Aquatic Microbial Habitats Within a Neotropical Rainforest: Bromeliads and pH-Associated Trends in Bacterial Diversity and Composition

Microbial Ecology

Volumn 61, Issue 3, 2011, Pages 529-542

  Goffredi, Shana K ^a   Kantor, Adam H ^a   Woodside, Walter T ^a  

^a OCCIDENTAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CARBON; NITROGEN; RNA 16S;

ARTICLE; BACTERIUM; BIODIVERSITY; BROMELIACEAE; CHEMISTRY; CLASSIFICATION; COSTA RICA; DNA SEQUENCE; GENETICS; MICROBIOLOGY; PH; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SOIL; TREE; TROPIC CLIMATE;

BACTERIA; BIODIVERSITY; BROMELIACEAE; CARBON; COSTA RICA; DNA, BACTERIAL; HYDROGEN-ION CONCENTRATION; NITROGEN; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL; TREES; TROPICAL CLIMATE;

ACIDOBACTERIA; AECHMEA; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; BETAPROTEOBACTERIA; FIRMICUTES; PLANCTOMYCETES; WERAUHIA;

EID: 79953751610     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-010-9781-8     Document Type: Article

References (48)

1. Beals EW (1984) Bray-Curtis ordination: an effective strategy for analysis of multivariate ecological data. Adv Ecol Res 14: 1-55.
2. Benlloch S, Rodriguez-Valera F, Martinez-Murcia AJ (1995) Bacterial diversity in two coastal lagoons deduced from 16S rDNA PCR amplification and partial sequencing. FEMS Microbiol Ecol 18: 267-280.
3. Benzing DH (1970) Foliar permeability and the absorption of minerals and organic nitrogen by certain tank bromeliads. Bot Gaz 131: 23-31.
4. Benzing DH (2000) Bromeliaceae: profile of an adaptive radiation. Cambridge University Press, Cambridge.
5. Benzing DH, Derr JA, Titus JE (1972) The water chemistry of microcosms associated with the bromeliad Aechmea bracteata. Amer Mid Natr 87: 60-70.
6. Bermudes D, Benzing DH (1991) Nitrogen fixation in association with Ecuadorean bromeliads. J Trop Ecol 7: 531-536.
7. Bissett A, Bowman J, Burke C (2006) Bacterial diversity in organically-enriched fish farm sediments. FEMS Microbiol Ecol 55: 48-56.
8. Brighigna L, Montaini P, Favilli F, Trejo AC (1992) Role of nitrogen-fixing bacterial microflora in the epiphytism of Tillandsia (Bromeliaceae). Am J Bot 79: 723-727.
9. Burkert U, Warnecke F, Babenzien D, Zwirnmann E, Pernthaler J (2003) Members of a readily enriched beta-proteobacterial clade are common in surface waters of a humic lake. Appl Environ Microbiol 69: 6550-6559.
10. Dedysh SN (2009) Exploring methanotroph diversity in acidic northern wetlands: molecular and cultivation-based studies. Microbiol 78: 665-669.
11. Dedysh SN, Khmelenina VN, Suzina NE, Trotsenko YA, Semrau JD, Liesack W, Tiedje JM (2002) Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog. Int J Syst Evol Microbiol 52: 251-261.
12. Dedysh SN, Pankratov TA, Belova SE, Kulichevskaya IS, Liesack W (2006) Phylogenetic analysis and in situ identification of bacteria community composition in an acidic Sphagnum peat bog. Appl Environ Microbiol 27: 2110-2117.
13. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072.
14. Eichorst SA, Breznak JA, Schmidt TM (2007) Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the Phylum Acidobacteria. Appl Environ Microbiol 73: 2708-2717.
15. Fish D (1983) Phytotelmata: terrestrial plants as hosts for aquatic insect communities. In: Frank JH, Lounibos LP (eds) Phytotelmata: flora and fauna. Plexus, New Jersey, pp 1-28.
16. Goffredi SK, Orphan VJ (2010) Bacterial community shifts in taxa and diversity in response to localized organic loading in the deep sea. Environ Microbiol 12: 344-363.
17. Guimaraes-Souza BA, Mendes GB, Bento L, Morotta H, Santoro AL, Esteves FA, Pinho L, Farjalla VF, Enrich-Prast A (2006) Limnological parameters in the water accumulated in tropical bromeliads. Acta Limnol Bras 18: 47-53.
18. Hanson RS, Netrusov AI, Tsuji K (1992) The obligate methanotrophic bacteria Methylococcus, Methylomonas, and Methylosinus. In: Balows A, Truper HG, Dworkin M, Harder W, Schleifer K-H (eds) The prokaryotes. Springer, New York, pp 2350-2364.
19. Hartman WH, Richardson CJ, Vilgalys R, Bruland GL (2008) Environmental and anthropogenic controls over bacterial communities in wetland soils. Proc Natl Acad Sci 105: 17842-17847.
20. Imhoff JF (2006) The phototrophic alpha-proteobacteria. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes, vol 5., pp 41-64.
21. Inselsbacher E, Cambui CA, Richter A, Stange CF, Mercier H, Wanek W (2007) Microbial activities and foliar uptake of nitrogen in the epiphytic bromeliad Vriesea gigantea. New Phytol 175: 311-320.
22. Jollès P, Muzzarelli RAA (1999) Chitin and Chitinases. Birkhäuser Verlag, Basel.
23. Kawahara N, Shigematsu K, Miyadai T, Kondo R (2009) Comparison of bacterial communities in fish farm sediments along an organic enrichment gradient. Aquaculture 287: 107-113.
24. Kulichevskaya IS, Guzev VS, Gorlenko VM, Liesack W, Dedysh SN (2006) Rhodoblastus sphagnicola sp. nov., a novel acidophilic purple non-sulfur bacterium from Sphagnum peat bog. Int J Syst Evol Microbiol 56: 1397-1402.
25. Laessle AM (1961) A micro-limnological study of Jamaican bromeliads. Ecol 42: 499-517.
26. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115-175, In.
27. Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75: 5111-5120.
28. Lopez LCS, Alves RRD, Rios RI (2009) Micro-environmental factors and the endemism of bromeliad aquatic fauna. Hydrobiol 625: 151-156.
29. Loy A, Schulz C, Lucker S, Schopfer-Wendels A, Stoecker K, Baranyi C, Lehner A, Wagner M (2005) 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales". Appl Environ Microbiol 71: 1373-1386.
30. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar EA (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
31. McCune B, Mefford MJ (2006) PC-ORD: multivariate analysis of ecological data, vol. MjM Software, Glenedon Beach.
32. Mehta MP, Butterfield DA, Baross JA (2003) Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the Juan de Fuca Ridge. Appl Environ Microbiol 69: 960-970.
33. Merwin MC, Rentmeester SA, Nadkarni NM (2003) The influence of host tree species on the distribution of epiphytic bromeliads in experimental monospecific plantations, La Selva, Costa Rica. Biotropica 35: 37-47.
34. Pittl E, Innerebner G, Wanek W, Insam H (2010) Microbial communities of arboreal and ground soils in the Esquinas rainforest, Costa Rica. Plant Soil 329: 65-74.
35. Richardson BA (1999) The bromeliad microcosm and the assessment of faunal diversity in a neotropical forest. Biotropica 31: 321-336.
36. Rui J, Peng J, Lu Y (2009) Succesion of bacterial populations during plant residue decomposition in rice field soil. Appl Environ Microbiol 75: 4879-4886.
37. Sait M, Davis KER, Janssen PH (2006) Effect of pH on isolation and distribution of members of subdivision 1 of the phylum Acidobacteria occurring in soil. Appl Environ Microbiol 72: 1852-1857.
38. Spring S (2006) The genera Leptothrix and Sphaerotilus. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The Prokaryotes, vol. 5., pp 758-777.
39. Sugden AM, Robins RJ (1979) Aspects of the ecology of vascular epiphytes in colombian cloud forests, I. The distribution of the epiphytic flora. Biotropica 11: 173-188.
40. Swofford DL (1998) PAUP*: phylogenetic analysis using parsimony (*and other methods). Sinauer, Sunderland.
41. van Veen WL, Mulder EG, Deinema MH (1978) The Sphaerotilus-Leptothrix group of bacteria. Microbiol Rev 42: 329-356.
42. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
43. Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM (2009) Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl Environ Microbiol 75: 2046-2056.
44. Winkler U, Zotz G (2008) Highly efficient uptake of phosphorus in epiphytic bromeliads. Ann Bot (Lond) 103: 477-484.
45. Xiao X, Yin X, Lin J, Sun L, You Z, Wang P, Wang F (2005) Chitinase genes in lake sediments of Ardley Island, Antarctica. Appl Environ Microbiol 71: 7904-7909.
46. Yamada A, Inoue T, Noda S, Hongoh Y, Ohkuma M (2007) Evolutionary trend of phylogenetic diversity of nitrogen fixation genes in the gut community of wood-feeding termites. Mol Ecol 16: 3768-3777.
47. Yarwood SA, Myrold DD, Högberg MN (2009) Termination of belowground C allocation by trees alters soil fungal and bacterial communities in a boreal forest. FEMS Microbiol Ecol 70: 151-162.
48. Zhang W, Ki J-S, Qian P-Y (2008) Microbial diversity in polluted harbor sediments I: bacterial community assessment based on four clone libraries of 16S rDNA. Estuar Coast Shelf Sci 76: 668-681.