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Optics Express

Optics Express

  • Editor: Andrew M. Weiner
  • Vol. 22, Iss. 18 — Sep. 8, 2014
  • pp: 21641–21656

Aquatic laser fluorescence analyzer: field evaluation in the northern Gulf of Mexico

Alexander Chekalyuk, Andrew Barnard, Antonietta Quigg, Mark Hafez, and Yan Zhao  »View Author Affiliations

Optics Express, Vol. 22, Issue 18, pp. 21641-21656 (2014)

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The new Aquatic Laser Fluorescence Analyzer (ALFA) provides spectral and temporal measurements of laser-stimulated emission (LSE) for assessment of phytoplankton pigments, community structure, photochemical efficiency (PY), and chromophoric dissolved organic matter (CDOM). The instrument was deployed in the Northern Gulf of Mexico to evaluate the ALFA analytical capabilities across the estuarine-marine gradient. The robust relationships between the pigment fluorescence and independent pigment measurements were used to validate the ALFA analytical algorithms and calibrate the instrument. The maximal PY magnitudes, PYm = PY(1-1.35·10−4PAR)−1, were estimated using the underway measurements of PY and photosynthetically active radiation (PAR). The chlorophyll (Chl) spatial patterns were calculated using the ratio of Chl fluorescence to PY to eliminate the effect of non-photochemical quenching on the underway Chl assessments. These measurements have provided rich information about spatial distributions of Chl, PYm, CDOM, and phytoplankton community structure, and demonstrated the utility of the ALFA instrument for oceanographic studies and bio-environmental surveys. The data suggest that the fluorescence measurements with 514 nm excitation can provide informative data for characterization of the CDOM-rich fresh, estuarine, and coastal aquatic environments.

© 2014 Optical Society of America

OCIS Codes
(010.4450) Atmospheric and oceanic optics : Oceanic optics
(140.0140) Lasers and laser optics : Lasers and laser optics
(300.0300) Spectroscopy : Spectroscopy
(280.4788) Remote sensing and sensors : Optical sensing and sensors

ToC Category:
Atmospheric and Oceanic Optics

Original Manuscript: June 18, 2014
Revised Manuscript: August 15, 2014
Manuscript Accepted: August 15, 2014
Published: August 29, 2014

Virtual Issues
Vol. 9, Iss. 11 Virtual Journal for Biomedical Optics

Alexander Chekalyuk, Andrew Barnard, Antonietta Quigg, Mark Hafez, and Yan Zhao, "Aquatic laser fluorescence analyzer: field evaluation in the northern Gulf of Mexico," Opt. Express 22, 21641-21656 (2014)

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  1. A. M. Chekalyuk and M. Hafez, “Advanced laser fluorometry of natural aquatic environments,” Limnol. Oceanogr. Methods 6, 591–609 (2008). [CrossRef]
  2. A. M. Chekalyuk and M. Hafez, “Photo-physiological variability in phytoplankton chlorophyll fluorescence and assessment of chlorophyll concentration,” Opt. Express 19(23), 22643–22658 (2011). [CrossRef] [PubMed]
  3. A. M. Chekalyuk, M. Landry, R. Goericke, A. G. Taylor, and M. Hafez, “Laser fluorescence analysis of phytoplankton across a frontal zone in the California Current ecosystem,” J. Plankton Res. 34(9), 761–777 (2012). [CrossRef]
  4. A. M. Chekalyuk and M. A. Hafez, “Next generation Advanced Laser Fluorometry (ALF) for characterization of natural aquatic environments: new instruments,” Opt. Express 21(12), 14181–14201 (2013). [CrossRef] [PubMed]
  5. D. Marie, F. Partensky, S. Jacquet, and D. Vaulot, “Enumeration and cell cycle analysis of natural populations of marine picoplankton by flow cytometry using the nucleic acid stain SYBR Green I,” Appl. Environ. Microbiol. 63(1), 186–193 (1997). [PubMed]
  6. A. S. McInnes, A. K. Shepard, E. J. Raes, A. M. Waite, and A. Quigg, “Carbon and Nitrogen Fixation: Simultaneous quantification of active communities and estimation of rates using Fluorescence in situ Hybridization and Flow Cytometry,” Appl. Environ. Microbiol. (submitted).
  7. M. D. Ohman, D. L. Rudnick, A. Chekalyuk, R. E. Davis, R. A. Feely, M. Kahru, H.-J. Kim, M. R. Landry, T. R. Martz, C. L. Sabine, and U. Send, “Autonomous ocean measurements in the California Current Ecosystem,” Oceanography (Wash. D.C.) 26(3), 18–25 (2013). [CrossRef]
  8. J. I. Goes, H. R. Gomes, A. M. Chekalyuk, E. J. Carpenter, J. P. Montoya, V. J. Coles, P. L. Yager, W. M. Berelson, D. G. Capone, R. A. Foster, D. K. Steinberg, A. Subramaniam, and M. A. Hafez, “Influence of Amazon River discharge on the biogeography of phytoplankton communities in the western tropical north Atlantic,” Prog. Oceanogr. 120, 29–40 (2014), doi:. [CrossRef]
  9. J. I. Goes, H. R. Gomes, E. M. Haugen, K. T. McKee, E. J. D’Sa, A. M. Chekalyuk, D. K. Stoecker, P. J. Stabeno, S.-I. Saitoh, and R. N. Sambrotto, “Fluorescence, pigment, and microscope characterization of Bering Sea phytoplankton community structure and photosynthetic competency in the presence of a Cold Pool during summer,” http://www.sciencedirect.com/science/article/pii/S0967064513004505
  10. A. M. Chekalyuk, “Optical analysis of emissions from stimulated liquids,” Patent application WO2013116769 A1 (2013). https://www.google.com/patents/WO2013116760A1?cl=en&dq=WO2013116760+A1&hl=en&sa=X&ei=N9FKUsJ4863gA8n8gcgB&ved=0CDkQ6AEwAA
  11. A. M. Chekalyuk and M. Hafez, “Analysis of spectral excitation for measurements of fluorescence constituents in natural waters,” Opt. Express 21(24), 29255–29268 (2013). [CrossRef] [PubMed]
  12. A. Barnard, A. M. Chekalyuk, A. Derr, W. Strubhar, M. A. Hafez, J. Pearson, C. Orrico, and C. Moore, “Aquatic Laser Fluorescence Analyzer (ALFA): A new instrument for characterization of natural aquatic environments,” AGU 2012 Ocean Sciences Meeting (2012). http://www.sgmeet.com/osm2012/viewabstract2.asp?AbstractID=11217 .; see also http://www.wetlabs.com/aquatic-laser-fluorescence-analyzer-alfa .
  13. R. E. Turner and N. N. Rabalais, “Coastal eutrophication near the Mississippi River delta,” Nature 368(6472), 619–621 (1994). [CrossRef]
  14. N. N. Rabalais, W. J. Wiseman, R. E. Turner, D. Justić, B. K. Gupta, and Q. Dortch, “Nutrient changes in the Mississippi River and system responses on the adjacent continental shelf,” Estuaries 19(2), 386–407 (1996).
  15. R. E. Turner and N. N. Rabalais, “Nitrogen and phosphorus phytoplankton growth limitation in the northern Gulf of Mexico,” Aquat. Microb. Ecol. 68(2), 159–169 (2013). [CrossRef]
  16. J. B. Sylvan, A. Quigg, S. Tozzi, and J. W. Ammerman, “Eutrophication-induced phosphorus limitation in the Mississippi River plume: evidence from fast repetition rate fluorometry,” Limnol. Oceanogr. 52(6), 2679–2685 (2007). [CrossRef]
  17. J. B. Sylvan, A. Quigg, S. Tozzi, and J. W. Ammerman, “Mapping phytoplankton community physiology on a river impacted continental shelf: testing a multifaceted approach,” Estuaries Coasts 34(6), 1220–1233 (2011). [CrossRef]
  18. A. Quigg, J. B. Sylvan, A. B. Gustafson, T. R. Fisher, R. L. Oliver, S. Tozzi, and J. W. Ammerman, “Going west: nutrient limitation of primary production in the Northern Gulf of Mexico and the importance of the Atchafalaya River,” Aquat. Geochem. 17(4-5), 519–544 (2011). [CrossRef]
  19. Y. Zhao and A. Quigg, “Nutrient limitation in Northern Gulf of Mexico (NGOM): phytoplankton communities and photosynthesis respond to nutrient pulse,” PLoS ONE 9(2), e88732 (2014), doi:. [CrossRef] [PubMed]
  20. Y. R. Qian, A. E. Jochens, M. C. Kennicutt, and D. C. Biggs, “Spatial and temporal variability of phytoplankton biomass and community structure over the continental margin of the northeast Gulf of Mexico based on pigment analysis,” Cont. Shelf Res. 23(1), 1–17 (2003). [CrossRef]
  21. B. A. Schaeffer, J. C. Kurtz, and M. K. Hein, “Phytoplankton community composition in nearshore coastal waters of Louisiana,” Mar. Pollut. Bull. 64(8), 1705–1712 (2012). [CrossRef] [PubMed]
  22. R. J. Olson, A. M. Chekalyuk, and H. M. Sosik, “Phytoplankton photosynthetic characteristics from fluorescence induction assays of individual cells,” Limnol. Oceanogr. 41(6), 1253–1263 (1996). [CrossRef]
  23. D. N. Klyshko and V. V. Fadeev, “Remote determination of concentration of impurities in water by the laser spectroscopy method with calibration by Raman scattering,” Sov. Phys. Dokl. 23, 55–59 (1978).
  24. F. E. Hoge and R. N. Swift, “Airborne simultaneous spectroscopic detection of laser-induced water Raman backscatter and fluorescence from chlorophyll a and other naturally occurring pigments,” Appl. Opt. 20(18), 3197–3205 (1981). [CrossRef] [PubMed]
  25. R. J. Exton, W. M. Houghton, W. E. Esaias, R. C. Harriss, F. H. Farmer, and H. H. White, “Laboratory analysis of techniques for remote sensing of estuarine parameters using laser excitation,” Appl. Opt. 22(1), 54–64 (1983). [CrossRef] [PubMed]
  26. T. J. Cowles, R. A. Desiderio, and S. Neuer, “In situ characterization of phytoplankton from vertical profiles of fluorescence emission spectra,” Mar. Biol. 115(2), 217–222 (1993). [CrossRef]
  27. M. Vernet, B. G. Mitchell, and O. Holm-Hansen, “Adaptation of Synechococcus in situ determined by variability in intracellular phycoerythrin-543 at a coastal station off the Southern California coast, USA,” Mar. Ecol. Prog. Ser. 63, 9–16 (1990). [CrossRef]
  28. A. Bricaud, M. Babin, A. Morel, and H. Claustre, “Variability in the chlorophyll-specific absorption coefficients of natural phytoplankton: Analysis and parameterization,” J. Geophys. Res. 100(C7), 13321–13332 (1995). [CrossRef]
  29. R. Williams and H. Claustre, “Photosynthetic pigments as biomarkers oof phytoplankton populations and processes involved in the transformation of particulate organic matter at the Biotrans site (47°N, 20°W),” Deep-Sea Res. Part A, Oceanograph. Res. Papers 38, 347–355 (1991). [CrossRef]
  30. D. M. Kehoe and A. Gutu, “Responding to color: the regulation of complementary chromatic adaptation,” Annu. Rev. Plant Biol. 57(1), 127–150 (2006). [CrossRef] [PubMed]
  31. B. Palenik, “Chromatic adaptation in marine Synechococcus strains,” Appl. Environ. Microbiol. 67(2), 991–994 (2001). [CrossRef] [PubMed]
  32. A. M. Chekalyuk, F. E. Hoge, C. W. Wright, R. N. Swift, and J. K. Yungel, “Airborne test of laser pump-and-probe technique for assessment of phytoplankton photochemical characteristics,” Photosynth. Res. 66(1-2), 45–56 (2000). [CrossRef] [PubMed]
  33. P. G. Falkowski and Z. Kolber, “Variations in chlorophyll fluorescence yields in phytoplankton in the world oceans,” Aust. J. Plant Physiol. 22(2), 341–355 (1995). [CrossRef]
  34. Z. S. Kolber, O. Prasil, and P. G. Falkowski, “Measurements of variable chlorophyll fluorescence using fast repetition rate techniques: Defining methodology and experimental protocols,” Biochem. Biophys. Acta 1367(1-3), 88–106 (1998). [CrossRef] [PubMed]

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