The bacterial diversity in a Brazilian non-disturbed mangrove sediment

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 98, Issue 4, 2010, Pages 541-551

  Dias, Armando C F ^a   Andreote, Fernando D ^a,b   Rigonato, Janaina ^a   Fiore, Marli Fátima ^a   Melo, Itamar S ^b   Araújo, Welington Luiz ^c  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b EMBRAPA CERRADOS   (Brazil)

^c CENA/USP ^*

Author keywords

Culture independent analysis; DGGE; Environmental factors; Tropical microbiology

Indexed keywords

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; ARTICLE; BACTEROIDETES; BETAPROTEOBACTERIA; BRAZIL; CONTROLLED STUDY; DELTAPROTEOBACTERIA; DENATURING GRADIENT GEL ELECTROPHORESIS; ECOSYSTEM; ENVIRONMENTAL FACTOR; FIRMICUTES; GEOGRAPHICAL VARIATION (SPECIES); MANGROVE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEASONAL VARIATION; SEDIMENT; UNINDEXED SEQUENCE;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; BACTERIA; BACTEROIDETES; BASE COMPOSITION; BETAPROTEOBACTERIA; BIODIVERSITY; BRAZIL; DELTAPROTEOBACTERIA; DNA, BACTERIAL; ECOSYSTEM; GAMMAPROTEOBACTERIA; GENETIC VARIATION; GEOLOGIC SEDIMENTS; POLYMERASE CHAIN REACTION; RHIZOPHORACEAE; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; TEMPERATURE;

ACIDOBACTERIA; ACTINOBACTERIA; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; BETAPROTEOBACTERIA; DELTAPROTEOBACTERIA; FIRMICUTES; GAMMAPROTEOBACTERIA; RHIZOPHORACEAE;

EID: 78149409938     PISSN: 00036072     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10482-010-9471-z     Document Type: Article

References (43)

1. DM Alongi 1988 Bacterial productivity and microbial biomass in tropical mangrove sediments Microb Ecol 15 59 79 10.1007/BF02012952
2. JI Baldani VM Reis VLD Baldani J Döbereiner 2002 A brief story of nitrogen fixation in sugarcane-reasons for success in Brazil Funct Plant Biol 29 417 423 10.1071/PP01083
3. SM Barns SL Takala CR Kuske 1999 Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment Appl Environ Microb 65 1731 1737 1:CAS:528:DyaK1MXitlarur4%3D
4. HC Birnboim J Doly 1979 Rapid alkaline extraction procedure for screening recombinant plasmid DNA Nucleic Acids Res 7 1513 1523 1:CAS:528: DyaL3cXlsVKrtQ%3D%3D 10.1093/nar/7.6.1513 388356
5. BC Crump CS Hopkinson ML Sogin JE Hobbie 2004 Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time Appl Environ Microbiol 70 1494 1505 1:CAS:528: DC%2BD2cXisVKju7g%3D 10.1128/AEM.70.3.1494-1505.2004 15006771
6. ACF Dias FD Andreote F Dini-Andreote PT Lacava ALB Sá IS Melo JL Azevedo WL Araújo 2009 Diversity and biotechnological potential of culturable bacteria from Brazilian mangrove sediment W J Microbiol Biotechnol 25 1305 1311 1:CAS:528:DC%2BD1MXnt1CisL4%3D 10.1007/s11274-009-0013-7
7. R Dixon D Kahn 2004 Genetic regulation of biological nitrogen fixation Nat Rev Microbiol 2 621 631 1:CAS:528:DC%2BD2cXlsl2ksLc%3D 10.1038/nrmicro954 15263897
8. NC Duke JO Meynecke S Dittmann, et al. 2007 A world without mangroves? Science 317 41 42 1:CAS:528:DC%2BD2sXns1Cruro%3D 10.1126/science.317.5834.41b 17615322
9. AL Flores-Mireles SC Winans G Holguin 2007 Molecular characterization of diazotrophic and denitrifying bacteria associated with mangrove roots Appl Environ Microbiol 73 7308 7321 1:CAS:528:DC%2BD1cXnsFyhsg%3D%3D 10.1128/AEM.01892-06 17827324
10. IF George MR Liles M Hartmann W Ludwig RM Goodman SN Agathos 2009 Changes in soil Acidobacteria communities after 2, 4, 6-trinitrotoluene contamination FEMS Microbiol Lett 296 159 166 1:CAS:528:DC%2BD1MXotFKjsb0%3D 10.1111/j.1574-6968.2009.01632.x 19459956
11. NCM Gomes H Heuer J Schonfeld R Costa L Mendonca-Hagler K Smalla 2001 Bacterial diversity of the rhizosphere of maize (Zea mays) grown in tropical soil studied by temperature gradient gel electrophoresis Plant Soil 232 167 180 1:CAS:528:DC%2BD3MXlsVCksLs%3D 10.1023/A:1010350406708
12. NCM Gomes LR Borges R Paranhos FN Pinto LCS Mendonça-Hagler K Smalla 2008 Exploring the diversity of bacterial communities in sediments of urban mangrove forests FEMS Microbiol Ecol 66 96 109 1:CAS:528: DC%2BD1cXht1ektL7K 10.1111/j.1574-6941.2008.00519.x
13. B Gonzalez-Acosta Y Bashan NY Hernandez-Saavedra F Ascencio G Cruz-Aguero 2006 Seasonal seawater temperature as the major determinant for populations of culturable bacteria in the sediments of an intact mangrove in an arid region FEMS Microbiol Ecol 55 311 321 1:CAS:528:DC%2BD28Xit1Snur0%3D 10.1111/j.1574-6941.2005.00019.x 16420638
14. AP Harrison Jr 1981 Acidiphilium cryptum gen. nov., sp. nov., heterotrophic bacterium from acidic mineral environments Int J Syst Bacteriol 31 327 332 10.1099/00207713-31-3-327
15. IS Henriques A Alves M Tacão A Almeida A Cunha A Correia 2006 Seasonal and spatial variability of free-living bacterial community composition along an estuarine gradient (Ria de Aveiro, Portugal) Est Coast Shelf Sci 68 139 148 10.1016/j.ecss.2006.01.015
16. H Heuer M Krsek P Baker K Smalla EMH Wellington 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 1:CAS:528:DyaK2sXlt1Wis7c%3D 9251210
17. G Holguin P Vazquez Y Bashan 2001 The role of sediment microorganisms in the productivity, conservation, and rehabilitation of mangrove ecosystems: an overview Biol Fertil Soils 33 265 278 1:CAS:528:DC%2BD3MXhs1Ggsbo%3D 10.1007/s003740000319
18. G Holguin PG Zamorano LED Bashan R Mendoza E Amador Y Bashan 2006 Mangrove health in an arid environment encroached by urban development-a case study Sci Total Environ 363 260 274 1:CAS:528:DC%2BD28XltFChtr4%3D 10.1016/j.scitotenv.2005.05.026 16112715
19. K Kathiresan BL Bingham 2001 Biology of mangroves and mangrove ecosystems Adv Mar Biol 40 81 251 10.1016/S0065-2881(01)40003-4
20. K Kathiresan M Selvam 2006 Evaluation of beneficial bacteria from mangrove soil Bot Mar 49 86 88 1:CAS:528:DC%2BD28Xis1ygsr4%3D 10.1515/BOT.2006.011
21. M Kimura 1980 A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide-sequences J Mol Evol 16 111 120 1:CAS:528:DyaL3MXmtFSktg%3D%3D 10.1007/BF01731581 7463489
22. KP Krishnan SO Fernandes GS Chandan PAL Bharathi 2007 Bacterial contribution to mitigation of iron and manganese in mangrove sediments Mar Pollut Bull 54 1427 1433 1:CAS:528:DC%2BD2sXhtVCmurvF 10.1016/j.marpolbul.2007. 05.023 17632183
23. E Kristensen GM King M Holmer GT Banta MH Jensen K Hansen N Bussarawit 1994 Sulfate reduction, acetate turnover and carbon metabolism in sediments of Ao Nam Bor mangrove, Phuket, Thailand Mar Ecol Prog Ser 109 245 255 1:CAS:528:DyaK2MXhvVKrsbo%3D 10.3354/meps109245
24. DJ Lane B Pace GJ Olsen DA Stahl ML Sogin NR Pace 1985 Rapid-determination of 16S ribosomal-RNA sequences for phylogenetic analyses Proc Natl Acad Sci USA 82 6955 6959 1:CAS:528:DyaL28XjtFalug%3D%3D 10.1073/pnas.82.20.6955 2413450
25. I Letunic P Bork 2006 Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation Bioinformatics 23 127 128 10.1093/bioinformatics/btl529 17050570
26. JB Liang YQ Chen CY Lan NFY Tam QJ Zan LN Huang 2007 Recovery of novel bacterial diversity from mangrove sediment Mar Biol 150 739 747 10.1007/s00227-006-0377-2
27. M Muhling J Woolven-Allen JC Murrell I Joint 2008 Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities ISME J 2 379 392 1:CAS:528:DC%2BD1cXlvVGrtbg%3D 10.1038/ismej.2007.97 18340335
28. G Muyzer EC de Waal AG Uitterlinden 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 1:CAS:528:DyaK3sXit1Kktrk%3D 7683183
29. N Saitou M Nei 1987 The neighbor-joining method-a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425 1:STN:280: DyaL1c7ovFSjsA%3D%3D 3447015
30. PD Schloss J Handelsman 2005 Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness Appl Environ Microbiol 71 1501 1506 1:CAS:528:DC%2BD2MXisVOisb8%3D 10.1128/AEM.71.3.1501-1506.2005 15746353
31. DL Semensatto Jr GCL Araujo RHF Funo J Santa-Cruz D Dias-Brito 2007 Metais e não-metais em sedimentos de um manguezal não- poluído, Ilha do Cardoso, Cananéia (SP) Rev Pesq Geoc 34 25 31
32. CAR Silva BD Smith PS Rainbow 2006 Comparative biomonitors of coastal trace metal contamination in tropical South America (N. Brazil) Mar Environ Res 61 439 455 1:CAS:528:DC%2BD28XjvVagsL4%3D 10.1016/j.marenvres.2006.02.001
33. EM Smith WM Kemp 2003 Planktonic and bacterial respiration along an estuarine gradient: responses to carbon and nutrient enrichment Aquat Microb Ecol 30 251 261 10.3354/ame030251
34. M Sogin HG Morrison JA Huber DM Welch SM Huse PR Neal JM Arrieta GJ Herndl 2006 Microbial diversity in the deep sea and the underexplored "rare biosphere" Proc Natl Acad Sci USA 103 12115 12120 1:CAS:528: DC%2BD28Xotlyisb4%3D 10.1073/pnas.0605127103 16880384
35. A Strangmann Y Bashan L Giani 2008 Methane in pristine and impaired mangrove soils and its possible effect on establishment of mangrove seedlings Biol Fertil Soils 44 511 519 1:CAS:528:DC%2BD1cXjsFKrsw%3D%3D 10.1007/s00374-007-0233-7
36. RG Taketani CA Yoshiura ACF Dias FD Andreote SM Tsai 2010 Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove Antonie van Leeuwenhoek 97 401 411 1:CAS:528:DC%2BC3cXktVCnsb4%3D 10.1007/s10482-010-9422-8 20195901
37. K Tamura J Dudley M Nei S Kumar 2007 MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 Mol Biol Evol 24 1596 1599 1:CAS:528:DC%2BD2sXpsVGrsL8%3D 10.1093/molbev/msm092 17488738
38. B Van Raij JAV Quaggio NM Silva 1986 Extraction of phosphorus, potassium, calcium and magnesium from soils by ion-exchange resin procedure Commun Soil Sci Plant Anal 17 547 566 10.1080/00103628609367733
39. Van Raij B, Cantarella H, Andrade JC, Quaggio JA (2001) Análise química para avaliação da fertilidade de solos tropicais. Instituto Agronômico, Campinas, p 285
40. WG Weisburg SM Barns DA Pelletier DJ Lane 1991 16S ribosomal DNA amplification for phylogenetic study J Bacteriol 173 697 703 1:CAS:528:DyaK3MXhsl2lurY%3D 1987160
41. JP Zehr BB Ward 2002 Nitrogen cycling in the ocean: new perspectives on processes and paradigms Appl Environ Microbiol 68 1015 1024 1:CAS:528: DC%2BD38XitV2qtbc%3D 10.1128/AEM.68.3.1015-1024.2002 11872445
42. HW Zhou CL Guo YS Wong NFY Tam 2006 Genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments FEMS Microbiol Lett 262 148 157 1:CAS:528:DC%2BD28XhtVOmtLvM 10.1111/j.1574-6968.2006.00379.x 16923069
43. HW Zhou TG Luanc F Zoub NFY Tam 2008 Different bacterial groups for biodegradation of three- and four-ring PAHs isolated from a Hong Kong mangrove sediment J Hazard Mat 152 1179 1185 1:CAS:528:DC%2BD1cXjt12mtLo%3D 10.1016/j.jhazmat.2007.07.116