Real-time in situ detection and quantification of bacteria in the Arctic environment

Linda Powers; Walther R. Ellis Jr.; Christopher R. Lloyd

doi:10.1142/s1793545813500387

[1] N. S. Hobson, I. Tothill, A. P. F. Turner, "Microbial detection," Biosens. Bioelectron 11, 455–477 (1996).

[2] M. Manafi, W. Kneifel, S. Bascomb, "Fluorogenic and chromogenic substrates used in bacterial diagnosis," Microbiol. Rev. 1991, 335–348 (1991).

[3] J. Oliver, "Recent findings on the viable but nonculturable state in pathogenic bacteria," FEMS Microbiol. Rev. 34, 415–425 (2010).

[4] N. Tarcea, M. Harz, P. R€osch, T. Frosch, M. Schmitt, H. Thiele, R. Hochleitner, J. Popp, "UV Raman spectroscopy — a technique for biological and mineralogical in-situ planetary studies," Spectrochim. Acta 68A, 1029–1035 (2007).

[5] M. Krause, P. R€osch, B. Radt, J. Popp, "Localizing and identifying living bacteria in an abiotic environment by a combination of Raman and fluorescence microscopy," Anal. Chem. 80, 8568–8575 (2008).

[6] M. Harz, P. R€osch, J. Popp, "Vibrational spectroscopy — a powerful tool for the rapid identifi- cation of microbial cells at the single-cell level," Cytometry 75A, 104–113 (2009).

[7] J. J. Ojeda, M. E. Romero-Gonzalez, S. A. Banwart, "Analysis of bacteria on steel surfaces using reflectance micro-Fourier transform infrared spectroscopy," Anal. Chem. 81, 6467–6473 (2009).

[8] M. S.Ammor, "Recent advances in the use of intrinsic fluorescence for bacterial identification and characterization," J. Fluorescence 17, 455–459 (2007).

[9] L. Powers, "Method and apparatus for sensing the presence of microbes," U.S. Patent 5,760, 406 (1998).

[10] L. Powers, "Method and apparatus for sensing the presence of microbes," U.S. Patent 5,968, 766 (1999).

[11] C. Estes, A. Duncan, B. Wade, C. Lloyd, W. Ellis Jr., L. Powers, "Reagentless detection of microorganisms by intrinsic fluorescence," Biosens. Bioelectron 18, 511–519 (2003).

[12] L. Powers, C. R. Lloyd, "Method and apparatus for detecting the presence of microbes and determining their physiological status," U.S. Patent 6,750, 006 (2004).

[13] L. Powers, C. R. Lloyd, "Method and apparatus for detecting and imaging the presence of biological materials," U.S. Patent 7,186, 990 B2 (2007a).

[14] L. Powers, C. R. Lloyd, "Method for detecting the presence of dormant cryptobiotic microorganisms," U.S. Patent 7,211, 377 B1 (2007b).

[15] B. Chance, The Harvey Lectures, Series 49, 1953– 1954, Academic Press, NY, pp. 145–175 (1955).

[16] B. Chance, B. Theorell, "Localization and kinetics of reduced pyridine nucleotide in living cells by micro- fluorimetry," J. Biol. Chem. 2234, 3044–3050 (1959).

[17] L. Duysens, J. Amesz, "Fluorescence spectrophotometry of reduced phosphopyridine nucleotide in intact cells in the near-ultraviolet and visible regions," Biochim. Biophys. Acta 24, 19–26 (1957).

[18] A. Alimova, A. Katz, H. E. Savage, M. Shah, G. Minko, D. V. Will, R. B. Rosen, S. A. McCormick, R. R. Alfano, "Native fluorescence and excitation spectroscopic changes in Bacillus subtilis and Staphylococcus aureus bacteria subjected to conditions of starvation," Appl. Opt. 42, 4080–4087 (2003).

[19] J. Lackowicz, Topics in Fluorescence Spectroscopy, Vol. 3, Plenum Press, New York (1991).

[20] K. Ka tovska, J. Elster, M. Stibal, H. antruckova, "Microbial assemblages in soil microbial succession after glacial retreat in Svalbard (high Arctic)," Microb. Ecol. 50, 396–407 (2005).

[21] S. M. Cheng, J. M. Foght, "Cultivation-independent and -dependent characterization of bacteria resident beneath John Evans glacier," FEMS Microbiol. Ecol. 59, 318–330 (2007).

[22] K. Katovska, M. Stibal, M. abacka, B. Cerna, H. antruckova, J. Elster, "Microbial community structure and ecology of subglacial sediments in two polythermal Svalbard glaciers characterized by epi- fluorescence microscopy and PLFA," Polar Biol. 30, 277–287 (2007).

[23] B. Lanoil, M. Skidmore, J. C. Priscu, S. Han, W. Foo, S. W. Vogel, S. Tulaczyk, H. Engelhardt, "Bacteria beneath the West Antarctic Ice Sheet," Environ. Microbiol. 11, 609–615 (2009).

[24] J. L. Wadham, S. Bottrell, M. Tranter, R. Raiswell, "Stable isotope evidence for microbial sulphate reduction at the bed of a polythermal high Arctic glacier," Earth Planet. Sci. Lett. 219, 341–355 (2004).

[25] S. Chakravorty, D. Helb, M. Burday, N. Connell, D. Alland, "A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria," J. Microbiol. Methods 69, 330–339 (2007).

[26] R. Atlas, Handbook of Media for Environmental Microbiology, 2nd edition, p. 634, Taylor & Francis, Boca Raton, FL (2005).

[27] L. Powers, C. R. Lloyd, "Method and apparatus for detecting the presence of microbes with frequency modulated multiwavelength intrinsic fluorescence," U.S. Patent 7,824, 883 (2010).

[28] B. R. Copeland, M. Chen, B. D. Wade, L. S. Powers, "A noise-driven strategy for background estimation and event detection in data streams," Signal Process. 86, 3739–3751 (2006).

[29] M. Sharp, J. Parkes, B. Craig, I. J. Fairchild, H. Lamb, M. Tranter, "Widespread bacterial populations at glacier beds and their relationship to rock weathering and carbon cycling," Geology 27, 107–110 (1999).

[30] M. L. Skidmore, J. Foght, M. J. Sharp, "Microbial life beneath a high Arctic glacier," Appl. Environ. Microbiol. 66, 3214–3220 (2000).

[31] J. A. Mikucki, A. Pearson, D. T. Johnston, A. V. Turchyn, J. Farquhar, D. P. Schrag, A. D. Anbar, J. C. Priscu, P. A. Lee, "A contemporary microbially maintained subglacial ferrous `ocean'," Science 324, 397–400 (2009).

[32] T. N. Srinivas, S. S. N. Rao, P. V. V. Reddy, M. S. Pratibha, B. Sailaja, B. Kavya, K. K. Hara, Z. Begum, S. M. Singh, S. Shivaji, "Bacterial diversity and bioprospecting for cold-active lipases, amylases and proteases, from culturable bacteria of Kongsfjorden and Ny-Alesund, Svalbard. Arctic," Curr. Microbiol. 59, 537–547 (2009).

[33] J. Foght, J. Aislabie, S. Turner, C. E. Brown, J. Ryburn, D. J. Saul, W. Lawson, "Culturable bacteria in subglacial sediments and ice from two southern hemisphere glaciers," Microb. Ecol. 47, 329–340 (2004).