Underwater application of quantitative PCR on an Ccean Mooring

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Preston, Christina M ^a   Harris, Adeline ^a   Ryan, John P ^a   Roman, Brent ^a   Marin, Roman ^a   Jensen, Scott ^a   Everlove, Cheri ^a   Birch, James ^a   Dzenitis, John M ^b   Pargett, Douglas ^a   Adachi, Masao ^c   Turk, Kendra ^d   Zehr, Jonathon P ^d   Scholin, Christopher A ^a  

^a MONTEREY BAY AQUARIUM RESEARCH INSTITUTE   (United States)

^b LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^c KOCHI UNIVERSITY   (Japan)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACID; DYES, REAGENTS, INDICATORS, MARKERS AND BUFFERS; PRIMER DNA; RIBOSOME RNA;

ARTICLE; BACTERIOPLANKTON; CRENARCHAEOTA; CYANOBACTERIUM; DENATURATION; DEVICE; DNA PROBE; ENVIRONMENTAL SAMPLE PROCESSOR; MARINE ENVIRONMENT; MICROFLUIDICS; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; SALINITY; SEASONAL VARIATION; SOLID PHASE EXTRACTION; SPRING; SUMMER; THERMODYNAMICS; ANIMAL; GENETICS; ISOLATION AND PURIFICATION; MARINE BIOLOGY; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEA;

CRENARCHAEOTA; CYANOBACTERIA;

ANIMALS; BASE SEQUENCE; DNA PRIMERS; DNA PROBES; INDICATORS AND REAGENTS; MARINE BIOLOGY; MICROFLUIDICS; OCEANS AND SEAS; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL; SOLID PHASE EXTRACTION;

EID: 79960940108     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0022522     Document Type: Article

References (58)

1. Giovannoni SJ, Rappe MS, (2000) Evolution, diversity, and molecular ecology of marine prokaryotes. In: Kirchman DL, editors. Microbial Ecology of the Ocean New York Wilery Interscience pp. 47-84.
2. DeLong EF, (2009) The microbial ocean from genomes to biomes. Nature 459: 200-206.
3. Zehr JP, Hewson I, Moisander PH, (2009) Molecular biology techniques and applications for ocean sensing. Ocean Sci 5: 101-113.
4. Heid CA, Stevens J, Livak KJ, Williams PM, (1996) Real time quantitative PCR. Genome Res 6: 986-994.
5. Suzuki MT, Taylor LT, DeLong EF, (2000) Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays. Appl Environ Microbiol 66: 4605-4614.
6. Suzuki MT, Preston CM, Chavez FP, DeLong EF, (2001) Quantitative mapping of bacterioplankton populations in seawater: Field tests across an upwelling plume in Monterey Bay. Aquat Microb Ecol 24: 117-127.
7. Short SM, Zehr JP, (2005) Quantitative analysis of nifh genes and transcripts from aquatic environments. Methods Enzymol 397: 380-394.
8. Smith CJ, Osborn AM, (2009) Advantages and limitations of quantitative PCR (q-PCR)-based approaches in microbial ecology. FEMS Microbiol Ecol 67: 6-20.
9. Whitman RL, Ge Z, Nevers MB, Boehm AB, Chern EC, et al. (2010) Relationship and variation of qPCR and culturable Enterococci estimates in ambient surface waters are predictable. Environmental Science & Technology 44: 5049-5054.
10. Fasham MJR, Balino BM, Bowles MC, Anderson R, Archer D, et al. (2001) A new vision of ocean biogeochemistry after a decade of the Joint Global Ocean Flux Study (JGOFS). Ambio pp. 4-31.
11. Karl DM, Dore JE, Lukas R, Michaels A, Bates NR, et al. (2001) Building the long-term picture: The U.S. JGOFS time-series programs. Oceanography 14: 6-17.
12. Karl DM, (2002) Nutrient dynamics in the deep blue sea. Trends in Microbiology 10: 410-418.
13. Paul JH, Scholin C, van Den Engh G, Perry MJ, (2007) In situ instrumentation. Oceanography 20: 58-66.
14. Bowler C, Karl DM, Colwell RR, (2009) Microbial oceanography in a sea of opportunity. Nature 459: 180-184.
15. Scholin C, Doucette G, Jensen S, Roman B, Pargett D, et al. (2009) Remote detection of marine microbes, small invertebrates, harmful algae, and biotoxins using the environmental sample processor (esp). Oceanography 22: 158-167.
16. Scholin CA, (2010) What are "Ecogenomic sensors?" - a review and thoughts for the future. Ocean Sci Discuss 6: 51-60.
17. Bruckner-Lea CJ, Tsukuda T, Dockendorff B, Follansbee JC, Kingsley MT, et al. (2002) Renewable microcolumns for automated DNA purification and flow-through amplification: From sediment samples through polymerase chain reaction. Analytica Chimica Acta 469: 129-140.
18. Belgrader P, Elkin CJ, Brown SB, Nasarabadi SN, Langlois RG, et al. (2003) A reusable flow-through polymerase chain reaction instrument for the continuous monitoring of infectious biological agents. Anal Chem 75: 3446-3450.
19. Chandler DP, Jarrell AE, (2004) Automated purification and suspension array detection of 16s rrna from soil and sediment extracts by using tunable surface microparticles. Appl Environ Microbiol 70: 2621-2631.
20. Fukuba T, Yamamoto T, Niganuma T, Fuji T, (2004) Microfabricated flow-through device for DNA amplification- towards in situ gene analysis. Chem Eng J 101: 151-156.
21. Hindson BJ, Brown SB, Marshall GD, McBride MT, Makarewicz AJ, et al. (2004) Development of an automated sample preparation module for environmental monitoring of biowarfare agents. Anal Chem 76: 3492-3497.
22. Hindson BJ, McBride MT, Makarewicz AJ, Henderer BD, Setlur US, et al. (2005) Autonomous detection of aerosolized biological agents by multiplexed immunoassay with polymerase chain reaction confirmation. Anal Chem 77: 284-289.
23. Straub TM, Dockendorff BP, QuiÒonez-DÌaz MD, Valdez CO, Shutthanandan JI, et al. (2005) Automated methods for multiplexed pathogen detection. Journal of Microbiological Methods 62: 303-316.
24. Casper ET, Patterson SS, Bhaunushali P, Farmer A, Smith M, et al. (2007) A handheld NASBA analyzer for the field detection and quantification of Karenia brevis. Harmful Algae 6: 112-118.
25. LaGier MJ, Fell JW, Goodwin KD, (2007) Electrochemical detection of harmful algae and other microbial contaminants in coastal waters using hand-held biosensors. Mar Pollut Bull 54: 757-770.
26. Hindson BJ, Gutierrez DM, Ness KD, Makarewicz AJ, Metz TR, et al. (2008) Development of an automated DNA purification module using a micro-fabricated pillar chip. Analyst 133: 248-255.
27. Regan JF, Makarewicz AJ, Hindson BJ, Metz TR, Gutierrez DM, et al. (2008) Environmental monitoring for biological threat agents using the autonomous pathogen detection system with multiplexed polymerase chain reaction. Anal Chem 80: 7422-7429.
28. Scholin CA, Massion EI, Mellinger E, Brown M, Wright DE, et al. The development and application of molecular probes and novel instrumentation for detection of harmful algae; 1998. Marine Technology Society pp. 367-370.
29. Goffredi SK, Jones WJ, Scholin CA, Marin R 3rd, Vrijenhoek RC, (2006) Molecular detection of marine invertebrate larvae. Mar Biotechnol 8: 149-160.
30. Greenfield DI, Marin R III, Jensen S, Massion E, Roman B, et al. (2006) Application of the environmental sample processor (esp) for quantifying Pseudo-nitzschia australis using ribosomal RNA-targeted probes in sandwich and fluorescent in situ hybridization. Limnology and Oceanography, Methods 4: 426-435.
31. Haywood AJS C.A., Marin R III, Steidinger KA, Heil C, Ray J, (2007) Molecular detection of the brevetoxin-producing dinoflagellate Karenia brevis and closely related species using rrna-targeted probes and a semiautomated sandwich hybridization assay. Journal of Phycology 43: 1271-1286.
32. Jones WJ, Preston CM, Marin R III, Scholin CA, Vrijenhoek RC, (2007) A robotic molecular method for in situ detection of marine invertebrate larvae. Molecular Ecology Resources 8: 540-550.
33. Greenfield DI, III RM, Doucette GJ, Mikulski C, Jensen S, et al. (2008) Field applications of the second-generation Environmental Sample Processor (ESP) for remote detection of harmful algae: 2006-2007. Limnol Oceanogr Methods pp. 667-679.
34. Doucette GJ, Mikulski GM, Jones KL, King KL, Greenfield DI, et al. (2009) Remote, subsurface detection of the algal toxin domoic acid onboard the environmental sample processor: Assay development and initial field trials. Harmful Algae 8: 880-888.
35. Preston CM, Marin R 3rd, Jensen SD, Feldman J, Birch JM, et al. (2009) Near real-time, autonomous detection of marine bacterioplankton on a coastal mooring in Monterey Bay, California, using rRNA-targeted DNA probes. Environ Microbiol 11: 1168-1180.
36. Ryan J, Greenfield D, Marin R III, Preston CM, Roman B, et al. (2011) Harmful phytoplankton ecology studies using an autonomous molecular analytical and ocean observing network. Limnol Oceanogr 56: 1255-1272.
37. Ottesen EA, Marin R III, Preston CM, Young CR, Ryan JP, et al. (2011) Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. ISME J.
38. Scholin CA, Massion EI, Wright D, Cline D, Mellinger E, et al. (2001) Aquatic autosampler device. U.S Patent Number 6187530.
39. Roman B, Scholin C, Jensen S, Marin R III, Massion E, et al. (2005) The 2nd generation Environmental Sample Processor: Evolution of a robotic underwater biochemical laboratory. OCEANS 2005 MTS/IEEE Conference Washington DC Marine Technology Society pp. 1-9.
40. Roman B, Scholin C, Jensen S, Massion E, Marin R III, et al. (2007) Controlling a robotic marine water sampler with the ruby scripting language. Journal of American Laboratory Automation 12: 56-61.
41. Tyrrell JV, Bergquist PR, Bergquist PL, Scholin CA, (2001) Detection and enumeration of Heterosigma akashiwo and Fibrocapsa japonica (Raphidophyceae) using RNA-targeted oligonucleotide probes. Phycologia 40: 457-467.
42. Ruzicka J, Marshall GD, (1990) Sequential injection: A new concept for chemical censors, process analysis and laboratory assays. Analytica Chimica Acta 237: 39-343.
43. Ahlfors C, Marshall GD, Wolcott DK, Olson DC, Van Overmeire B, (2005) Measurement of unbound bilirubin by the peroxidase test using zone fluidics. Clin Chim Acta 365: 75-85.
44. Paerl R, Turk K, Beinart R, Chavez F, Zehr JP, (in press) Seasonal change in Synechococcus and Synechococcus narB subgroup abundances at monterey bay monitoring site m0. Environmental Microbiology.
45. Scholin CA, Doucette GJ, Cambella AD, (2008) Prospects for developing automated systems for in situ detection of harmful algae and their toxins. In: Babin M, Roesler C, Cullen J, editors. Paris, France UNESCO Publishing pp. 413-462.
46. Johnson KS, Coletti LJ, (2002) In situ ultraviolet spectrophotometry for high resolution and long term monitoring of nitrate, bromide and bisulfide in the ocean. Deep-Sea Res I 49: 1291-1305.
47. Ryan JP, Johnson SB, Sherman A, Rajan K, Py F, et al. (2010) Mobile autonomous process sampling within coastal ocean observing systems. Limnol Oceanogr Methods 8: 394-402.
48. Church MJ, Short CM, Jenkins BD, Karl DM, Zehr JP, (2005) Temporal patterns of nitrogenase gene (nifh) expression in the oligotrophic North Pacific Ocean. Appl Environ Microbiol 71: 5362-5370.
49. Dong LF, Smith CJ, Papaspyrou S, Stott A, Osborn AM, et al. (2009) Changes in benthic denitrification, nitrate ammonification, and anammox process rates and nitrate and nitrite reductase gene abundances along an estuarine nutrient gradient (the Colne Estuary, United Kingdom). Appl Environ Microbiol 75: 3171-3179.
50. Santoro AE, Casciotti KL, Francis CA, (2010) Activity, abundance and diversity of nitrifying archaea and bacteria in the central California current. Environ Microbiol 12: 1989-2006.
51. Bostrom KH, Simu K, Hagstrom A, Riemann L, (2004) Optimization of DNA extraction for quantitative marine bacterioplankton community analysis. Limnol Oceanogr Methods 2: 365-373.
52. Rowan AK, Davenport RJ, Snape JR, Fearnside D, Barer MR, et al. (2005) Development of a rapid assay for determining the relative abundance of bacteria. Appl Environ Microbiol 71: 8481-8490.
53. Mincer TJ, Church MJ, Taylor LT, Preston C, Karl DM, et al. (2007) Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ Microbiol 9: 1162-1175.
54. Paerl RW, Johnson KS, Walsh RM, Worden AZ, Chavez FP, et al. (2011) Differential distributions of synechococcus subgroups across the California Current system. Front Microbio 2 (Article 59): 1-22.
55. Karner MB, DeLong EF, Karl DM, (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409: 507-510.
56. Wuchter C, Abbas B, Coolen MJ, Herfort L, van Bleijswijk J, et al. (2006) Archaeal nitrification in the ocean. Proc Natl Acad Sci U S A 103: 12317-12322.
57. Herfort L, Schouten S, Abbas B, Veldhuis MJ, Coolen MJ, et al. (2007) Variations in spatial and temporal distribution of archaea in the North Sea in relation to environmental variables. FEMS Microbiol Ecol 62: 242-257.
58. Ryan JP, McManus MA, Sullivan JM, (2010) Interacting physical, chemical and biological forcing of phytoplankton thin-layer variability in Monterey Bay, California. Continental Shelf Research 30: 7-16.