Development and comparison of SYBR Green quantitative real-time PCR assays for detection and enumeration of sulfate-reducing bacteria in stored swine manure

Journal of Applied Microbiology

Volumn 105, Issue 6, 2008, Pages 2143-2152

  Spence, C ^a,b   Whitehead, T R ^a   Cotta, M A ^a  

^a NATIONAL CENTER FOR AGRICULTURAL UTILIZATION RESEARCH   (United States)

^b U S DEPARTMENT OF AGRICULTURE   (United States)

Author keywords

dsrA; Real time PCR; Sulfate reducing bacteria; Swine manure; SYBR Green

Indexed keywords

BACTERIA; ECOSYSTEMS; FERTILIZERS; POLYMERASE CHAIN REACTION; SULFUR COMPOUNDS;

DETECTION AND ENUMERATIONS; DISSIMILATORY SULPHITE REDUCTASE GENE; PRIMER SETS; REAL-TIME PCR; REAL-TIME PCR ASSAY; REDUCTASE GENES; SULFITE REDUCTASE; SULPHATE REDUCING BACTERIA; SWINE MANURE; SYBR GREEN;

MANURES;

SULFITE REDUCTASE; SULFUR;

BIOASSAY; COMPARATIVE STUDY; DETECTION METHOD; MANURE; MICROBIAL COMMUNITY; PIG; POLYMERASE CHAIN REACTION; REAL TIME; SPECIES DIVERSITY; SULFATE-REDUCING BACTERIUM;

ARTICLE; BACTERIAL GENE; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; CLONE; CONTROLLED STUDY; DESULFOBULBUS; DESULFOVIBRIO; DIETARY INTAKE; ECOSYSTEM; GENE SEQUENCE; GENETIC VARIABILITY; MANURE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; QUANTITATIVE ASSAY; REAL TIME POLYMERASE CHAIN REACTION; RELIABILITY; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SULFATE REDUCING BACTERIUM; SWINE;

DESULFOBULBUS; DESULFOBULBUS SP.; DESULFOVIBRIO SP.; SUIDAE;

EID: 56649086758     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2008.03900.x     Document Type: Article

References (37)

1. Amann, R.I., Ludwig, W. Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59, 143.
2. Clark, O.G., Morin, B., Zhang, Y., Sauer, W.C. Feddes, J.J. (2005a) Preliminary investigation of air bubbling and dietary sulfur reduction to mitigate hydrogen sulfide and odor from swine waste. J Environ Qual 34, 2018 2023.
3. Clark, O.G., Moehn, S., Edeogu, I. Leonard, J. (2005b) Manipulation of dietary protein and nonstarch polysaccharide to control swine manure emissions. J Environ Qual 34, 1461 1466.
4. Cook, K.L., Whitehead, T.R., Spence, C. Cotta, M.A. (2008) Evaluation of the sulfate-reducing bacterial population associated with stored swine slurry. Anaerobe 14, 172 180.
5. Cotta, M.A., Whitehead, T.R. Zeltwanger, R.L. (2003) Isolation, characterization and comparison of bacteria from swine faeces and manure storage pits. Environ Microbiol 5, 737 745.
6. Dhillon, A., Teske, A., Dillon, J., Stahl, D.A. Sogin, M.L. (2003) Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Appl Environ Microbiol 69, 2765 2772.
7. Donham, K.J. (2000) The concentration of swine production. Effects on swine health, productivity, human health, and the environment. Vet Clin North Am Food Anim Pract 16, 559 597.
8. Foti, M., Sorokin, D.Y., Lomans, B., Mussman, M., Zacharova, E.E., Pimenov, N.V., Kuenen, J.G. Muyzer, G. (2007) Diversity, activity, and abundance of sulfate-reducing bacteria in saline and hypersaline soda lakes. Appl Environ Microbiol 73, 2093 2100.
9. Harms, G., Layton, A.C., Dionisi, H.M., Gregory, I.R., Garrett, V.M., Hawkins, S.A., Robinson, K.G. Sayler, G.S. (2003) Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant. Environ Sci Technol 37, 343 351.
10. Hill, J.E., Hemmingsen, S.M., Goldade, B.G., Dumonceaux, T.J., Klassen, J., Zijlstra, R.T., Goh, S.H. Van Kessel, A.G. (2005) Comparison of ileum microflora of pigs fed corn-, wheat-, or barley-based diets by chaperonin-60 sequencing and quantitative PCR. Appl Environ Microbiol 71, 867 875.
11. Ito, T., Okabe, S., Satoh, H. Watanabe, Y. (2002) Successional development of sulfate-reducing bacterial populations and their activities in a wastewater biofilm growing under microaerophilic conditions. Appl Environ Microbiol 68, 1392 1402.
12. Kjeldsen, K.U., Loy, A., Jakobsen, T.F., Thomsen, T.R., Wagner, M. Ingvorsen, K. (2007) Diversity of sulfate-reducing bacteria from an extreme hypersaline sediment, Great Salt Lake (Utah). FEMS Microbiol Ecol 60, 287 298.
13. Klappenbach, J.A., Saxman, P.R., Cole, J.R. Schmidt, T.M. (2001) rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res 29, 181 184.
14. Klein, M., Friedrich, M., Roger, A.J., Hugenholtz, P., Fishbain, S., Abicht, H., Blackall, L.L., Stahl, D.A. et al. (2001) Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J Bacteriol 183, 6028 6035.
15. Kondo, J., Nedwell, D.B., Purdy, K.J. de Queiroz Silva, S. (2004) Detection and enumeration of sulphate-reducing bacteria in estuarine sediments by competitive PCR. Geomicrobiol J 21, 145 157.
16. Leloup, J., Quillet, L., Berthe, T. Petit, F. (2006) Diversity of the dsrAB (dissimilatory sulfite reductase) gene sequences retrieved from two contrasting mudflats of the Seine estuary, France. FEMS Microbiol Ecol 55, 230 238.
17. Leloup, J., Loy, A., Knab, N.J., Borowski, C., Wagner, M. Jorgensen, B.B. (2007) Diversity and abundance of sulfate-reducing microorganisms in the sulfate and methane zones of a marine sediment, Black Sea. Environ Microbiol 9, 131 142.
18. Leser, T.D., Amenuvor, J.Z., Jensen, T.K., Lindecrona, R.H., Boye, M. Moller, K. (2002) Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl Environ Microbiol 68, 673 690.
19. Manz, W., Eisenbrecher, M., Neu, T.R. Szewzyk, U. (1998) Abundance and spatial organization of Gram-negative sulfate-reducing bacteria in activated sludge investigated by in situ probing with specific 16S rRNA targeted oligonucleotides. FEMS Microbiol Ecol 25, 43 61.
20. Minz, D., Flax, J.L., Green, S.J., Muyzer, G., Cohen, Y., Wagner, M., Rittmann, B.E. Stahl, D.A. (1999) Diversity of sulfate-reducing bacteria in oxic and anoxic regions of a microbial mat characterized by comparative analysis of dissimilatory sulfite reductase genes. Appl Environ Microbiol 65, 4666 4671.
21. Nanninga, H.J. Gottschal, J.C. (1987) Properties of Desulfovibrio carbinolicus sp. nov. and other sulfate-reducing bacteria isolated from an anaerobic-purification plant. Appl Environ Microbiol 53, 802 809.
22. Odom, J.M. Peck, H.D. Jr. (1984) Hydrogenase, electron-transfer proteins, and energy coupling in the sulfate-reducing bacteria Desulfovibrio. Annu Rev Microbiol 38, 551 592.
23. Panetta, D.M., Powers, W.J., Xin, H., Kerr, B.J. Stalder, K.J. (2006) Nitrogen excretion and ammonia emissions from pigs fed modified diets. J Environ Qual 4, 1297 1308.
24. Perez-Jimenez, J.R., Young, L.Y. Kerkhof, L.J. (2001) Molecular characterization of sulfate-reducing bacteria in anaerobic hydrocarbon-degrading consortia and pure cultures using the dissimilatory sulfite reductase (dsrAB) genes. FEMS Microbiol Ecol 35, 145 150.
25. Snell-Castro, R., Godon, J.J., Delgenés, J.-P. Dabert, P. (2005) Characterisation of the microbial diversity in a pig manure storage pit using small subunit rDNA sequence analysis. FEMS Microbiol Ecol 52, 229 242.
26. Sutton, A.L., Kephart, K.B., Verstegen, M.W., Canh, T.T. Hobbs, P.J. (1999) Potential for reduction of odorous compounds in swine manure through diet modification. J Anim Sci 77, 430 439.
27. Tajima, K., Nonaka, I., Higuchi, K., Takusari, N., Kurihara, M., Takenaka, A., Mitsumori, M., Kajikawa, H. et al. (2007) Influence of high temperature and humidity on rumen bacterial diversity in Holstein heifers. Anaerobe 13, 57 64.
28. Tamura, K., Dudley, J., Nei, M. Kumar, S. (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24, 1596 1599.
29. Wagner, M., Roger, A.J., Flax, J.L., Brusseau, G.A. Stahl, D.A. (1998) Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J Bacteriol 180, 2975 2982.
30. Ward, D.M., Weller, R. Bateson, M.M. (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345, 63 65.
31. Whitehead, T.R. Cotta, M.A. (2001) Characterisation and comparison of microbial populations in swine faeces and manure storage pits by 16S rDNA gene sequence analyses. Anaerobe 7, 181 187.
32. Whitehead, T.R. Cotta, M.A. (2004) Isolation and identification of hyper-ammonia producing bacteria from swine manure storage pits. Curr Microbiol 48, 20 26.
33. Whitehead, T.R., Cotta, M.A., Collins, M.D. Lawson, P.A. (2004) Hespellia stercorisuis gen. nov., sp. nov. and Hespellia porcina sp. nov., isolated from swine manure storage pits. Int J Syst Evol Microbiol 54, 241 245.
34. Whitehead, T.R., Cotta, M.A., Collins, M.D., Falsen, E. Lawson, P.A. (2005) Bacteroides coprosuis sp. nov., isolated from swine-manure storage pits. Int J Syst Evol Microbiol 55, 2515 2518.
35. Whitford, M.F., Forster, R.J., Beard, C.E., Gong, J. Teather, R.M. (1998) Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes. Anaerobe 4, 153 163.
36. Widdel, F. (1988) Microbiology and ecology of sulfate- and sulfur-reducing bacteria. In Biology of Anaerobic Microorganisms ed. Zehnder, A.J.B. pp. 469 585. New York : John Wiley & Sons.
37. Zahn, J.A., Hatfield, J.L., Do, Y.S., DiSpirito, A.A., Laird, D.A. Pfeiffer, R.L. (1997) Characterization of volatile organic emissions and wastes from a swine production facility. J Environ Qual 26, 1687 1696.