Dr. Ruth Carmichael

Dr. Ruth Carmichael


Professor, University of South Alabama
Senior Marine Scientist III, Dauphin Island Sea Lab
Ph.D. 2004, Boston University


Emphasis: Marine Ecosystem Response

Research Interests

My research focuses on marine ecosystem responses; understanding relationships between organisms and their environment and specific biological and physiological responses to environmental change.  In particular, I am interested in the mechanisms by which anthropogenic-driven perturbations affect coastal habitats and species.  I give special focus to commercially important coastal bivalves, horseshoe crabs, manatees and dolphins.

I use a variety of approaches to make these assessments.  I measure how perturbations affect habitat and food quality for consumers, and then determine the extent to which these effects may be transferred up coastal food webs in terms of change in growth, survival, and physiology.  I also employ natural abundance stable isotopes to trace N and C sources from consumers to their food sources and ultimately to N and C sources from land.  I use this information to discern trophic interactions, define linkages between anthropogenic factors and organism responses, assess nutritional importance of food sources, discern physiological state of organisms, and historically trace responses to environmental change.

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Current Research Grants

National Fish and Wildlife Foundation (NFWF) - Alabama Marine Mammal Conservation and Recovery Program. 2015-2020

Alabama Division of Wildlife and Freshwater Fisheries - Aerial mapping of manatee thermal refugia in Alabama waters: Defining essential habitat. 2015-2017

U.S. Fish and Wildlife Service - Decadal scale documentation of endangered West Indian manatee habitat use in the northern Gulf of Mexico west of Florida. 2016-2018

WHOI Sea Grant Program - A history of mercury impacts to Waquoit Bay, MA clams. 2014-2017


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Cloyed, C.S., K.P. DaCosta, M.R. Hodanbosi, and R.H. Carmichael. The effects of lipid extraction on δ13C and δ15N values and use of lipid-correction models across tissues, taxa and trophic groups. Methods Ecol Evol. 00:1-12. DOI: 10.1111/2041-210X.13386.

Deming, A.C., N.L. Wingers, D. P. Moore, D. Rotstein, R. S. Wells, R. Ewing, M. R. Hodanbosi, and R. H. Carmichael. Health Impacts and Recovery From Prolonged Freshwater Exposure in a Common Bottlenose Dolphin (Tursiops truncatus) Front. Vet. Sci.. Vol. 7(235). doi.org/10.3389/fvets.2020.00235.

Collins, M.K., R.H. Carmichael, D.S. Rotstein, J.H. Byrd, and A.C. Deming. Suspected broadhead arrow injuries in two common bottlenose dolphins (Tursiops truncatus) along the Alabama Coast. Marine Mammal Science. DOI: 10.1111/mms.12667.

Hays, G.C., H. Bailey, S.J. Bograd, W.D. Bowen, C. Campagna, R.H. Carmichael, and et. al.. Translating Marine Animal Tracking Data into Conservation Policy and Management Trends in Ecology & Evolution. 2491. doi.org/10.1016/j.tree.2019.01.009.
Gancel, H.N., R.H. Carmichael, K. Park, J.W. Krause, and S. Rikard. Field Mark-Recapture of Calcein-Stained Larval Oysters (Crassostrea virginica) in a Freshwater-Dominated Estuary. Estuaries and Coasts. doi.org/10.1007/s12237-019-00582-6.
Sequeira, A.M.M., M.R. Heupel, M.-A. Lea, V.M. Eguiluz, C.M. Duarte, M.G. Meekan, M. Thums, H.J. Calich, R.H. Carmichael, D.P. Costa, L.C. Ferreira, J. Fernandez-Garcia, R. Harcourt, A.-L. Harrison, I. Jonsen, C.R. McMahon, D.W. Sims, R.P. Wilson, and G.C. Hays. The importance of sample size in marine megafauna tagging studies. Ecological Applications. 0(0). e01947.

Cloyed, C.S., E.E. Hieb, M.K. Collins, K.P. DaCosta, and R.H. Carmichael. Linking use of ship channels by West Indian Manatees (Trichechus manatus) to seasonal migration and habitat use. frontiers in Marine Science. 6:318. doi: 10.3389/fmars.2019.00318.

Murray, R., R.H. Carmichael, M.K. Collins, M.L. Russell, and A.C. Deming. Dead or Alive: Use of Elemental Analysis to Determine Status of Stranded Perinate Bottlenose Dolphins (Tursiops truncatus). Gulf and Caribbean Research. Vol. 30 (1)

Patterson, H.K. and R.H. Carmichael. Dissolved oxygen concentration affects Delta 15N values in oyster tissues: implications for stable isotope ecology Ecosphere. Volume9(3). Article e02154.

Grüss, A., M.D. Drexler, C.H. Ainsworth, J.J. Roberts, R.H. Carmichael, N.F. Putman, P.M. Richards, E. Chancellor, E.A. Babcock, and M.S. Love.. Improving the spatial allocation of marine mammal and sea turtle biomasses in spatially explicit ecosystem models. Marine Ecology Progress Series. Vol. 602: 255–274.

D'Ambra, I., W.M. Graham, R.H. Carmichael, F.J. Hernandez, Jr.. Dietary overlap between jellyfish and forage fish in the northern Gulf of Mexico. Marine Ecology Progress Series. Vol. 587; 31-40.

Sequeira, A. M. M., J. Rodríguez, V. Eguíluz, R. Harcourt, M. Hinde, D. Sims, C. Duarte, D. Costa, Fernández-Gracia, L. Ferreira, G. Hays, M. Heupe, M. Meekan, A. Aven, F. Bailleul, A. Baylis, M. Berumen, C. Braun, J. Burns, J. Caley, R. Campbell, R. H. Carmichael, et al.. Convergence of marine megafauna movement patterns in coastal and open oceans PNAS. p.201716173.

Darrow, E. S., R. H. Carmichael, C. F. T. Andrus, H. E. Jackson. From middens to modern estuaries, oyster shells sequester source-specific nitrogen. Geochimica et Cosmochimica Acta 202:39-56

Krause, J., E. Darrow, R. Pickering, R. H. Carmichael, A. Larson, J. Basaldua. Reactive Silica Fractions in Coastal Lagoon Sediments from the Northern Gulf of Mexico. Cont. Shelf Res. 151(2017):8-14. doi: 10.1016/j.csr.2017.09.014
Hohn, A., L. Thomas, C. Booth, R. H. Carmichael, J. Litz, D. Shannon, S. Shippee, C. Sinclair, S. Smith, T. R. Speakman, M. Tumlin, E. Zolman.. Assigning Stranded Dolphins to Stock using Stable Isotope Ratios following the Deepwater Horizon Oil Spill. Endanger. Species Res. 33:235-252.

Hieb, E.E., R.H. Carmichael, A. Aven, C. Nelson-Seely, N. Taylor. . Sighting demographics of the West Indian manatee (Trichechus manatus) in the north central Gulf of Mexico. Endangered Species Research 32:321-332

Fauquier, D. A., J. Litz, S. Sanchez, K. Colegrove, L. Schwacke, L. Hart, J. Saliki, C. Smith, T. Goldstein, S. Bowen-Stevens, W. McFee, E. Fougeres, B. Mase-Guthrie, E. Stratton, R. Ewing, S. Venn-Watson, R. H. Carmichael, C. Clemons-Chevis, D. Shannon, S. Shippee, S. Smith, L. Staggs, M. Tumlin, N. Wingers, T. Rowles. Evaluation of Morbillivirus Exposure in Cetaceans from the Northern Gulf of Mexico 2010-2014. Endangered Species Research, 33:211-220.

Oczkowski, A., T. Gumbley, B. Carter, R. Carmichael, A. Humphries. . Frontiers in Marine Science Frontiers Mar Sci. DOI:10.3389/fmars.2016.00079.

Colegrove, K., S. Venn-Watson, J. Litz, M. J. Kinsel, K. A. Terio, E. Fougeres, Ruth Ewing, D. A. Pabst, W. A. McLellan, S. Raverty, J. Saliki, S. Fire, G. Rappucci, S. Bowen-Stevens, L. Noble, A. Costidis, M. Barbieri, C. Field, S. Smith, R. H. Carmichael, C. Chevis, W. Hatchett, D. Shannon, M. Tumlin, G. Lovewell, W. McFee, T. Rowles. Fetal distress and in utero Brucella pneumonia in perinatal bottlenose dolphins (Tursiops truncatus) during the Northern Gulf of Mexico unusual mortality event: 2010 through 2013 Dis. Aquat. Org. 119:1-16

Darrow, E. S., R. H. Carmichael, K. R. Calci, W. Burkhardt III. Land-use related changes to sedimentary organic matter in tidal creeks of the northern Gulf of Mexico Limnol. Oceanogr. 10.1002/lno.10453

Patterson H. K., R. H. Carmichael. The effect of lipid extraction on carbon and nitrogen stable isotope ratios in oyster tissues: Implications for glycogen‐rich species Rapid Commun. Mass Sp. 30(24):2594-600.

2015                Dalrymple, J. D. and R. H. Carmichael*. Effects of age class on N removal capacity of oysters and implications for bioremediation. MEPS 528: 205-220. (G)

2015                Venn-Watson, S., K. M. Colegrove, J. Litz, M. Kinsel, K. Terio, J. Saliki, S. Fire, R. H. Carmichael, C. Chevis, W. Hatchett, J. Pitchford, M. Tumlin, C. Field, S. Smith, R. Ewing, D. Fauquier, G. Lovewell, H. Whitehead, D. Rotstein, W. McFee, E. Fougeres, T. Rowles. Adrenal Gland and Lung Lesions in Gulf of Mexico Common Bottlenose Dolphins (Tursiops truncatus) Found Dead following the Deepwater Horizon Oil Spill. PLoS ONE. 10(5): e0126538. DOI:10.1371/journal.pone.0126538

2015                Venn-Watson, S., L. Garrison, J. Litz, E. Fougeres, B. Mase, G. Rappucci, E. Stratton, R. H. Carmichael, D. Odell, D. Shannon, S. Shippee, S. Smith L. Staggs, M. Tumlin, H. Whitehead, T. Rowles. Demographic clusters identified within the northern Gulf of Mexico common bottlenose dolphin (Tursiops truncatus) unusual mortality event: January 2010- June 2013. PLoS ONE. 10(2): e0117248. doi:10.1371/journal.pone.0117248

2015                D'Ambra, I., W. M. Graham, R. H. Carmichael, F. J. Hernandez, Jr. Fish rely on scyphozoan hosts as a primary food source: evidence from stable isotope analysis. Mar. Biol. 162:247-252. Feature Article, Highlighted in Harrod 2015 Mar. Biol. Editorial 162:245-246. (G)

2014                Aven, A., R. H. Carmichael, M. Ajemian, S. Powers. Passive acoustic monitoring mitigates GPS tag loss by tracked manatees. Mar. Freshwater Res. Published online 26 Nov 2014 (G)

2014                Kellogg L., A. Smyth, M. W. Luckenbach, R. H. Carmichael, B. L. Brown, J. C. Cornwell, Michael F. Piehler, M. S. Owens, D. J. Dalrymple, C. Higgins. Use of oysters to mitigate eutrophication in coastal waters. Est Coast Shelf Sci. 151:156-168.

2014                Litz, J., M. Baran, R. H. Carmichael, K. Colegrove, S. Fire, E. Fougeres, R. Hardy, S. Holmes, W. Jones, B. MaseGuthrie1, D. Odell, P. Rosel, D. Shannon, J. Saliki, S. Shippee, S. Smith, E. Stratton, S. BowenStevens, M. Tumlin, H. Whitehead, G. Worthy, T. Rowles. A review of historical unusual mortality events in the Gulf of Mexico (1990-2009): providing context for the complex and long-lasting Northern Gulf of Mexico Cetacean UME. Dis. Aquat. Org. 112:161-175.

2014                Patterson H. K., A. Boettcher, R. H. Carmichael. Biomarkers of dissolved oxygen stress in oysters: A tool for restoration and management efforts. PLoS ONE 9(8): e104440. DOI:10.1371/journal.pone.0104440.(G)

2014                Martin, J., H. Edwards, F. Bled, C. Fonnesbeck, J. Dupuis, B. Gardner, S. Koslovsky, A. Aven, L. Ward-Geiger, R. H. Carmichael, D. Fagan, M. Ross, and J. Royle. Maximum number of manatees in areas potentially affected by the Gulf oil spill. PLoS ONE 9(3): e91683. DOI:10.1371/journal.pone.0091683.

2014                D’Ambra, I., R. H. Carmichael, W. M. Graham. Determination of δ13C and δ15N and trophic fractionation in jellyfish: implications for food web ecology. Mar. Biol. 161:473-480. (G)

2013                D'Ambra, I., W. M. Graham, R. H. Carmichael, A. Malej, V. Onofri. Predation patterns and prey quality of medusae in a semi-enclosed marine lake: implications for food web energy transfer in coastal marine ecosystems. J. Plankton Res. 35:1305-1312. DOI: 10.1093/plankt/fbt065. (G)

2012                Carmichael, R. H.* A. Jones, H. Patterson, W. Walton, A. Pérez-Huerta, E. Overton, M. Dailey, K. Willett. Assimilation of oil-derived elements by oysters due to the Deepwater Horizon oil spill. Environ. Sci. Technol. 46:12787-12795.  DOI: 10.1021/es302369h Featured by Gulf of Mexico Research Initiative http://gulfresearchinitiative.org/studies-indicate-that-oyster-tissue-and-shell-were-similar-in-pre-and-post-oil-spill-conditions/

2012                Prado, P., R. H. Carmichael, S. Watts, J. Cebrian, and K. L. Heck, Jr. Diet-dependent δ13Cand δ15N fractionation among sea urchin (Lytechinus variegatus) tissues: Implications for food web models. Mar. Ecol. Prog. Ser. 462:175-190.

2012                Carmichael, R. H.*, W. Graham, A. Aven, G. Worthy, S. Howden. Were multiple stressors a ‘perfect storm’ for northern Gulf of Mexico bottlenose dolphins in 2011? PloS ONE 7(7): e41155. doi:10.1371/journal.pone.0041155.  Featured in Nature News http://www.nature.com/news/perfect-storm-hit-gulf-of-mexico-dolphins-1.11011

2012                Carmichael, R. H.*, W. Walton, H. Clark. Bivalve enhanced N removal from coastal estuaries. Can. J. Fish. Aquat. Sci. 69:1131-1149.

2012                Carmichael, R.H.*, A. Shriver, and I. Valiela. Bivalve response to estuarine eutrophication: The balance between enhanced food supply and habitat alternations. J. Shellfish Res. 31: 1-11.

2012                Carmichael, R. H.* and E. Brush. Three decades of horseshoe crab rearing: A review of conditions for captive growth and survival. Rev. Aquac. 4: 32-43.

2012                Biancani, P. J., R. H. Carmichael*, J. H. Daskin, K. R. Calci, W. Burkhardt III. Seasonal and spatial effects of wastewater effluent on growth, survival, and accumulation of microbial contaminants by oysters in Mobile Bay, Alabama. Est Coasts. 35:121-131. CESN highlight article. (G)

2012                Drymon, J. M., S. P. Powers, R. H. Carmichael. Trophic plasticity in the Atlantic sharpnose shark (Rhizoprionodon terraenovae) from the north central Gulf of Mexico. Environ. Biol. Fish. 95:21-35.

2010                Graham, W., R. H. Condon, R. H. Carmichael, I. D’Ambra, H. K. Patterson, F. J. Hernandez, Jr. Oil carbon entered the coastal planktonic food web during the Deepwater Horizon oil spill. Environ. Res. Lett. 5(045301):1-6. 2010 Highlight.

2010                Kovacs, C., J. Daskin, H. Patterson, R. H. Carmichael*. Crassostrea virginica shells record local variation in wastewater inputs to a coastal estuary. Aquatic Biol. 9:77-84.  (U)

2009                Pabody, C., R. H. Carmichael*, L. Rice, M. Ross.  West Indian manatees in Mobile Bay, Alabama:  A new sighting network adds to twenty years of historical data on extralimital populations. Gulf Mexico Sci. 27:52-61.  (T)

2009                Carmichael, R. H.*, E. Gaines, Z. Sheller, A. Tong, A. Clapp, I. Valiela. Diet composition of juvenile horseshoe crabs: Implications for growth and survival of natural and cultured stocks, p. 521-534. In J. Tanacredi, M. Botton, D. Smith [eds.], Biology and Conservation of Horseshoe Crabs. Springer, New York.

2009                Smith, D., M. Millard, R. H. Carmichael. Status and assessment of Limulus polyphemus along the western Atlantic. p. 361-386. In J. Tanacredi, M. Botton, D. Smith [eds.], Biology and Conservation of Horseshoe Crabs. Springer, New York.

2008                Carmichael, R. H.*, T. Hattenrath, I. Valiela, R. H. Michener. Nitrogen stable isotopes in the shell of Mercenaria mercenaria trace wastewater inputs from watersheds to estuarine ecosystems. Aquatic Biol. 4:99-111. Feature Article.

2008                Daskin, J. H., K. Calci, W. Burkhardt, III, R. H. Carmichael*. Use of N stable isotope and alternative microbial analysis to define wastewater influence in Mobile Bay, AL. Mar. Pollut. Bull. 56:860-868.  (U)

2007                Bowen, J., K. Kroeger, G. Tomasky, W. J. Pabich, , M. L. Cole, R. H. Carmichael, I. Valiela. A review of land-estuary coupling by groundwater discharge to New England estuaries:  Mechanisms and effects. Applied Geochemistry. 22:175-191.

2005                Carmichael, R. H.* and I. Valiela. Coupling of near-bottom seston and surface sediment composition: Changes with nutrient enrichment and implications for estuarine food supply and biogeochemical processing. Limnol. Oceanogr. 50:97-105.

2004                Carmichael, R. H.*, A. Shriver, I. Valiela. Changes in shell and soft tissue growth, tissue composition, and survival of quahogs, Mercenaria mercenaria, and softshell clams, Mya arenaria, in response to eutrophic-driven changes in food supply and habitat. J. Exp. Mar. Biol. Ecol. 313: 75-104.

2004                Rutecki, D., R. H. Carmichael, I. Valiela.  Magnitude of harvest of Atlantic horseshoe crabs, Limulus polyphemus, in Pleasant Bay, MA. Estuaries 27:179-187. (G)

2004                Carmichael, R. H.*, B. Annette, I. Valiela. N loading to Pleasant Bay, Cape Cod:  Application of models and stable isotopes to detect incipient nutrient enrichment of estuaries. Mar. Pollut. Bull. 48: 137-143.

2004                Carmichael, R. H.* Effects of eutrophication on Mya arenaria and Mercenaria mercenaria: Growth, survival, and physiological responses to changes in food supply and habitat in estuaries receiving different N loads. Ph.D. Thesis, Boston University.

2004                Carmichael, R. H.*, D. Rutecki, B. Annett, E. Gaines, I. Valiela.  Position of horseshoe crabs in estuarine food webs: N and C stable isotopic study of foraging ranges and diet composition. J. Exp. Mar. Biol. Ecol. 299: 231-253.

2003                Carmichael, R. H.*, D. Rutecki, I. Valiela.  Abundance and population structure of the Atlantic horseshoe crab, Limulus polyphemus, in Pleasant Bay, Cape Cod. Mar. Ecol. Prog. Ser. 246:225-239.

2003                O'Connell, C. W., S. P. Grady, A. S. Leschen, R. H. Carmichael, I. Valiela.  Stable isotopic assessment of site loyalty and relationships between size and trophic position of the Atlantic horseshoe crab, Limulus polyphemus, in Cape Cod estuaries. Biol. Bull. 205:254-255.

2002                Weiss, E., R. H. Carmichael, I. Valiela.  The effect of nitrogen loading on growth of quahogs and softshell clams through changes in food supply.  Aquaculture  211:275-289.

2002                Shriver, A. C., R. H. Carmichael, I. Valiela.  Growth, condition, reproductive potential, and mortality of bay scallops, Argopecten irradians, in response to eutrophic-driven changes in food resources. J. Exp. Mar. Biol. Ecol. 279:21-40.

2002                Gaines, E., R. H. Carmichael*, S. P. Grady, I. Valiela.  Stable isotopic evidence for changing nutritional sources of juvenile horseshoe crabs. Biol. Bull. 203:228-230. (U)

2002                Suggs, D., R. H. Carmichael, S. P. Grady, I. Valiela.  Effects of individual size on pairing in horseshoe crabs. Biol. Bull. 203: 225-227. (U)

2001                Grady, S., D. Rutecki, R. H. Carmichael, I. Valiela.  Age structure of the Pleasant Bay population of Crepidula fornicata: A possible tool for estimating horseshoe crab age. Biol. Bull. 201:296-297. (U)

2001                Fila, L., R. H. Carmichael, A. Shriver, I. Valiela.  Stable N isotopic signatures in Bay scallop tissue, feces, and pseudofeces in Cape Cod estuaries subject to different N loads. Biol. Bull. 201: 294-296. (U)

1996                Herrold R. E., A. Marchini, S. Fruehling, R. Longnecker. Glycoprotein 110 (gp110), the Epstein-Barr Virus homolog of Herpes Simplex Virus Glycoprotein B (gB), is essential for Epstein-Barr replication in vivo. J Virol. 70: 2049-2054.

1996                Fruehling S., S. K. Lee, R. E. Herrold, B. Frech, G. Laux, E. Kremmer, F. A. Grasser, R. Longnecker. Identification of Latent Membrane Protein 2A (LMP2A) domains essential for the LMP2A dominant-negative effect on B-lymphocyte surface immunoglobulin signal transduction. J Virol. 70: 6216-6226.

*Carmichael is corresponding author. T, G, U = Technician, graduate student, or undergraduate student as first author working under Carmichael.

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  • Marine Conservation Biology
  • Marine Invertebrate Zoology
  • Scientific Communication
  • Stable Isotope Ecology Seminar
  • Biology and Conservation of Horseshoe Crabs
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