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2016
A. Garcia, Polonio, J. C., Polli, A. D., Santos, C. M., Rhoden, S. A., Quecine, M. C., Azevedo, J. L., and Pamphile, J. A., Rhizosphere bacteriome of the medicinal plant Sapindus saponaria L. revealed by pyrosequencing, vol. 15, no. 4, p. -, 2016.
Conflicts of interestThe authors declare no conflict of interest.ACKNOWLEDGMENTSResearch supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (grant #311534/2014-7 and #447265/2014-8) and Fundação Araucária (grant FA-#276/2014), and by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) via scholarship to A. Garcia, J.C. Polonio, A.D. Polli, and C.M. Santos.REFERENCESde Oliveira Costa LE, de Queiroz MV, Borges AC, de Moraes CA, et al (2012). Isolation and characterization of endophytic bacteria isolated from the leaves of the common bean (Phaseolus vulgaris). Braz. J. Microbiol. 43: 1562-1575. http://dx.doi.org/10.1590/S1517-83822012000400041 Gans J, Wolinsky M, Dunbar J, et al (2005). Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387-1390. http://dx.doi.org/10.1126/science.1112665 Garcia A, Rhoden SA, Bernardi-Wenzel J, Orlandelli RC, et al (2012a). Antimicrobial activity of crude extracts of endophytic fungi isolated from the medicinal plant Sapindus saponaria L. J. Appl. Pharm. Sci. 2: 35-40. García A, Rhoden SA, Rubin Filho CJ, Nakamura CV, et al (2012b). Diversity of foliar endophytic fungi from the medicinal plant Sapindus saponaria L. and their localization by scanning electron microscopy. Biol. Res. 45: 139-148. http://dx.doi.org/10.4067/S0716-97602012000200006 García-Salamanca A, Molina-Henares MA, van Dillewijn P, Solano J, et al (2013). Bacterial diversity in the rhizosphere of maize and the surrounding carbonate-rich bulk soil. Microb. Biotechnol. 6: 36-44. http://dx.doi.org/10.1111/j.1751-7915.2012.00358.x Hallmann J and Berg G (2006). Spectrum and population dynamics of bacterial root endophytes. In: Microbial root endophytes (Schulz B, Boyle C and Sieber TN, eds.). Springer-Verlag, Berlin, Heidelberg, 15-31. Johnston-Monje D, Lundberg DS, Lazarovits G, Reis VM, et al (2016). Bacterial populations in juvenile maize rhizospheres originate from both seed and soil. Plant Soil 405: 337-355. http://dx.doi.org/10.1007/s11104-016-2826-0 Kemmitt SJ, Wright D, Goulding KWT, Jones DL, et al (2006). pH regulation of carbon and nitrogen dynamics in two agricultural soils. Soil Biol. Biochem. 38: 898-911. http://dx.doi.org/10.1016/j.soilbio.2005.08.006 Keswani J, Whitman WB, et al (2001). Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes. Int. J. Syst. Evol. Microbiol. 51: 667-678. http://dx.doi.org/10.1099/00207713-51-2-667 Mendes R, Kruijt M, de Bruijn I, Dekkers E, et al (2011). Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332: 1097-1100. http://dx.doi.org/10.1126/science.1203980 Miguel PSB, Delvaux JC, de Oliveira MNV, Monteiro LCP, et al (2013). Diversity of endophytic bacteria in the fruits of Coffea canephora. Afr. J. Microbiol. Res. 7: 586-594. http://dx.doi.org/10.5897/AJMR12.2036 Morgan JAW and Whipps JM (2001). Methodological approaches to the study of rhizosphere carbon flow and microbial population dynamics. In: The rhizosphere. Biochemistry and organic substances at the soil-plant interface. 1st edn. (Pinton R, Varanini Z and Nannipieri P, eds.). Marcel Dekker, New York, 373-409. Nacke H, Thürmer A, Wollherr A, Will C, et al (2011). Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS One 6: e17000. http://dx.doi.org/10.1371/journal.pone.0017000 Nielsen AT, Liu WT, Filipe C, GradyLJret al (1999). Identification of a novel group of bacteria in sludge from a deteriorated biological phosphorus removal reactor. Appl. Environ. Microbiol. 65: 1251-1258. Pelczar MJ, Jr., Chan ECS and Krieg NR (2011). Microbiologia: Conceitos e Aplicações. 2nd edn. Pearson Education do Brasil, São Paulo. Pelegrini DD, Tsuzuki JK, Amado CAB, Cortez DAG, et al (2008). Biological activity and isolated compounds in Sapindus saponaria L. and other plants of the genus Sapindus. Lat. Am. J. Pharm. 27: 922-927. Polonio JC, Almeida TT, Garcia A, Mariucci GE, et al (2015). Biotechnological prospecting of foliar endophytic fungi of guaco (Mikania glomerata Spreng.) with antibacterial and antagonistic activity against phytopathogens. Genet. Mol. Res. 14: 7297-7309. http://dx.doi.org/10.4238/2015.July.3.5 Qi X, Wang E, Xing M, Zhao W, et al (2012). Rhizosphere and non-rhizosphere bacterial community composition of the wild medicinal plant Rumex patientia. World J. Microbiol. Biotechnol. 28: 2257-2265. http://dx.doi.org/10.1007/s11274-012-1033-2 Rhoden SA, Garcia A, Bongiorno VA, Azevedo JL, et al (2012). Antimicrobial activity of crude extracts of endophytic fungi isolated from the medicinal plant Trichilia elegans A Juss. J. Appl. Pharm. Sci. 2: 57-59. Roesch LF, Fulthorpe RR, Riva A, Casella G, et al (2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1: 283-290. Schloss PD, Handelsman J, et al (2006). Toward a census of bacteria in soil. PLOS Comput. Biol. 2: e92. http://dx.doi.org/10.1371/journal.pcbi.0020092 Schulz B, Boyle C, et al (2005). The endophytic continuum. Mycol. Res. 109: 661-686. http://dx.doi.org/10.1017/S095375620500273X Silva-Lacerda GR, Santana RC, Vicalvi-Costa MC, Solidônio EG, et al (2016). Antimicrobial potential of actinobacteria isolated from the rhizosphere of the Caatinga biome plant Caesalpinia pyramidalis Tul. Genet. Mol. Res. 15: 15017488. http://dx.doi.org/10.4238/gmr.15017488 Singh BK, Bardgett RD, Smith P, Reay DS, et al (2010). Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nat. Rev. Microbiol. 8: 779-790. http://dx.doi.org/10.1038/nrmicro2439 Winston ME, Hampton-Marcell J, Zarraonaindia I, Owens SM, et al (2014). Understanding cultivar-specificity and soil determinants of the cannabis microbiome. PLoS One 9: e99641. http://dx.doi.org/10.1371/journal.pone.0099641    
2013
S. A. Rhoden, Garcia, A., Azevedo, J. L., and Pamphile, J. A., In silico analysis of diverse endophytic fungi by using ITS1-5,8S-ITS2 sequences with isolates from various plant families in Brazil, vol. 12, pp. 935-950, 2013.
Abreu LM, Costa SS, Pfenning LH, Takahashi JA, et al. (2012). Chemical and molecular characterization of Phomopsis and Cytospora-like endophytes from different host plants in Brazil. Fungal Biol. 116: 249-260. http://dx.doi.org/10.1016/j.funbio.2011.11.008 PMid:22289771   Alexopoulos CJ, Mims CW and Blackwell M (1996). Introductory Mycology. John Wiley & Sons Inc., New York.   Altschul SF, Gish W, Miller W, Myers EW, et al. (1990). Basic Local Alignment Search Tool. J. Mol. Biol. 215: 403-410. PMid:2231712   Arnold AE (2008). Tropical Forest Community Ecology. In: Endophytic Fungi: Hidden Components of Tropical Community Ecology (Carson W and Schnitzer S, eds.). Blackwell Scientific, Inc., Malden, 254-271. PMid:18257039   Arnold AE, Henk DA, Eells RL, Lutzoni F, et al. (2007). Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR. Mycologia 99: 185-206. http://dx.doi.org/10.3852/mycologia.99.2.185 PMid:17682771   Arnold AE, Miadlikowska J, Higgins KL, Sarvate SD, et al. (2009). A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification? Syst. Biol. 58: 283-297. http://dx.doi.org/10.1093/sysbio/syp001 PMid:20525584   Azevedo JL, Maccheroni W Jr, Pereira JO and Araújo WL (2000). Endophytic microorganisms: a review on insect control and recent advances on tropical plants. EJB: Eletron. J. Biotechnol. 3: 40-65.   Bellemain E, Carlsen T, Brochmann C, Coissac E, et al. (2010). ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol. 10: 189. http://dx.doi.org/10.1186/1471-2180-10-189 PMid:20618939 PMCid:2909996   Bernardi-Wenzel J, Garcia A, Filho CJ, Prioli AJ, et al. (2010). Evaluation of foliar fungal endophyte diversity and colonization of medicinal plant Luehea divaricata (Martius et Zuccarini). Biol. Res. 43: 375-384. PMid:21526263   Chen SH, Lin CY and Kuo CM (2005). In silico analysis of crustacean hyperglycemic hormone family. Mar. Biotechnol. 7: 193-206. http://dx.doi.org/10.1007/s10126-004-0020-5 PMid:15933902   Felsenstein J (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791. http://dx.doi.org/10.2307/2408678   Gai CS, Lacava PT, Maccheroni W Jr, Glienke C, et al. (2009). Diversity of endophytic yeasts from sweet orange and their localization by scanning electron microscopy. J. Basic Microbiol. 49: 441-451. http://dx.doi.org/10.1002/jobm.200800328 PMid:19798655   Gilbert LB, Chae L, Kasuga T and Taylor JW (2011). Array Comparative Genomic Hybridizations: assessing the ability to recapture evolutionary relationships using an in silico approach. BMC Genomics 12: 456. http://dx.doi.org/10.1186/1471-2164-12-456 PMid:21936922 PMCid:3196971   Higgins KL, Arnold AE, Miadlikowska J, Sarvate SD, et al. (2007). Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages. Mol. Phylogenet. Evol. 42: 543-555. http://dx.doi.org/10.1016/j.ympev.2006.07.012 PMid:17005421   Jasinski JPP and Payette S (2007). Holocene occurrence of Lophodermium piceae, a black spruce needle endophyte and possible paleoindicator of boreal forest health. Quaternary Res. 67: 50-56. http://dx.doi.org/10.1016/j.yqres.2006.07.008   Kirk PM, Cannon PF, Minter DW and Stalpers JA (2008). Ainsworth & Bisby's Dictionary of the Fungi. CAB International, Wallingford.   Kogel KH, Franken P and Huckelhoven R (2006). Endophyte or parasite - what decides? Curr. Opin. Plant Biol. 9: 358-363. http://dx.doi.org/10.1016/j.pbi.2006.05.001 PMid:16713330   Koulman A, Lane GA, Christensen MJ, Fraser K, et al. (2007). Peramine and other fungal alkaloids are exuded in the guttation fluid of endophyte-infected grasses. Phytochemistry 68: 355-360. http://dx.doi.org/10.1016/j.phytochem.2006.10.012 PMid:17126863   MMA/SBF. Ministério do Meio Ambiente SdBeF (2002). Biodiversidade Brasileira: Avaliação e Identificação de Áreas e Ações Prioritárias para Conservação, Utilização Sustentável e Repartição de Benefícios da Biodiversidade Brasileira. SBF, Brasília. Available at [http://www.mma.gov.br/estruturas/chm/_arquivos/biodivbr.pdf]. Accessed May 15, 2012.   Palsson B (2000). The challenges of in silico biology: Moving from a reductionist paradigm to one that views cells as systems will necessitate changes in both the culture and the practice of research. Nat. Biotechnol. 18: 1147-1150. http://dx.doi.org/10.1038/81125 PMid:11062431   Pamphile JA and Azevedo JL (2002). Molecular characterization of endophytic strains of Fusarium verticillioides (Fusarium moniliforme) from maize (Zea mays L.). World J. Microbiol. Biotechnol. 18: 391-396. http://dx.doi.org/10.1023/A:1015507008786   Rhoden SA, Garcia A, Rubin Filho CJ, Azevedo JL, et al. (2012). Phylogenetic diversity of endophytic leaf fungus isolates from the medicinal tree Trichilia elegans (Meliaceae). Genet. Mol. Res. 11: 2513-2522. http://dx.doi.org/10.4238/2012.June.15.8 PMid:22782630   Rocha ACS, Garcia D, Uetanabaro APT, Carneiro RTO, et al. (2011). Foliar endophytic fungi from Hevea brasiliensis and their antagonism on Microcyclus ulei. Fungal Divers. 47: 75-84. http://dx.doi.org/10.1007/s13225-010-0044-2   Rosa LH, Gonçalves VN, Caligiorne RB, Alves TMA, et al. (2010). Leishmanicidal, trypanocidal, and cytotoxic activities of endophytic fungi associated with bioactive plants in Brazil. Braz. J. Microbiol. 41: 420-430. http://dx.doi.org/10.1590/S1517-83822010000200024   Rubini MR, Silva-Ribeiro RT, Pomella AW, Maki CS, et al. (2005). Diversity of endophytic fungal community of cacao (Theobroma cacao L.) and biological control of Crinipellis perniciosa, causal agent of Witches' Broom Disease. Int. J. Biol. Sci. 1: 24-33. http://dx.doi.org/10.7150/ijbs.1.24 PMid:15951847 PMCid:1140355   Saikkonen K, Wali P, Helander M and Faeth SH (2004). Evolution of endophyte-plant symbioses. Trends Plant Sci. 9: 275-280. http://dx.doi.org/10.1016/j.tplants.2004.04.005 PMid:15165558   Saitou N and Nei M (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425. PMid:3447015   Sette LD, Passarini MRZ, Delarmelina C, Salati F, et al. (2006). Molecular characterization and antimicrobial activity of endophytic fungi from coffee plants. World J. Microb. Biot. 22: 1185-1195. http://dx.doi.org/10.1007/s11274-006-9160-2   Souza AQL, Souza ADL, Astolfi-Filho S, Belém-Pinheiro ML, et al. (2004). Atividade antimicrobiana de fungos endofíticos isolados de plantas tóxicas da Amazônia: Palicourea longiflora (Aubl.) rich e Strychnos cogens bentham. Acta Amaz. 34: 185-195. http://dx.doi.org/10.1590/S0044-59672004000200006   Strobel GA (2003). Endophytes as sources of bioactive products. Microbes Infect. 5: 535-544. http://dx.doi.org/10.1016/S1286-4579(03)00073-X   Strobel GA, Hess WM, Ford E, Sidhu RS, et al. (1996). Taxol from fungal endophytes and the issue of biodiversity. J. Ind. Microbiol. Biot. 17: 417-423. http://dx.doi.org/10.1007/BF01574772   Stuart RM, Romao AS, Pizzirani-Kleiner AA, Azevedo JL, et al. (2010). Culturable endophytic filamentous fungi from leaves of transgenic imidazolinone-tolerant sugarcane and its non-transgenic isolines. Arch. Microbiol. 192: 307-313. http://dx.doi.org/10.1007/s00203-010-0557-9 PMid:20191263   Tamura K, Peterson D, Peterson N, Stecher G, et al. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731-2739. http://dx.doi.org/10.1093/molbev/msr121 PMid:21546353 PMCid:3203626   Vaz AB, Mota RC, Bomfim MR, Vieira ML, et al. (2009). Antimicrobial activity of endophytic fungi associated with Orchidaceae in Brazil. Can. J. Microbiol. 55: 1381-1391. http://dx.doi.org/10.1139/W09-101 PMid:20029530   Victoria FC, da Maia LC and de Oliveira AC (2011). In silico comparative analysis of SSR markers in plants. BMC Plant Biol. 11: 15. http://dx.doi.org/10.1186/1471-2229-11-15 PMid:21247422 PMCid:3037304   Vieira ML, Hughes AF, Gil VB, Vaz AB, et al. (2012). Diversity and antimicrobial activities of the fungal endophyte community associated with the traditional Brazilian medicinal plant Solanum cernuum Vell. (Solanaceae). Can. J. Microbiol. 58: 54-66. http://dx.doi.org/10.1139/w11-105 PMid:22182199   Wickert E, de Goes A, de Macedo Lemos EG, de Souza A, et al. (2009). Relações filogenéticas e diversidade de isolados de Guignardia spp oriundos de diferentes hospedeiros nas regiões ITS1-5,8S-ITS2. Rev. Bras. Frutic. 31: 360-380. http://dx.doi.org/10.1590/S0100-29452009000200010
J. Bernardi-Wenzel, Garcia, A., Azevedo, J. L., and Pamphile, J. A., Molecular characterization by amplified ribosomal DNA restriction analysis and antimicrobial potential of endophytic fungi isolated from Luehea divaricata (Malvaceae) against plant pathogenic fungi and pathogenic bacteria, vol. 12, pp. 5072-5084, 2013.
2012
S. A. Rhoden, Garcia, A., Filho, C. J. Rubin, Azevedo, J. L., and Pamphile, J. A., Phylogenetic diversity of endophytic leaf fungus isolates from the medicinal tree Trichilia elegans (Meliaceae), vol. 11, pp. 2513-2522, 2012.
Agusta A, Ohashi K and Shibuya H (2006). Composition of the endophytic filamentous fungi isolated from the tea plant Camellia sinensis. J. Nat. Med. 60: 268-272. http://dx.doi.org/10.1007/s11418-006-0038-2   Arnold AE and Herre EA (2003). Canopy cover and leaf age affect colonization by tropical fungal endophytes: ecological pattern and process in Theobroma cacao (Malvaceae). Mycologia 95: 388-389. http://dx.doi.org/10.2307/3761880 PMid:21156627   Arnold AE, Henk DA, Eells RL, Lutzoni F, et al. (2007). Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR. Mycologia 99: 185-206. http://dx.doi.org/10.3852/mycologia.99.2.185 PMid:17682771   Azevedo JL, Maccheroni Jr W, Pereira JO and Araujo WL (2000). Endophytic Microorganism: A Review on Insect Control and Recent Advances on Tropical Plants. Electron. J. Biotechnol. Available at [http://www.ejbiotechnology. info/content/vol3/issue1/full/4/index.html]. PMCid:3333147   Bernardi-Wenzel J, Garcia A, Filho CJ, Prioli AJ, et al. (2010). Evaluation of foliar fungal endophyte diversity and colonization of medicinal plant Luehea divaricata (Martius et Zuccarini). Biol. Res. 43: 375-384. PMid:21526263   Chareprasert S, Piapukiew J, Thienhirun S, Whalley AJS, et al. (2006). Endophytic fungi of teak leaves Tectona grandis L. and rain tree leaves Samanea saman Merr. World J. Microbiol. Biotechnol. 22: 481-486. http://dx.doi.org/10.1007/s11274-005-9060-x   Crozier J, Thomas SE, Aime MC, Evans HC, et al. (2006). Molecular characterization of fungal endophytic morphospecies isolated from stems and pods of Theobroma cacao. Plant Pathol. 55: 783-791. http://dx.doi.org/10.1111/j.1365-3059.2006.01446.x   de Souza LA, Moscheta SI, Mourão SMK and Silvério A (2001). Morphology and anatomy of the flowers of Trichilia catigua A. Juss., T. elegans A. Juss. and T. pallida Sw. (Meliaceae). Brazilian Arch. Biol. 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