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A. C. Fdos Santos, Marques, E. L. S., Gross, E., Souza, S. S., Dias, J. C. T., Brendel, M., and Rezende, R. P., Detection by denaturing gradient gel electrophoresis of ammonia-oxidizing bacteria in microcosms of crude oil-contaminated mangrove sediments, vol. 11, pp. 190-201, 2012.
Amorim JH, Macena TN, Lacerda GV Jr, Rezende RP, et al. (2008). An improved extraction protocol for metagenomic DNA from a soil of the Brazilian Atlantic Rainforest. Genet. Mol. Res. 7: 1226-1232. PMid:19065757 Arp DJ, Yeager CM and Hyman MR (2001). Molecular and cellular fundamentals of aerobic cometabolism of trichloroethylene. Biodegradation 12: 81-103. PMid:11710592 Atlas RM (1995). Biorremediation of Petroleum Pollutants. University of Louisville, Lousville. Bartha R and Pramer D (1965). Features of a flask and method for measuring the persistence and biological effects of pesticides in soil. Soil Sci. 100: 68-70. Bock E, Koops HP, Harms H and Ahlers B (1991). The Biochemistry of Nitrifying Organisms. In: Variations in Autotrophic Life (Shively JM and Barton LL, eds.). Academic Press, San Diego, 171-200. Bordenave S, Goni-Urriza MS, Caumette P and Duran R (2007). Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat. Appl. Environ. Microbiol. 73: 6089-6097. PMid:17704271    PMCid:2075027 Bothe H, Jost G, Schloter M, Ward BB, et al. (2000). Molecular analysis of ammonia oxidation and denitrification in natural environments. FEMS Microbiol. Rev. 24: 673-690. PMid:11077158 Brazil (1965). Federal Law No. 4.771, of September 15, 1965. Brasília, 1965. Available at []. Accessed October 7, 2011. Burton SA and Prosser JI (2001). Autotrophic ammonia oxidation at low pH through urea hydrolysis. Appl. Environ. Microbiol. 67: 2952-2957. PMid:11425707    PMCid:92966 CONAMA (1985). Conselho Nacional do Meio Ambiente. Resolution nº 04/1985, of September 18, 1985. Available at []. Accessed October 07, 2011. Evans FF, Rosado AS, Sebastian GV, Casella R, et al. (2004). Impact of oil contamination and biostimulation on the diversity of indigenous bacterial communities in soil microcosms. FEMS Microbiol. Ecol. 49: 295-305. Gieseke A, Tarre S, Green M and de Beer D (2006). Nitrification in a biofilm at low pH values: role of in situ microenvironments and acid tolerance. Appl. Environ. Microbiol. 72: 4283-4292. PMid:16751543    PMCid:1489657 Harayama S, Kasai Y and Hara A (2004). Microbial communities in oil-contaminated seawater. Curr. Opin. Biotechnol. 15: 205-214. PMid:15193328 Heuer H, Krsek M, Baker P, Smalla K, et al. (1997). Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63: 3233-3241. PMid:9251210    PMCid:168621 Hollocher TC, Tate ME and Nicholas DJ (1981). Oxidation of ammonia by Nitrosomonas europaea. Definite 18O-tracer evidence that hydroxylamine formation involves a monooxygenase. J. Biol. Chem. 256: 10834-10836. PMid:7287737 Islam KR and Weil RR (2000). Soil quality indicator properties in mid-Atlantic soils as influenced by conservation management. J. Soil Water Conserv. 55: 69-78. Jia Z and Conrad R (2009). Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ. Microbiol. 11: 1658-1671. PMid:19236445 Junier P, Kim OS, Junier T, Ahn TS, et al. (2009). Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon. Appl. Microbiol. Biotechnol. 83: 175-188. PMid:19274459    PMCid:2845890 Karlen DL, Andrews SS and Doran JW (2001). Soil quality: Current concepts and applications. Adv. Agron. 74: 1-40. Kasai Y, Kishira H, Syutsubo K and Harayama S (2001). Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident. Environ. Microbiol. 3: 246-255. PMid:11359510 Kathiresan K and Bingham BL (2001). Biology of mangroves and mangrove ecosystems. Adv. Mar. Biol. 40: 81-251. Koops H-P, Purkhold U, Pommerening-Röser A, Timmermann G, et al. (2006). The Lithoautotrophic Ammonia-Oxidizing Bacteria. In: The Prokaryotes (Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, et al., eds.). Vol. 2. Springer, New York, 778-811. Leahy JG and Colwell RR (1990). Microbial degradation of hydrocarbons in the environment. Microbiol. Rev. 54: 305- 315. PMid:2215423    PMCid:372779 Maciel BM, Santos AC, Dias JC, Vidal RO, et al. (2009). Simple DNA extraction protocol for a 16S rDNA study of bacterial diversity in tropical landfarm soil used for bioremediation of oil waste. Genet. Mol. Res. 8: 375-388. PMid:19440973 McCaig AE, Embley TM and Prosser JI (1994). Molecular analysis of enrichment cultures of marine ammonia oxidisers. FEMS Microbiol. Lett. 120: 363-367. PMid:8076810 Muyzer G, de Waal EC and Uitterlinden AG (1993). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59: 695-700. PMid:7683183    PMCid:202176 Nicol GW, Leininger S, Schleper C and Prosser JI (2008). The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ. Microbiol. 10: 2966-2978. PMid:18707610 Nicolaisen MH and Ramsing NB (2002). Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria. J. Microbiol. Methods 50: 189-203. Prosser JI (1989). Autotrophic nitrification in bacteria. Adv. Microb. Physiol. 30: 125-181. Rotthauwe JH, Witzel KP and Liesack W (1997). The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63: 4704-4712. PMid:9406389    PMCid:168793 Sayavedra-Soto LA, Hommes NG, Alzerreca JJ, Arp DJ, et al. (1998). Transcription of the amoC, amoA and amoB genes in Nitrosomonas europaea and Nitrosospira sp. NpAV. FEMS Microbiol. Lett. 167: 81-88. PMid:9785456 Stephen JR, Kowalchuk GA, Bruns MAV, McCaig AE, et al. (1998). Analysis of beta-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing. Appl. Environ. Microbiol. 64: 2958-2965. PMid:9687457    PMCid:106799 Vanneli T and Hooper AB (1992). Oxidation of nitrapyrin to 6-chloropicolinic acid by the ammonia-oxidizing bacterium Nitrosomonas europaea. Appl. Environ. Microbiol. 58: 2321-2325. PMid:16348740    PMCid:195775 Vannelli T, Logan M, Arciero D and Hooper AB (1990). Degradation of halogenated aliphatics by the ammonia-oxidizing bacterium Nitrosomonas europaea. Appl. Environ. Microbiol. 56: 1169-1171. PMid:2339874    PMCid:184364 Zhang LM, Wang M, Prosser JI, Zheng YM, et al. (2009). Altitude ammonia-oxidizing bacteria and archaea in soils of Mount Everest. FEMS Microbiol. Ecol. 70: 52-61. PMid:19780828
J. H. Amorim, Vidal, R. O., Lacerda-Junior, G. V., Dias, J. C. T., Brendel, M., Rezende, R. P., and Cascardo, J. C. M., A simple boiling-based DNA extraction for RAPD profiling of landfarm soil to provide representative metagenomic content, vol. 11, pp. 182-189, 2012.
Amorim JH, Macena TN, Lacerda GV Jr, Rezende RP, et al. (2008). An improved extraction protocol for metagenomic DNA from a soil of the Brazilian Atlantic Rainforest. Genet. Mol. Res. 7: 1226-1232. PMid:19065757 Ashburner M, Ball CA, Blake JA, Botstein D, et al. (2000). Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25: 25-29. PMid:10802651    PMCid:3037419 Daniel R (2004). The soil metagenome - a rich resource for the discovery of novel natural products. Curr. Opin. Biotechnol. 15: 199-204. PMid:15193327 Ewing B, Hillier L, Wendl MC and Green P (1998). Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175-185. PMid:9521921 Huson DH, Auch AF, Qi J and Schuster SC (2007). MEGAN analysis of metagenomic data. Genome Res. 17: 377-386. PMid:17255551    PMCid:1800929 Johnson PL and Slatkin M (2006). Inference of population genetic parameters in metagenomics: a clean look at messy data. Genome Res. 16: 1320-1327. PMid:16954540    PMCid:1581441 Kanehisa M and Goto S (2000). KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28: 27-30. PMid:10592173    PMCid:102409 Maciel BM, Dias JC, Dos Santos AC, Argolo Filho RC, et al. (2007). Microbial surfactant activities from a petrochemical landfarm in a humid tropical region of Brazil. Can. J. Microbiol. 53: 937-943. PMid:17898850 McHardy AC and Rigoutsos I (2007). What’s in the mix: phylogenetic classification of metagenome sequence samples. Curr. Opin. Microbiol. 10: 499-503. PMid:17933580 Riesenfeld CS, Schloss PD and Handelsman J (2004). Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38: 525-552. PMid:15568985 Robe P, Nalin R, Capellano C, Vogel TM, et al. (2003). Extraction of DNA from soil. Eur. J. Soil. Biol. 39: 183-190. Roh C, Villatte F, Kim BG and Schmid RD (2006). Comparative study of methods for extraction and purification of enviromental DNA from soil and sludge samples. Appl. Biochem. Biotech. 134: 97-112. Rondon MR, August PR, Bettermann AD, Brady SF, et al. (2000). Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66: 2541-2547. PMid:10831436    PMCid:110579 Sambrook J, Fritsch EF and Maniatis T (1989). Molecular Cloning: A Laboratory Manual. 3rd edn. Cold Spring Harbor Laboratory Press, New York. Schloss PD and Handelsman J (2003). Biotechnological prospects from metagenomics. Curr. Opin. Biotechnol. 14: 303-310. Smit AFA, Hubley R and Green P (2004). RepeatMasker Open-3.0. 1996-2007. Streit WR and Schmitz RA (2004). Metagenomics - the key to the uncultured microbes. Curr. Opin. Microbiol. 7: 492-498. PMid:15451504 Yun J, Kang S, Park S, Yoon H, et al. (2004). Characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library. Appl. Environ. Microbiol. 70: 7229-7235. PMid:15574921    PMCid:535135
B. M. Maciel, Dias, J. C. T., Romano, C. C., Sriranganathan, N., Brendel, M., and Rezende, R. P., Detection of Salmonella Enteritidis in asymptomatic carrier animals: comparison of quantitative real-time PCR and bacteriological culture methods, vol. 10, pp. 2578-2588, 2011.
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M. Brendel, Marisco, G., Ganda, I., Wolter, R., and Pungartnik, C., DNA repair mutant pso2 of Saccharomyces cerevisiae is sensitive to intracellular acetaldehyde accumulated by disulfiram-mediated inhibition of acetaldehyde dehydrogenase, vol. 9, pp. 48-57, 2010.
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