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2016
E. L. S. Marques, Dias, J. C. T., Silva, G. S., Pirovani, C. P., Rezende, R. P., Marques, E. L. S., Dias, J. C. T., Silva, G. S., Pirovani, C. P., and Rezende, R. P., Effect of organic matter enrichment on the fungal community in limestone cave sediments, vol. 15, p. -, 2016.
E. L. S. Marques, Dias, J. C. T., Silva, G. S., Pirovani, C. P., Rezende, R. P., Marques, E. L. S., Dias, J. C. T., Silva, G. S., Pirovani, C. P., and Rezende, R. P., Effect of organic matter enrichment on the fungal community in limestone cave sediments, vol. 15, p. -, 2016.
T. Fdos Santos, Melo, T. A., Santos, D. S., Rezende, R. P., Dias, J. C. T., Romano, C. C., Santos, T. Fdos, Melo, T. A., Santos, D. S., Rezende, R. P., Dias, J. C. T., and Romano, C. C., Efficacy of oral administration of lactic acid bacteria isolated from cocoa in a fermented milk preparation: reduction of colitis in an experimental rat model, vol. 15, p. -, 2016.
T. Fdos Santos, Melo, T. A., Santos, D. S., Rezende, R. P., Dias, J. C. T., Romano, C. C., Santos, T. Fdos, Melo, T. A., Santos, D. S., Rezende, R. P., Dias, J. C. T., and Romano, C. C., Efficacy of oral administration of lactic acid bacteria isolated from cocoa in a fermented milk preparation: reduction of colitis in an experimental rat model, vol. 15, p. -, 2016.
F. M. O. Sousa, Moura, S. R., Quinto, C. A., Dias, J. C. T., Pirovani, C. P., Rezende, R. P., Sousa, F. M. O., Moura, S. R., Quinto, C. A., Dias, J. C. T., Pirovani, C. P., and Rezende, R. P., Functional screening for cellulolytic activity in a metagenomic fosmid library of microorganisms associated with coral, vol. 15, p. -, 2016.
F. M. O. Sousa, Moura, S. R., Quinto, C. A., Dias, J. C. T., Pirovani, C. P., Rezende, R. P., Sousa, F. M. O., Moura, S. R., Quinto, C. A., Dias, J. C. T., Pirovani, C. P., and Rezende, R. P., Functional screening for cellulolytic activity in a metagenomic fosmid library of microorganisms associated with coral, vol. 15, p. -, 2016.
2012
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. http://dx.doi.org/10.4238/vol7-4gmr509 PMid:19065757 Arp DJ, Yeager CM and Hyman MR (2001). Molecular and cellular fundamentals of aerobic cometabolism of trichloroethylene. Biodegradation 12: 81-103. http://dx.doi.org/10.1023/A:1012089908518 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. http://dx.doi.org/10.1097/00010694-196507000-00011 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. http://dx.doi.org/10.1128/AEM.01352-07 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. http://dx.doi.org/10.1111/j.1574-6976.2000.tb00566.x PMid:11077158 Brazil (1965). Federal Law No. 4.771, of September 15, 1965. Brasília, 1965. Available at [http://www.lei.adv.br]. 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. http://dx.doi.org/10.1128/AEM.67.7.2952-2957.2001 PMid:11425707    PMCid:92966 CONAMA (1985). Conselho Nacional do Meio Ambiente. Resolution nº 04/1985, of September 18, 1985. 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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. http://dx.doi.org/10.1111/j.1462-2920.2009.01891.x 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. http://dx.doi.org/10.1007/s00253-009-1923-x PMid:19274459    PMCid:2845890 Karlen DL, Andrews SS and Doran JW (2001). Soil quality: Current concepts and applications. Adv. Agron. 74: 1-40. http://dx.doi.org/10.1016/S0065-2113(01)74029-1 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. http://dx.doi.org/10.1046/j.1462-2920.2001.00185.x PMid:11359510 Kathiresan K and Bingham BL (2001). Biology of mangroves and mangrove ecosystems. Adv. Mar. Biol. 40: 81-251. http://dx.doi.org/10.1016/S0065-2881(01)40003-4 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. 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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. http://dx.doi.org/10.1111/j.1462-2920.2008.01701.x 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. http://dx.doi.org/10.1016/S0167-7012(02)00026-X Prosser JI (1989). Autotrophic nitrification in bacteria. Adv. Microb. Physiol. 30: 125-181. http://dx.doi.org/10.1016/S0065-2911(08)60112-5 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. 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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. http://dx.doi.org/10.4238/vol7-4gmr509 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. http://dx.doi.org/10.1038/75556 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. http://dx.doi.org/10.1016/j.copbio.2004.04.005 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. http://dx.doi.org/10.1101/gr.5969107 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. http://dx.doi.org/10.1101/gr.5431206 PMid:16954540    PMCid:1581441 Kanehisa M and Goto S (2000). KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28: 27-30. http://dx.doi.org/10.1093/nar/28.1.27 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. http://dx.doi.org/10.1139/W07-052 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. http://dx.doi.org/10.1016/j.mib.2007.08.004 PMid:17933580 Riesenfeld CS, Schloss PD and Handelsman J (2004). Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38: 525-552. http://dx.doi.org/10.1146/annurev.genet.38.072902.091216 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. http://dx.doi.org/10.1016/S1164-5563(03)00033-5 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. http://dx.doi.org/10.1385/ABAB:134:2:97 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. http://dx.doi.org/10.1128/AEM.66.6.2541-2547.2000 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. http://dx.doi.org/10.1016/S0958-1669(03)00067-3 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. http://dx.doi.org/10.1016/j.mib.2004.08.002 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. http://dx.doi.org/10.1128/AEM.70.12.7229-7235.2004 PMid:15574921    PMCid:535135
2011
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.
Agron PG, Walker RL, Kinde H, Sawyer SJ, et al. (2001). Identification by subtractive hybridization of sequences specific for Salmonella enterica serovar Enteritidis. Appl. Environ. Microbiol. 67: 4984-4991. http://dx.doi.org/10.1128/AEM.67.11.4984-4991.2001 PMid:11679316    PMCid:93261 APHA - American Public Health Association (1992). Compendium of Methods for the Microbiological Examination of Foods. 3rd edn. American Public Health Association, Washington. Boutaga K, van Winkelhoff AJ, Vandenbroucke-Grauls CM and Savelkoul PH (2003). Comparison of real-time PCR and culture for detection of Porphyromonas gingivalis in subgingival plaque samples. J. Clin. Microbiol. 41: 4950-4954. http://dx.doi.org/10.1128/JCM.41.11.4950-4954.2003 PMid:14605122    PMCid:262485 Buh GM, Cankar K, Zel J and Gruden K (2008). Comparison of different real-time PCR chemistries and their suitability for detection and quantification of genetically modified organisms. 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Food Microbiol. 35: 239-250. http://dx.doi.org/10.1016/S0168-1605(97)01241-5 De Medici D, Croci L, Delibato E, Di Pasquale S, et al. (2003). Evaluation of DNA extraction methods for use in combination with SYBR green I real-time PCR to detect Salmonella enterica serotype Enteritidis in poultry. Appl. Environ. Microbiol. 69: 3456-3461. http://dx.doi.org/10.1128/AEM.69.6.3456-3461.2003 PMid:12788750    PMCid:161507 Deng SX, Cheng AC, Wang MS and Cao P (2007). Gastrointestinal tract distribution of Salmonella enteritidis in orally infected mice with a species-specific fluorescent quantitative polymerase chain reaction. World J. Gastroenterol. 13: 6568-6574. http://dx.doi.org/10.3748/wjg.13.6568 PMid:18161929 Deng SX, Cheng AC, Wang MS, Cao P, et al. (2008). Quantitative studies of the regular distribution pattern for Salmonella enteritidis in the internal organs of mice after oral challenge by a specific real-time polymerase chain reaction. World J. 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Clin. Microbiol. Antimicrob. 7: 18. http://dx.doi.org/10.1186/1476-0711-7-18 PMid:18817537    PMCid:2566554 Maciel BM, Argôlo Filho RC, Freitas ES, Kruschewsky FF, et al. (2004). Ocorrência de sorotipos exóticos de Salmonella encontrados em cães assintomáticos nos distritos do município de Ilhéus / BA - Brasil. Braz. J. Vet. Res. Anim. Sci. 41: 247-253. Maciel BM, Argolo Filho RC, Nogueira SS, Dias JC, et al. (2010). High prevalence of Salmonella in tegu lizards (Tupinambis merianae), and susceptibility of the serotypes to antibiotics. Zoonoses Public Health 57: e26-e32. http://dx.doi.org/10.1111/j.1863-2378.2009.01283.x PMid:19968856 Malorny B, Hoorfar J, Hugas M, Heuvelink A, et al. (2003). Interlaboratory diagnostic accuracy of a Salmonella specific PCR-based method. Int. J. Food Microbiol. 89: 241-249. http://dx.doi.org/10.1016/S0168-1605(03)00154-5 Malorny B, Paccassoni E, Fach P, Bunge C, et al. (2004). Diagnostic real-time PCR for detection of Salmonella in food. Appl. Environ. 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Application of SYBR green real-time PCR assay for specific detection of Salmonella spp. in dairy farm environmental samples. Int. J. Food Microbiol. 102: 161-171. http://dx.doi.org/10.1016/j.ijfoodmicro.2004.12.020 PMid:15913820 Nga TV, Karkey A, Dongol S, Thuy HN, et al. (2010). The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens. BMC Infect. Dis. 10: 125. http://dx.doi.org/10.1186/1471-2334-10-125 PMid:20492644    PMCid:2886058 O’Brien JDP (1990). Aspects of Salmonella enteritidis control in poultry. Worlds Poult. Sci. J. 46: 119-124. http://dx.doi.org/10.1079/WPS19900015 Perelle S, Dilasser F, Malorny B, Grout J, et al. (2004). Comparison of PCR-ELISA and LightCycler real-time PCR assays for detecting Salmonella spp. in milk and meat samples. Mol. Cell Probes 18: 409-420. http://dx.doi.org/10.1016/j.mcp.2004.07.001 PMid:15488381 Pintar K, Cook A, Pollari F, Ravel A, et al. (2007). Quantitative effect of refrigerated storage time on the enumeration of Campylobacter, Listeria, and Salmonella on artificially inoculated raw chicken meat. J. Food Prot. 70: 739-743. PMid:17388068 Temelli S, Kahya S, Eyigor A and Carli KT (2010). Incidence of Salmonella Enteritidis in chicken layer flocks in Turkey: Results by real-time polymerase chain reaction and International Organization for Standardization culture methods. Poult. Sci. 89: 1406-1410. http://dx.doi.org/10.3382/ps.2010-00796 PMid:20548068 WHO-GFN (2009). WHO Global Foodborne Infections Network Country Databank - A resource to link human and non-human sources of Salmonella. Available at [http://www.who.int/gfn/activities/CDB_poster_Sept09.pdf]. Accessed June 27, 2009. Wolffs PF, Glencross K, Thibaudeau R and Griffiths MW (2006). Direct quantitation and detection of salmonellae in biological samples without enrichment, using two-step filtration and real-time PCR. Appl. Environ. 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T. F. Santos, Santana, L. K. A., Santos, A. C. F., Silva, G. S., Romano, C. C., Dias, J. C. T., and Rezende, R. P., Lactic acid bacteria dynamics during spontaneous fermentation of cocoa beans verified by culture-independent denaturing gradient gel electrophoresis, vol. 10, pp. 2702-2709, 2011.
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