supplies to conduct these analyses. To scale up our conceptual ideas on N-retention capacity of the Cahaba River stretching from Helena, AL, to its junction with the Alabama River (~200 river kilometers), we are requesting CFS funds to purchase a self-contained YSI sensor that can be deployed in the field to measure several water chemistry parameters simultaneously (nitrate, chlorophyll a, turbidity, temperature, and conductivity). Large-scale changes in water chemistry along the river can then be measured in “realtime” to allow us to look for spatial and temporal patterns suggesting nutrient retention mechanisms functioning at this large spatial scale. This is a unique opportunity for ecological processing along the river to be “scaled up” such that funding agencies can better appreciate the broader importance of this work, and increase our ability to earn grants. Funds are requested to increase the impact of this research through conference presentations and publications.

4. External Funding Opportunities Strengthened

An NSF proposal will be submitted in July, 2013, to the Geomorphology Landuse Dynamics program. This CFS funding would decrease the budget request for this proposal by covering a portion of the equipment costs, making the proposal more competitive. $450,000

An NSF pre-proposal will be submitted to the Ecosystems Panel for co-review by Geography Spatial Science in Jan., 2014. Full proposal submissions in July, 2014. CFS funding would allow us to collect additional data for inclusion, making our submission more competitive. $700,000

5. Budget and Budget Justification

$13,000 YSI data sondes, which includes a five port sensor platform for measuring water column nitrate, conductivity, temperature, pH, chlorophyll a, and turbidity. Cost also includes calibration/storage chamber, maintenance kit, power pack, weight kit, and 50-foot cable.

$6,893 Funds to support a masters student for four months (15 June-15 Aug, 2013 & June, July 2014). Salary will be $1,600/month with fringe at 7.7% x salary ($555 for 4 months).

$3,000 Computer for the new post-doc, including a 2.9GHz Quad-core Intel Core i5, 16GB 1600MHz DDR3 SDRAM, 3TB Serial ATA Drive @ 7200 rpm, and a time capsule 3TB

$1,000 Computer software (MATLAB, Adobe Illustrator and Photoshop, Microsoft Visual Studio) $5,000 Travel funds for the post-doctoral fellow to attend the annual meeting of the American Geophysical Union (AGU) in San Francisco, and a second meeting at a more ecology-focused meeting (ASLO, ESA, or SFS). Total of 3 meetings for two years.

$3,107 Supplies for water chemistry and MIMS analyses. Includes facility costs for water chemistry parameters, as well as stable isotope measurements at an off-campus facility. Will also cover costs for reagents, sampling containers, gas tanks for the instruments, etc.

6. Research Timeline

Summer 2013 Fall 2013 Spring 2014 Summer 2014 Fall 2014 Spring 2015 Summer 2015
Objective 1 data collection x x x
Objective 2 data collection x x x
Meeting presentations x x x
Model development x x x x x x
Proposal submission x x x x

7. References Cited

Argentina JE, Freeman MC, Freeman BJ (2010). The response of stream fish to local and reach-scale variation in the occurrence of a benthic aquatic macrophyte. Freshwater Biology 55: 643-653.

Bishop, J, (2013). Geomorphic and geologic controls determining the distribution of bedrock shoals in the Cahaba River of Alabama, unpublished Master’s thesis, University of Alabama.

Davenport LJ (1996). The Cahaba lily: its distribution and status in Alabama. Journal of the Alabama Academy of Science 67: 222-233.

Duncan, W, Poole, GC, and Meyer, JL, (2009). Large channel confluence influence geomorphic heterogeneity of a southeastern United States river. Water Resources Research, 45:W10405, 1-9. doi:10.1029/2008WR007454. EPA, (2013). National Rivers and Streams Assessment (NRSA) 2008-2009 Draft Report, Accessed on March 1, 2013.

Lydeard C, Cowie RH, Ponder WF, Bogan AE, Bouchet P, Clark SA et al (2004). The global decline of nonmarine mollusks. Bioscience 54: 321-330.

Tatariw C, Chapman E, Sponseller R, Mortazavi B, Edmonds J (2013). Denitrification in a mid-sized river: interactions between geomorphology and microbial community structure. In press, Ecology

Travel to Joint Aquatic Sciences Meeting (JASM), Portland, OR, May 2014

  • April 4th, 2019
  • in News

Travel support for 10 graduate students ($1000 each) to attend and give presentations at the Joint Aquatic Sciences Meeting (JASM). The theme of the meeting was “ Bridging Genes to Ecosystems: Aquatic Science at a Time of Rapid Change”.

See meeting website at

Students supported for travel awards to Joint Aquatic Sciences Meeting (JASM) and (major advisor):

  • Bernard, Rebecca (Mortazavi)
  • Garcia-Soto, Gabriela (Lopez-Bautista)
  • Chapman, Elise (Edmonds)
  • Jones, Joshua (Cherry)
  • Davis, William (Powell)
  • Kendrick, Michael (Huryn)
  • Demi, Lee (Benstead)
  • Melton, James (Lopez-Bautista)
  • DePriest, Scotty (Lopez-Bautista)
  • Nelson, Daniel (Benstead)