Microbial Diversity of Brazilian Biomes

  • Thiago Bruce
  • Alinne de Castro
  • Ricardo Kruger
  • Cristiane C. Thompson
  • Fabiano L. Thompson
Chapter
Part of the Advances in Microbial Ecology book series (AMIE)

Abstract

Brazil is a megabiodiverse country with approximately 20% of the total number of described species on the planet (Mittermeier et al. 2004). It has the largest tropical forest cover (>6 million km2, corresponding to approximately 30 times the area of the United Kingdom or approx. 20 times the area of Germany) and one of the largest marine realms (>4 million km2) of the planet. The diversity of biomes (e.g., the Amazon and Atlantic Forests, Southern Plains or Pampas, Cerrado (a savanna-like vegetation), Pantanal (wetlands), Caatinga, coral reefs, oceanic islands, mangroves, salt marshes, coastal environments, and deep sea; (IBGE 2004)) allows for the diversification of a variety of life forms. Between 1999 and 2009, more than 1,200 new species of plants and vertebrates were discovered only in the Amazon region, corresponding to one new discovery every 3 days (WWF 2010). There is indeed a considerable amount of literature on the biodiversity of plants and animals in Brazil. Their diversity is used as a basic parameter in the implementation of management actions on priority areas for conservation and protection (Myers et al. 2000). Studies on the microbial diversity are comparatively much scarcer. For instance, only recently the microbial diversity of Amazon and Cerrado soils and the marine realm have been studied in a systematic way. The aim of this chapter was to establish an overview on the microbial diversity studies (N = 150) carried out in Brazil mainly in the last 5 years, including taxonomic studies based on cultured microorganisms and culture-independent studies based on molecular fingerprints and 16S rRNA clone libraries. The chapter focuses mainly on prokaryotes with environmental (e.g., coral holobionts), agricultural (e.g., crop promoting), and biotechnological importance (e.g., bioremediation).

Keywords

Cellulose Hydrocarbon Polycyclic Aromatic Hydrocarbon Bacillus Sewage 

Notes

Acknowledgments

The authors thank CNPq, CAPES, FAPERJ, and FAP-DF for funding.

References

  1. Aboim MCR, Coutinho HLC, Peixotoc RS, Barbosa JC, Rosado AS (2008) Soil bacterial community structure and soil quality in a slash-and-burn cultivation system in Southeastern Brazil. Appl Soil Ecol 38:100–108CrossRefGoogle Scholar
  2. Abreu F, Martins JL, Silveira TS, Keim CN, de Barros HGPL et al (2007) ‘Candidatus Magnetoglobus multicellularis’, a multicellular, magnetotactic prokaryote from a hypersaline environment. Int J Syst Evol Microbiol 57:1318–1322PubMedCrossRefGoogle Scholar
  3. Adesemoye A, Torbert H, Kloepper J (2009) Plant growth-promoting rhizobacteria allow reduced application rates of chemical fertilizers. Microb Ecol 58:921–929PubMedCrossRefGoogle Scholar
  4. Adriano EA, Arana S, Alves AL, Silva MRM, Ceccarelli PS et al (2009) Myxobolus cordeiroi n. sp., a parasite of Zungaro jahu (Siluriformes: Pimelodiade) from Brazilian pantanal: morphology, phylogeny and histopathology. Vet Parasitol 162:221–229PubMedCrossRefGoogle Scholar
  5. Albino U, Saridakis DP, Ferreira MC, Hungria M, Vinuesa P et al (2006) High diversity of diazotrophic bacteria associated with the carnivorous plant Drosera villosa var. villosa growing in oligotrophic habitats in Brazil. Plant Soil 287:199–207CrossRefGoogle Scholar
  6. Almeida WI, Vieira RP, Cardoso AM, Silveira CB, Costa RG et al (2009) Archaeal and bacterial communities of heavy metal contaminated acidic waters from zinc mine residues in Sepetiba Bay. Extremophiles 13:263–271PubMedCrossRefGoogle Scholar
  7. Alves N, Neto OSM, Silva BSO, de Moura RL, Francini RB et al (2010) Diversity and pathogenic potential of vibrios isolated from Abrolhos Bank corals. Environ Microbiol Rep 2:90–95CrossRefGoogle Scholar
  8. Alves-Prado HF, Pavezzi FC, Leite RSR, de Oliveira VM, Sette LD et al (2010) Screening and production study of microbial xylanase producers from Brazilian Cerrado. Appl Biochem Biotechnol 161:333–346PubMedCrossRefGoogle Scholar
  9. Amado-Filho G, Salgado L, Rebelo M, Rezende C, Karez C et al (2008) Heavy metals in benthic organisms from Todos os Santos Bay, Brazil. Braz J Biol 68:95–100PubMedCrossRefGoogle Scholar
  10. Andreote F, Mendes R, Dini-Andreote F, Rossetto P, Labate C et al (2008) Transgenic tobacco revealing altered bacterial diversity in the rhizosphere during early plant development. Antonie Van Leeuwenhoek 93:415–424PubMedCrossRefGoogle Scholar
  11. Andreote F, Carneiro R, Salles J, Marcon J, Labate C et al (2009) Culture-independent assessment of rhizobiales-related alphaproteobacteria and the diversity of methylobacterium in the rhizosphere and rhizoplane of transgenic eucalyptus. Microb Ecol 57:82–93PubMedCrossRefGoogle Scholar
  12. Araujo J, Kruger R Characterization of cerrado soils’ bacterial diversity. unpublishedGoogle Scholar
  13. Auch AF, von Jan M, Klenk HP, Göker M (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2(1):117–34Google Scholar
  14. Azevedo C, Casal G, Matos P, Matos E (2008) A new species of Myxozoa, Henneguya rondoni n. sp. (Myxozoa), from the peripheral nervous system of the Amazonian fish, Gymnorhamphichthys rondoni (Teleostei). J Eukaryot Microbiol 55:229–234PubMedCrossRefGoogle Scholar
  15. Azevedo C, Casal G, Mendonça I, Matos E (2009a) Fine structure of Henneguya hemiodopsis sp. n. (Myxozoa), a parasite of the gills of the Brazilian teleostean fish Hemiodopsis microlepes (Hemiodontidae). Memórias do Instituto Oswaldo Cruz 104:975–979PubMedGoogle Scholar
  16. Azevedo C, Casal G, Garcia P, Matos P, Teles-Grilo L et al (2009b) Ultrastructural and phylogenetic data of Chloromyxum riorajum sp. nov. (Myxozoa), a parasite of the stingray Rioraja agassizii in Southern Brazil. Dis Aquat Organ 85:41–51PubMedCrossRefGoogle Scholar
  17. Azevedo C, Casal G, Matos P, Ferreira I, Matos E (2009c) Light and electron microscopy of the spore of Myxobolus heckelii n. sp. (Myxozoa), parasite from the Brazilian fish Centromochlus heckelii (Teleostei, Auchenipteridae). J Eukaryot Microbiol 56:589–593PubMedCrossRefGoogle Scholar
  18. Azevedo C, Casal G, Mendonça I, Carvalho E, Matos P et al (2010) Light and electron microscopy of Myxobolus sciades n. sp. (Myxozoa), a parasite of the gills of the Brazilian fish Sciades herzbergii (Block, 1794) (Teleostei: Ariidae). Memórias do Instituto Oswaldo Cruz 105:203–207PubMedCrossRefGoogle Scholar
  19. Azevedo C, Casal G, Marques D, Silva E, Matos E (2011) Ultrastructure of Myxobolus brycon n. sp. (Phylum Myxozoa), parasite of the piraputanga fish Brycon hilarii (Teleostei) from Pantanal (Brazil). J Eukaryot Microbiol 58:88–93PubMedCrossRefGoogle Scholar
  20. Barbosa AC, Cadete RM, Gomes FCO, Lachance M-A, Rosa CA (2009) Candida materiae sp. nov., a yeast species isolated from rotting wood in the Atlantic Rain Forest. Int J Syst Evol Microbiol 59:2104–2106PubMedCrossRefGoogle Scholar
  21. Barbosa A, Morais C, Morais P, Rosa L, Pimenta R et al (2011) Wickerhamiella pagnoccae sp. nov. and Candida tocantinsensis sp. nov., two ascomycetous yeasts from flower bracts of Heliconia psittacorum (Heliconiaceae). Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.032466-0, ijs.0.032466-032460
  22. Barneah O, Ben-Dov E, Kramarsky-Winter E, Kushmaro A (2007) Characterization of black band disease in Red Sea stony corals. Environ Microbiol 9:1995–2006PubMedCrossRefGoogle Scholar
  23. Beneduzi A, Peres D, da Costa PB, Bodanese Zanettini MH, Passaglia LMP (2008a) Genetic and phenotypic diversity of plant-growth-promoting bacilli isolated from wheat fields in southern Brazil. Res Microbiol 159:244–250PubMedCrossRefGoogle Scholar
  24. Beneduzi A, Peres D, Vargas LK, Bodanese-Zanettini MH, Passaglia LMP (2008b) Evaluation of genetic diversity and plant growth promoting activities of nitrogen-fixing bacilli isolated from rice fields in South Brazil. Appl Soil Ecol 39:311–320CrossRefGoogle Scholar
  25. Beneduzi A, Costa PB, Parma M, Melo IS, Bodanese-Zanettini MH et al (2010) Paenibacillus riograndensis sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Triticum aestivum. Int J Syst Evol Microbiol 60:128–133PubMedCrossRefGoogle Scholar
  26. Borneman J, Triplett E (1997) Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl Environ Microbiol 63:2647–2653PubMedGoogle Scholar
  27. Brasil MD, Baldani JL, Baldani VLD (2005) Occurrence and diversity diazotrophic bacteria associated to forage grasses of the Pantanal in the state of Mato Grosso do Sul. Revista Brasileira De Ciencia Do Solo 29:179–190CrossRefGoogle Scholar
  28. Brito EMS, Guyoneaud R, Goñi-Urriza M, Ranchou-Peyruse A, Verbaere A et al (2006) Characterization of hydrocarbonoclastic bacterial communities from mangrove sediments in Guanabara Bay, Brazil. Res Microbiol 157:752–762PubMedCrossRefGoogle Scholar
  29. Bruce T, Martinez I, Maia Neto O, Vicente A, Kruger R et al (2010) Bacterial community diversity in the Brazilian Atlantic forest soils. Microb Ecol 60:840–849PubMedCrossRefGoogle Scholar
  30. Bruce T, Meirelles P, Garcia G, Paranhos R, Rezende C et al (2011) Total ecology of the Abrolhos reef Bank. SubmmitedGoogle Scholar
  31. Cadete RM, Santos RO, Melo MA, Mouro A, Gonçalves DL et al (2009) Spathaspora arborariae sp. nov., a d-xylose-fermenting yeast species isolated from rotting wood in Brazil. FEMS Yeast Res 9:1338–1342PubMedCrossRefGoogle Scholar
  32. Carvalho F, Vazoller R, Foronda A, Pellizari V (2007) Phylogenetic study of species in pristine and polluted aquatic samples from a tropical Atlantic Forest ecosystem. Curr Microbiol 55:288–293PubMedCrossRefGoogle Scholar
  33. Casal G, Matos E, Azevedo C (2006) A new mixozoan parasite from the amazonian fish Metynnis argenteus (Teleostei, characidae): light electronic microscope observations. J Parasitol 92:817–821PubMedCrossRefGoogle Scholar
  34. Casal G, Matos E, Teles-Grilo ML, Azevedo C (2008) A new microsporidian parasite, Potaspora morhaphis n. gen., n. sp. (Microsporidia) infecting the Teleostean fish, Potamorhaphis guianensis from the River Amazon. Morphological, ultrastructural and molecular characterization. Parasitology 135:1053–1064PubMedCrossRefGoogle Scholar
  35. Casal G, Matos E, Teles-Grilo ML, Azevedo C (2009a) Morphological and genetical description of Loma psittaca sp. n. isolated from the Amazonian fish species Colomesus psittacus. Parasitol Res 105:1261–1271PubMedCrossRefGoogle Scholar
  36. Casal G, Garcia P, Matos P, Monteiro E, Matos E et al (2009b) Fine structure of Chloromyxum menticirrhi n. sp. (Myxozoa) infecting the urinary bladder of the marine teleost Menticirrhus americanus (Sciaenidae) in Southern Brazil. Eur J Protistol 45:139–146PubMedCrossRefGoogle Scholar
  37. Casal G, Matos E, Teles-Grilo L, Azevedo C (2010) Ultrastructural and molecular characterization of a new microsporidium parasite from the Amazonian fish, Gymnorhamphichthys rondoni (Rhamphichthyidae). J Parasitol 96:1155–1163PubMedCrossRefGoogle Scholar
  38. Cenciani K, Lambais MR, Cerri CC, de Azevedo LCB, Feigl BJ (2009) Bacteria diversity and microbial biomass in forest, pasture and fallow soils in the southwestern Amazon basin. Revista Brasileira De Ciencia Do Solo 33:907–916CrossRefGoogle Scholar
  39. Chen W-M, James EK, Coenye T, Chou J-H, Barrios E et al (2006) Burkholderia mimosarum sp. nov., isolated from root nodules of Mimosa spp. from Taiwan and South America. Int J Syst Evol Microbiol 56:1847–1851PubMedCrossRefGoogle Scholar
  40. Chen W-M, de Faria SM, James EK, Elliott GN, Lin K-Y et al (2007) Burkholderia nodosa sp. nov., isolated from root nodules of the woody Brazilian legumes Mimosa bimucronata and Mimosa scabrella. Int J Syst Evol Microbiol 57:1055–1059PubMedCrossRefGoogle Scholar
  41. Chen W-M, de Faria SM, Chou J-H, James EK, Elliott GN et al (2008) Burkholderia sabiae sp. nov., isolated from root nodules of Mimosa caesalpiniifolia. Int J Syst Evol Microbiol 58:2174–2179PubMedCrossRefGoogle Scholar
  42. Chimetto LA, Brocchi M, Thompson CC, Martins RCR, Ramos HR et al (2008) Vibrios dominate as culturable nitrogen-fixing bacteria of the Brazilian coral Mussismilia hispida. Syst Appl Microbiol 31:312–319PubMedCrossRefGoogle Scholar
  43. Chimetto LA, Brocchi M, Gondo M, Thompson CC, Gomez-Gil B et al (2009) Genomic diversity of vibrios associated with the Brazilian coral Mussismilia hispida and its sympatric zoanthids (Palythoa caribaeorum, Palythoa variabilis and Zoanthus solanderi). J Appl Microbiol 106:1818–1826PubMedCrossRefGoogle Scholar
  44. Chimetto LA, Cleenwerck I, Brocchi M, Willems A, De Vos P et al (2010a) Marinomonas brasiliensis sp. nov. isolated from the coral Mussismilia hispida and reclassification of Marinomonas basaltis as a later synonym of Marinomonas communis. Int J Syst Evol Microbiol 61:1170–1175, ijs.0.024661-024660PubMedCrossRefGoogle Scholar
  45. Chimetto LA, Cleenwerck I, Thompson CC, Brocchi M, Willems A et al (2010b) Photobacterium jeanii sp. nov., isolated from corals and zoanthids. Int J Syst Evol Microbiol 60:2843–2848PubMedCrossRefGoogle Scholar
  46. Chimetto LA, Cleenwerck I, Brocchi M, Willems A, De Vos P et al (2011a) Marinobacterium coralli sp. nov., isolated from mucus of coral (Mussismilia hispida). Int J Syst Evol Microbiol 61:60–64PubMedCrossRefGoogle Scholar
  47. Chimetto LA, Cleenwerck I, Alves N Jr, Silva BS, Brocchi M et al (2011b) Vibrio communis sp. nov., isolated from the marine animals Mussismilia hispida, Phyllogorgia dilatata, Palythoa caribaeorum, Palythoa variabilis and Litopenaeus vannamei. Int J Syst Evol Microbiol 61:362–368PubMedCrossRefGoogle Scholar
  48. Chimetto L, Cleenwerck I, Moreira APB, Brocchi M, Willems A et al (2011) Vibrio variabilissp. nov. and Vibrio marinus sp. nov., isolated from Palythoa caribaeorum. Int J Syst Evol Microbiol 61:3009–3015, ijs.0.026997-026990PubMedCrossRefGoogle Scholar
  49. Clementino MM, Fernandes CC, Vieira RP, Cardoso AM, Polycarpo CR et al (2007) Archaeal diversity in naturally occurring and impacted environments from a tropical region. J Appl Microbiol 103:141–151PubMedCrossRefGoogle Scholar
  50. Clementino MM, Vieira RP, Cardoso AM, Nascimento APA, Silveira CB et al (2008) Prokaryotic diversity in one of the largest hypersaline coastal lagoons in the world. Extremophiles 12:595–604PubMedCrossRefGoogle Scholar
  51. Coelho MRR, Da Mota FF, Carneiro NP, Marriel IE, Paiva E et al (2007) Diversity of Paenibacillus spp. in the rhizosphere of four sorghum (Sorghum bicolor) cultivars sown with two contrasting levels of nitrogen fertilizer assessed by rpoB-based PCR-DGGE and sequencing analysis. J Microbiol Biotechnol 17:753–760PubMedGoogle Scholar
  52. Coelho G, Douanla-Meli C, Langer E, Langer G (2010) Hypochnella verrucospora (Basidiomycota, Atheliales), a neotropical new species with ornamented basidiospores. Mycologia 102:1158–1162PubMedCrossRefGoogle Scholar
  53. Coenye T, Gevers D, de Peer YV, Vandamme P, Swings J (2005) Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 29:147–167PubMedGoogle Scholar
  54. Costa R, Gomes NCM, Peixoto RS, Rumjanek N, Berg G et al (2006) Diversity and antagonistic potential of Pseudomonas spp. associated to the rhizosphere of maize grown in a subtropical organic farm. Soil Biol Biochem 38:2434–2447CrossRefGoogle Scholar
  55. Cury JC, Araujo FV, Coelho-Souza SA, Peixoto RS, Oliveira JAL et al (2011) Microbial diversity of a Brazilian Coastal Region influenced by an upwelling system and anthropogenic activity. PLoS One 6:e16553PubMedCrossRefGoogle Scholar
  56. da Mota FF, Gomes EA, Paiva E, Seldin L (2005) Assessment of the diversity of Paenibacillus species in environmental samples by a novel rpoB-based PCR-DGGE method. FEMS Microbiol Ecol 53:317–328PubMedCrossRefGoogle Scholar
  57. da Silva J, Barreto R, Pereira O (2008) Pseudocercospora cryptostegiae-madagascariensis sp. nov. on Cryptostegia madagascariensis, an exotic vine involved in major biological invasions in Northeast Brazil. Mycopathologia 166:87–91PubMedCrossRefGoogle Scholar
  58. Dall’Agnol L, Martins R, Vallinoto A, Ribeiro K (2008) Diversity of Chromobacterium violaceum isolates from aquatic environments of state of Pará, Brazilian Amazon. Memorias Do Instituto Oswaldo Cruz 103:678–682PubMedCrossRefGoogle Scholar
  59. de Castro AP, Quirino BF, Pappas G, Kurokawa AS, Neto EL et al (2008) Diversity of soil fungal communities of Cerrado and its closely surrounding agriculture fields. Arch Microbiol 190:129–139PubMedCrossRefGoogle Scholar
  60. de Castro AP, Araujo SD, Reis AMM, Moura RL, Francini RB et al (2010) Bacterial community associated with healthy and diseased reef coral Mussismilia hispida from Eastern Brazil. Microb Ecol 59:658–667PubMedCrossRefGoogle Scholar
  61. de O Santos E, Alves N Jr, Dias GM, Mazotto AM, Vermelho A et al (2011) Genomic and proteomic analyses of the coral pathogen Vibrio coralliilyticus reveal a diverse virulence repertoire. ISME J 5(9):1471–1483CrossRefGoogle Scholar
  62. de Oliveira VM, Manfio GP, da Costa Coutinho HL, Keijzer-Wolters AC, van Elsas JD (2006) A ribosomal RNA gene intergenic spacer based PCR and DGGE fingerprinting method for the analysis of specific rhizobial communities in soil. J Microbiol Methods 64:366–379PubMedCrossRefGoogle Scholar
  63. de Souza M, Moreira F, Cruz L, Miana de Faria S, Marsh T, Martínez-Romero E et al (2006) Azorhizobium doebereinerae sp. nov. microsymbiont of Sesbania virgata (Caz.) Pers. Syst Appl Microbiol 29:197–206CrossRefGoogle Scholar
  64. Dias RJP, Cabral AF, Siqueira-Castro ICV, da Silva-Neto ID, D’Agosto M (2010a) Morphometric study of a Brazilian strain of Carchesium polypinum (Ciliophora: Peritrichia) attached to Pomacea figulina (Mollusca: Gastropoda), with notes on a high infestation. Zoologia 27:483–488Google Scholar
  65. Dias ACF, Andreote FD, Rigonato J, Fiore MF, Melo IS et al (2010b) The bacterial diversity in a Brazilian non-disturbed mangrove sediment. Antonie Van Leeuwenhoek, Int J Gen Mol Microbiol 98:541–551CrossRefGoogle Scholar
  66. Evans HC, Elliot SL, Hughes DP (2011) Hidden diversity behind the zombie-ant fungus Ophiocordyceps unilateralis: four new species described from carpenter ants in Minas Gerais, Brazil. PLoS ONE 6:e17024PubMedCrossRefGoogle Scholar
  67. Faoro H, Alves AC, Souza EM, Rigo LU, Cruz LM et al (2010) Influence of soil characteristics on the diversity of bacteria in the Southern Brazilian Atlantic forest. Appl Environ Microbiol 76:4744–4749PubMedCrossRefGoogle Scholar
  68. Fernando S, Wang J, Sparling K, Paranhos R, Garcia G et al (2011) A core microbiome of the major South Atlantic reef builder coral Mussismilia. SubmmitedGoogle Scholar
  69. Fontana LF, Mendonça Filho JG, Pereira Netto AD, Sabadini-Santos E, de Figueiredo Jr AG et al (2010) Geomicrobiology of cores from Suruí Mangrove – Guanabara Bay – Brazil. Mar Pollut Bull 60:1674–1681PubMedCrossRefGoogle Scholar
  70. Fontes M, Suzuki M, Cottrell M, Abreu P (2011) Primary production in a subtropical stratified coastal lagoon—contribution of anoxygenic phototrophic bacteria. Microb Ecol 61:223–237PubMedCrossRefGoogle Scholar
  71. Fuentefria AM, Suh S-O, Landell MF, Faganello J, Schrank A et al (2008) Trichosporon insectorum sp. nov., a new anamorphic basidiomycetous killer yeast. Mycol Res 112:93–99PubMedCrossRefGoogle Scholar
  72. Gabardo IT, Meniconi MFG, Falcão LV, Vital NAA, Pereira RCL et al (2000) Hydrocarbon and ecotoxicity in seawater and sediment samples of Guanabara Bay after the oil spill in January 2000. In: Proceedings 2001 international oil spill conference. American Petroleum Institute Publ., pp. 941–950Google Scholar
  73. Gomes NCM, Borges LR, Paranhos R, Pinto FN, Mendonca-Hagler LCS et al (2008) Exploring the diversity of bacterial communities in sediments of urban mangrove forests. FEMS Microbiol Ecol 66:96–109CrossRefGoogle Scholar
  74. Gomes NCM, Flocco CG, Costa R, Junca H, Vilchez R et al (2010a) Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia. FEMS Microbiol Ecol 74:276–290PubMedCrossRefGoogle Scholar
  75. Gomes NCM, Cleary DFR, Pinto FN, Egas C, Almeida A et al (2010b) Taking root: enduring effect of rhizosphere bacterial colonization in mangroves. PLoS One 5:e14065PubMedCrossRefGoogle Scholar
  76. Gregoracci et al (2012) Structuring of bacterioplankton diversity in a large tropical Bay. PLOS ONE, in pressPubMedCrossRefGoogle Scholar
  77. Grossman JM, O’Neill BE, Tsai SM, Liang BQ, Neves E et al (2010) Amazonian anthrosols support similar microbial communities that differ distinctly from those extant in adjacent, unmodified soils of the same mineralogy. Microb Ecol 60:192–205PubMedCrossRefGoogle Scholar
  78. Hahn MW, Kasalicky V, Jezbera J, Brandt U, Simek K (2010) Limnohabitans australis sp. nov., isolated from a freshwater pond, and emended description of the genus Limnohabitans. Int J Syst Evol Microbiol 60:2946–2950PubMedCrossRefGoogle Scholar
  79. Hardoim CCP, Costa R, Araujo FV, Hajdu E, Peixoto R et al (2009) Diversity of bacteria in the marine sponge Aplysina fulva in Brazilian coastal waters. Appl Environ Microbiol 75:3331–3343PubMedCrossRefGoogle Scholar
  80. Hungria M, Astolfi-Filho S, Chueire LMO, Nicolás MF, Santos EBP et al (2005) Genetic characterization of Chromobacterium isolates from black water environments in the Brazilian Amazon. Lett Appl Microbiol 41:17–23PubMedCrossRefGoogle Scholar
  81. Hungria M, Chueire LMO, Megias M, Lamrabet Y, Probanza A et al (2006) Genetic diversity of indigenous tropical fast-growing rhizobia isolated from soybean nodules. Plant Soil 288:343–356CrossRefGoogle Scholar
  82. IBGE (2004) Mapas de biomas do Brasil. Instituto Brasileiro de Geografia e EstatísticaGoogle Scholar
  83. Inácio J, Landell MF, Valente P, Wang P-H, Wang Y-T et al (2008) Farysizyma gen. nov., an anamorphic genus in the Ustilaginales to accommodate three novel epiphytic basidiomycetous yeast species from America, Europe and Asia. FEMS Yeast Res 8:499–508PubMedCrossRefGoogle Scholar
  84. Jesus ED, Marsh TL, Tiedje JM, Moreira FMD (2009) Changes in land use alter the structure of bacterial communities in Western Amazon soils. ISME J 3:1004–1011CrossRefGoogle Scholar
  85. Kim JS, Sparovek G, Longo RM, De Melo WJ, Crowley D (2007) Bacterial diversity of terra preta and pristine forest soil from the Western Amazon. Soil Biol Biochem 39:684–690CrossRefGoogle Scholar
  86. Korenblum E, Valoni E, Penna M, Seldin L (2010) Bacterial diversity in water injection systems of Brazilian offshore oil platforms. Appl Microbiol Biotechnol 85:791–800PubMedCrossRefGoogle Scholar
  87. Lambais MR, Crowley DE, Cury JC, Büll RC, Rodrigues RR (2006) Bacterial diversity in tree canopies of the Atlantic Forest. Science 312:1917PubMedCrossRefGoogle Scholar
  88. Landell MF, Inacio J, Fonseca A, Vainstein MH, Valente P (2009) Cryptococcus bromeliarum sp. nov., an orange-coloured basidiomycetous yeast isolated from bromeliads in Brazil. Int J Syst Evol Microbiol 59:910–913PubMedCrossRefGoogle Scholar
  89. Landell MF, Billodre R, Ramos JP, Leoncini O, Vainstein MH et al (2010) Candida aechmeae sp. nov. and Candida vrieseae sp. nov., novel yeast species isolated from the phylloplane of bromeliads in Southern Brazil. Int J Syst Evol Microbiol 60:244–248PubMedCrossRefGoogle Scholar
  90. Leão ZMAN, Kikuchi RKP (2005) A relic coral fauna threatened by global changes and human activities, Eastern Brazil. Mar Pollut Bull 51:599–611PubMedCrossRefGoogle Scholar
  91. Lemke M, Lienau E, Rothe J, Pagioro T, Rosenfeld J et al (2009) Description of freshwater bacterial assemblages from the upper Paraná river floodpulse system, Brazil. Microb Ecol 57:94–103PubMedCrossRefGoogle Scholar
  92. Lima HN, Schaefer CER, Mello JWV, Gilkes RJ, Ker JC (2002) Pedogenesis and pre-Colombian land use of “Terra Preta Anthrosols” (“Indian black earth”) of Western Amazonia. Geoderma 110:1–17CrossRefGoogle Scholar
  93. Lima AS, Nobrega RSA, Barberi A, da Silva K, Ferreira DF et al (2009) Nitrogen-fixing bacteria communities occurring in soils under different uses in the Western Amazon Region as indicated by nodulation of siratro (Macroptilium atropurpureum). Plant Soil 319:127–145CrossRefGoogle Scholar
  94. Lins-de-Barros M, Vieira R, Cardoso A, Monteiro V, Turque A et al (2010) Archaea, bacteria, and algal plastids associated with the reef-building corals Siderastrea stellata and Mussismilia hispida from Búzios, South Atlantic Ocean, Brazil. Microb Ecol 59:523–532PubMedCrossRefGoogle Scholar
  95. Luvizotto D, Marcon J, Andreote F, Dini-Andreote F, Neves A et al (2010) Genetic diversity and plant-growth related features of Burkholderia spp. from sugarcane roots. World J Microbiol Biotechnol 26:1829–1836CrossRefGoogle Scholar
  96. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66:506–577PubMedCrossRefGoogle Scholar
  97. Maciel BM, Santos ACF, Dias JCT, Vidal RO, Dias RJC 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 8:375–388PubMedCrossRefGoogle Scholar
  98. Maciel-Souza MD, Macrae A, Volpon AGT, Ferreira PS, Mendonca-Hagler LC (2006) Chemical and microbiological characterization of mangrove sediments after a large oil-spill in Guanabara Bay, RJ, Brazil. Braz J Microbiol 37:262–266CrossRefGoogle Scholar
  99. Mann CC (2002) The real dirt on rainforest fertility. Science 297:920–923PubMedCrossRefGoogle Scholar
  100. Mao-Jones J, Ritchie KB, Jones LE, Ellner SP (2010) How microbial community composition regulates coral disease development. PLoS Biol 8:e1000345PubMedCrossRefGoogle Scholar
  101. Marris E (2005) Conservation in Brazil: the forgotten ecosystem. Nature 437:944–945PubMedCrossRefGoogle Scholar
  102. Martins JL, Silveira TS, Silva KT, Lins U (2009) Salinity dependence of the distribution of multicellular magnetotactic prokaryotes in a hypersaline lagoon. Int Microbiol 12:193–201PubMedGoogle Scholar
  103. MdF F, Neilan BA, Copp JN, Rodrigues JLM, Tsai SM et al (2005) Characterization of nitrogen-fixing cyanobacteria in the Brazilian Amazon floodplain. Water Res 39:5017–5026CrossRefGoogle Scholar
  104. Mendes R, Pizzirani-Kleiner AA, Araujo WL, Raaijmakers JM (2007) Diversity of cultivated endophytic bacteria from sugarcane: genetic and biochemical characterization of Burkholderia cepacia complex isolates. Appl Environ Microbiol 73:7259–7267PubMedCrossRefGoogle Scholar
  105. Menezes CBA, Bonugli-Santos RC, Miqueletto PB, Passarini MRZ, Silva CHD et al (2010) Microbial diversity associated with algae, ascidians and sponges from the north coast of São Paulo state, Brazil. Microbiol Res 165:466–482PubMedCrossRefGoogle Scholar
  106. Milanin T, Eiras JC, Arana S, Maia AA, Alves AL et al (2010) Phylogeny, ultrastructure, histopathology and prevalence of Myxobolus oliveirai sp. nov., a parasite of Brycon hilarii (Characidae) in the Pantanal wetland, Brazil. Memórias do Instituto Oswaldo Cruz 105:762–769PubMedCrossRefGoogle Scholar
  107. Miransari M (2011) Arbuscular mycorrhizal fungi and nitrogen uptake. Arch Microbiol 193:77–81PubMedCrossRefGoogle Scholar
  108. Mittermeier RA, Robles-Gil P, Hoffmann M, Pilgrim JD, Brooks TM, Mittermeier CG, Lamoreux JL, Fonseca G (2004) Hotspots revisited: earth’s biologically richest and most endangered terrestrial ecoregions. CEMEX, Mexico CityGoogle Scholar
  109. Monteiro J, Vollú R, Coelho M, Alviano C, Blank A et al (2009) Comparison of the bacterial community and characterization of plant growth-promoting rhizobacteria from different genotypes of Chrysopogon zizanioides (L.) Roberty (Vetiver) rhizospheres. J Microbiol 47:363–370PubMedCrossRefGoogle Scholar
  110. Muyzer G, Stams AJM (2008) The ecology and biotechnology of sulphate-reducing bacteria. Nat Rev Microbiol 6:441–454PubMedGoogle Scholar
  111. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403:853–858PubMedCrossRefGoogle Scholar
  112. Nakatani AS, Martines AM, Nogueira MA, Fagotti DSL, Oliveira AG et al (2011) Changes in the genetic structure of bacteria and microbial activity in an agricultural soil amended with tannery sludge. Soil Biol Biochem 43:106–114CrossRefGoogle Scholar
  113. Pace NR, Stahl DA, Lane DJ, Olsen GJ (1985) Analyzing natural microbial populations by rRNA sequences. ASM News 51:4–12Google Scholar
  114. Pagnocca FC, Legaspe MFC, Rodrigues A, Ruivo CCC, Nagamoto NS et al (2010) Yeasts isolated from a fungus-growing ant nest, including the description of Trichosporon chiarellii sp. nov., an anamorphic basidiomycetous yeast. Int J Syst Evol Microbiol 60:1454–1459PubMedCrossRefGoogle Scholar
  115. Peixoto R, Chaer G, Carmo F, Araújo F, Paes J et al (2011) Bacterial communities reflect the spatial variation in pollutant levels in Brazilian mangrove sediment. Antonie Van Leeuwenhoek 99:341–354PubMedCrossRefGoogle Scholar
  116. Pereira AA, Hungria M, Franchini JC, Kaschuk G, de Oliveira LM et al (2007) Qualitative and quantitative changes in soil microbiota and biological nitrogen fixation under different soybean managements. Revista Brasileira De Ciencia Do Solo 31:1397–1412CrossRefGoogle Scholar
  117. Pereira LF, Costa CRL Jr, Brasileiro BTRV, de Morais MA Jr (2011) Lachancea mirantina sp. nov., an ascomycetous yeast isolated from the cachaca fermentation process. Int J Syst Evol Microbiol 61:989–992PubMedCrossRefGoogle Scholar
  118. Perin L, Martinez-Aguilar L, Paredes-Valdez G, Baldani JI, Estrada-de los Santos P et al (2006) Burkholderia silvatlantica sp. nov., a diazotrophic bacterium associated with sugar cane and maize. Int J Syst Evol Microbiol 56:1931–1937PubMedCrossRefGoogle Scholar
  119. Ramos PL, Van Trappen S, Thompson FL, Rocha RCS, Barbosa HR et al (2010) Screening for endophytic nitrogen-fixing bacteria in Brazilian sugarcane varieties used in organic farming and description of Stenotrophomonas pavanii sp. nov. Int J Syst Evol Microbiol 61:926–931, ijs.0.019372-019370PubMedCrossRefGoogle Scholar
  120. Reis AMM, Araújo SD Jr, Moura RL, Francini-Filho RB, Pappas G Jr et al (2009) Bacterial diversity associated with the Brazilian endemic reef coral Mussismilia braziliensis. J Appl Microbiol 106:1378–1387PubMedCrossRefGoogle Scholar
  121. Ribeiro RA, Barcellos FG, Thompson FL, Hungria M (2009) Multilocus sequence analysis of Brazilian Rhizobium microsymbionts of common bean (Phaseolus vulgaris L.) reveals unexpected taxonomic diversity. Res Microbiol 160:297–306PubMedCrossRefGoogle Scholar
  122. Rodrigues DF, da C Jesus E, Ayala-del-Rio HL, Pellizari VH, Gilichinsky D et al (2009) Biogeography of two cold-adapted genera: Psychrobacter and Exiguobacterium. ISME J 3:658–665PubMedCrossRefGoogle Scholar
  123. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AKM et al (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290PubMedGoogle Scholar
  124. Roesch LFW, Camargo FAO, Bento FM, Triplett EW (2008) Biodiversity of diazotrophic bacteria within the soil, root and stem of field-grown maize. Plant Soil 302:91–104CrossRefGoogle Scholar
  125. Rosa CA, Lachance M-A, Teixeira LCRS, Pimenta RS, Morais PB (2007a) Metschnikowia cerradonensis sp. nov., a yeast species isolated from ephemeral flowers and their nitidulid beetles in Brazil. Int J Syst Evol Microbiol 57:161–165PubMedCrossRefGoogle Scholar
  126. Rosa CA, Pagnocca FC, Lachance M-A, Ruivo CCC, Medeiros AO et al (2007b) Candida flosculorum sp. nov. and Candida floris sp. nov., two yeast species associated with tropical flowers. Int J Syst Evol Microbiol 57:2970–2974PubMedCrossRefGoogle Scholar
  127. Rosa CA, Jindamorakot S, Limtong S, Nakase T, Pagnocca FC et al (2009a) Candida golubevii sp. nov, an asexual yeast related to Metschnikowia lunata. Int J Syst Evol Microbiol 60:704–706, ijs.0.014050-014050PubMedCrossRefGoogle Scholar
  128. Rosa CA, Morais PB, Lachance M-A, Santos RO, Melo WGP et al (2009b) Wickerhamomyces queroliae sp. nov. and Candida jalapaonensis sp. nov., two yeast species isolated from Cerrado ecosystem in North Brazil. Int J Syst Evol Microbiol 59:1232–1236PubMedCrossRefGoogle Scholar
  129. Rosa CA, Jindamorakot S, Limtong S, Nakase T, Lachance M-A et al (2009c) Synonymy of the yeast genera Moniliella and Trichosporonoides and proposal of Moniliella fonsecae sp. nov. and five new species combinations. Int J Syst Evol Microbiol 59:425–429PubMedCrossRefGoogle Scholar
  130. Ruivo CCC, Lachance M-A, Rosa CA, Bacci M Jr, Pagnocca FC (2006) Candida heliconiae sp. nov., Candida picinguabensis sp. nov. and Candida saopaulonensis sp. nov., three ascomycetous yeasts from Heliconia velloziana (Heliconiaceae). Int J Syst Evol Microbiol 56:1147–1151PubMedCrossRefGoogle Scholar
  131. Santos R, Cadete R, Badotti F, Mouro A, Wallheim D et al (2011) Candida queiroziae sp. nov., a cellobiose-fermenting yeast species isolated from rotting wood in Atlantic Rain Forest. Antonie Van Leeuwenhoek 99:635–642PubMedCrossRefGoogle Scholar
  132. Schmidt TM, DeLong EF, Pace NR (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 173:4371–4378PubMedGoogle Scholar
  133. Sekar R, Mills DK, Remily ER, Voss JD, Richardson LL (2006) Microbial communities in the surface mucopolysaccharide layer and the black band microbial mat of black band-diseased Siderastrea siderea. Appl Environ Microbiol 72:5963–5973PubMedCrossRefGoogle Scholar
  134. Sette LD, Simioni KCM, Vasconcellos SP, Dussan LJ, Neto EVS et al (2007) Analysis of the composition of bacterial communities in oil reservoirs from a southern offshore Brazilian basin. Antonie Van Leeuwenhoek 91:253–266PubMedCrossRefGoogle Scholar
  135. Siqueira-Castro ICV, Paiva TdS, Silva-Neto IDd (2009) Morphology of Parastrongylidium estevesi comb. nov. and Deviata brasiliensis sp. nov. (Ciliophora: Stichotrichia) from a sewage treatment plant in Rio de Janeiro, Brazil. Zoologia (Curitiba, Impresso) 26:774–786CrossRefGoogle Scholar
  136. Souchie EL, Saggin-Junior OJ, Silva EMR, Campello EFC, Azcon R et al (2006) Communities of P-solubilizing bacteria, fungi and arbuscular mycorrhizal fungi in grass pasture and secondary forest of Paraty, RJ Brazil. Anais Da Academia Brasileira De Ciencias 78:183–193PubMedCrossRefGoogle Scholar
  137. Sousa OV, Macrae A, Menezes FGR, Gomes NCM, Vieira RHSF et al (2006) The impact of shrimp farming effluent on bacterial communities in mangrove waters, Ceará, Brazil. Mar Pollut Bull 52:1725–1734PubMedCrossRefGoogle Scholar
  138. Souza RFd, Coelho RRR, Macrae A, Soares RMA, Nery DdCM et al (2008) Streptomyces lunalinharesii sp. nov., a chitinolytic streptomycete isolated from cerrado soil in Brazil. Int J Syst Evol Microbiol 58:2774–2778PubMedCrossRefGoogle Scholar
  139. Taketani R, Tsai S (2010a) The influence of different land uses on the structure of archaeal communities in Amazonian anthrosols based on 16S rRNA and amoA genes. Microb Ecol 59:734–743PubMedCrossRefGoogle Scholar
  140. Taketani R, Tsai S (2010b) The influence of different land uses on the structure of archaeal communities in Amazonian anthrosols based on 16S rRNA and amoA genes. Microb Ecol 59:734–743PubMedCrossRefGoogle Scholar
  141. Taketani R, Franco N, Rosado A, van Elsas J (2010a) Microbial community response to a simulated hydrocarbon spill in mangrove sediments. J Microbiol 48:7–15PubMedCrossRefGoogle Scholar
  142. Taketani R, Yoshiura C, Dias A, Andreote F, Tsai S (2010b) Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove. Antonie Van Leeuwenhoek 97:401–411PubMedCrossRefGoogle Scholar
  143. Teather RM, Wood PJ (1982) Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 43:777–780PubMedGoogle Scholar
  144. Thompson C, Vicente A, Souza R, Vasconcelos A, Vesth T et al (2009) Genomic taxonomy of vibrios. BMC Evol Biol 9:258PubMedCrossRefGoogle Scholar
  145. Thompson F, Bruce T, Gonzalez A, Cardoso A, Clementino M et al (2011) Coastal bacterioplankton community diversity along a latitudinal gradient in Latin America by means of V6 tag pyrosequencing. Arch Microbiol 193:105–114PubMedCrossRefGoogle Scholar
  146. Turque AS, Cardoso AM, Silveira CB, Vieira RP, Freitas FAD et al (2008) Bacterial communities of the marine sponges Hymeniacidon heliophila and Polymastia janeirensis and their environment in Rio de Janeiro, Brazil. Mar Biol 155:135–146CrossRefGoogle Scholar
  147. Turque AS, Batista D, Silveira CB, Cardoso AM, Vieira RP et al (2010) Environmental shaping of sponge associated archaeal communities. PLoS One 5:e15774PubMedCrossRefGoogle Scholar
  148. Valverde A, Delvasto P, Peix A, Velazquez E, Santa-Regina I et al (2006) Burkholderia ferrariae sp. nov., isolated from an iron ore in Brazil. Int J Syst Evol Microbiol 56:2421–2425PubMedCrossRefGoogle Scholar
  149. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K et al (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438PubMedGoogle Scholar
  150. Varga J, Kocsube S, Toth B, Frisvad JC, Perrone G et al (2007) Aspergillus brasiliensis sp. nov., a biseriate black Aspergillus species with world-wide distribution. Int J Syst Evol Microbiol 57:1925–1932PubMedCrossRefGoogle Scholar
  151. Vieira R, Clementino M, Cardoso A, Oliveira D, Albano R et al (2007) Archaeal communities in a tropical estuarine ecosystem: Guanabara Bay, Brazil. Microb Ecol 54:460–468PubMedCrossRefGoogle Scholar
  152. Vieira RP, Gonzalez AM, Cardoso AM, Oliveira DN, Albano RM et al (2008) Relationships between bacterial diversity and environmental variables in a tropical marine environment, Rio de Janeiro. Environ Microbiol 10:189–199PubMedGoogle Scholar
  153. Viola LB, Attias M, Takata CSA, Campaner M, De Souza W et al (2009) Phylogenetic analyses based on small subunit rRNA and glycosomal glyceraldehyde-3-phosphate dehydrogenase genes and ultrastructural characterization of two snake trypanosomes: Trypanosoma serpentis n. sp. from Pseudoboa nigra and Trypanosoma cascavelli from Crotalus durissus terrificus. J Eukaryot Microbiol 56:594–602PubMedCrossRefGoogle Scholar
  154. Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F (2007) Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol 9:2707–2719PubMedCrossRefGoogle Scholar
  155. WWF (2010) Amazônia Viva! Uma década de descobertas 1999–2009Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Thiago Bruce
    • 1
  • Alinne de Castro
    • 2
  • Ricardo Kruger
    • 2
  • Cristiane C. Thompson
    • 3
  • Fabiano L. Thompson
    • 1
  1. 1.Laboratory of Microbiology, Institute of BiologyFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
  2. 2.Laboratory of EnzymologyUniversity of Brasilia (UNB)BrasiliaBrazil
  3. 3.Laboratory of Microbial GeneticsInstitute Oswaldo Cruz (IOC-FIOCRUZ)Rio de JaneiroBrazil

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