Metagenomic analysis of a freshwater toxic cyanobacteria bloom

FEMS Microbiology Ecology

Volumn 64, Issue 1, 2008, Pages 9-27

  Pope, Phillip B ^a   Patel, Bharat K C ^a  

^a GRIFFITH UNIVERSITY   (Australia)

Author keywords

Australia; Cyanobacteria; Cylindrospermopsis; Freshwater; Metagenomics

Indexed keywords

RNA 16S;

COMMUNITY COMPOSITION; CYANOBACTERIUM; FRESHWATER; GENOMICS; PHYLOGENETICS;

ACTINOBACTERIA; APHANIZOMENON; ARTICLE; AUSTRALIA; BACTERIAL ARTIFICIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL METABOLISM; BACTERIAL OVERGROWTH; CELL COUNT; CHLOROFLEXI; CYANOBACTERIUM; CYLINDROSPERMOPSIS; FRESHWATER ENVIRONMENT; GAMMAPROTEOBACTERIA; GENE LIBRARY; GENE SEQUENCE; GENETIC ANALYSIS; MOLECULAR CLONING; MOLECULAR WEIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYTOPLANKTON; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; UNINDEXED SEQUENCE; VERRUCOMICROBIUM;

AUSTRALIA; BACTERIA; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CYANOBACTERIA; DNA, BACTERIAL; FRESH WATER; GENE LIBRARY; GENES, RRNA; GENOME, BACTERIAL; GENOMICS; PHYLOGENY; PLANKTON; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

AUSTRALASIA; AUSTRALIA;

ACTINOBACTERIA; APHANIZOMENON; BACTERIA (MICROORGANISMS); BACTEROIDETES; CHLOROFLEXI; CHLOROFLEXI (CLASS); CYANOBACTERIA; CYLINDROSPERMOPSIS; GAMMAPROTEOBACTERIA; PLANCTOMYCETES; PROTEOBACTERIA; VERRUCOMICROBIUM;

EID: 40549100750     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2008.00448.x     Document Type: Article

References (33)

1. Altschul SF, Gish W, Miller W, Myers EW lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215 : 403 410.
2. Borodovsky M McIninch J (1993) GeneMark: parallel gene recognition for both DNA strands. Comput Chem 17 : 123 133.
3. Burford MA O'Donohue MJ (2006) A comparison of phytoplankton community assemblages in artificially and naturally mixed subtropical water reservoirs. Freshwater Biol 51 : 973 982.
4. Carmichael WW, He JW, Carmichael WW, Eschendor J, He ZR Juan YM (1988) Partial structural determination of hepatotoxic peptides from Microcystis aeruginosa (cyanobacterium) collecterd in ponds of central China. Toxicon 26 : 1213 1217.
5. Chefetz B, Tarchitzky J, Deshmukh AP, Hatcher PG Chen Y (2002) Structural characterization of soil organic matter and humic acids in particle-size fractions of an agricultural soil. Soil Sci Soc Am J 66 : 129 141.
6. Colberg PJ Young LY (1985) Aromatic and Volatile Acid Intermediates Observed during Anaerobic Metabolism of Lignin-Derived Oligomers. Appl Environ Microbiol 49 : 350 358.
7. Curtis TP, Sloan WT Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99 : 10494.
8. Felsenstein J (2006) PHYLIP (Phylogeny Inference Package) version 3.66. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
9. Ferrandez A, Prieto MA, Garcia JL Diaz E (1997) Molecular characterization of PadA, a phenylacetaldehyde dehydrogenase from Escherichia coli. FEBS Lett 406 : 23 27.
10. Glockner FO, Fuchs B Amann R (1999) Bacterioplankton composition of lakes and oceans: a comparison based on fluorescence in situ hybridization. Appl Environ Microbiol 65 : 3721 3726.
11. Hall TA (1998) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41 : 95 98.
12. Harada K-i, Ohtani I, Iwamoto K, Suzuki M, Watanabe MF, Watanabe M Terao K (1994) Isolation of cylindrospermopsin from a cyanobacterium Umezakia natans and its screening method. Toxicon 32 : 73 84.
13. Izaguirre G Taylor WD (2004) A guide to geosmin- and MIB-producing cyanobacteria in the United States. Water Sci Technol 49 : 19 24.
14. Jain R, Rivera MC Lake JA (1999) Horizontal gene transfer among genomes: the complexity hypothesis. 96 : 3801 3806.
15. Jiménez JI, Miñambres B, García JL Díaz E (2002) Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ Microbiol 4 : 824 841.
16. Markowitz VM, Korzeniewski F, Palaniappan K et al 2006) The integrated microbial genomes (IMG) system. Nucleic Acids Res 34 : D344 D348.
17. Mohamed M, Ismail W, Heider J Fuchs G (2002) Aerobic metabolism of phenylacetic acids in Azoarcus evansii. Archiv Microbiol 178 : 180 192.
18. Namikoshi M Rinehart KL (1996) Bioactive compounds produced by cyanobacteria. J Ind Microbiol 17 : 373 384.
19. Nesbø CL, Boucher Y, Dlutek M Ford Doolittle W (2005) Lateral gene transfer and phylogenetic assignment of environmental fosmid clones. Environ Microbiol 7 : 2011 2026.
20. Olivera ER, Minambres B, Garcõa B, Muniz C, Moreno MA Ferrandez A (1998) Molecular characterization of the phenylacetic acid catabolic pathway in Pseudomonas putida U: the phenylacetyl-CoA catabolon. Proc Natl Acad Sci USA 95 : 6419 6424.
21. Ollagnier-de Choudens S, Loiseau L, Sanakis Y, Barras F Fontecave M (2005) Quinolinate synthetase, an iron-sulfur enzyme in NAD biosynthesis. FEBS Lett 579 : 3737 3743.
22. Redburn AC Patel BKC (1993) Phylogenetic analysis of Desulfotomaculum thermobenzoicum using polymerase chain-amplified 16S rRNA-specific DNA. FEMS Microbiol Lett 115 : 33 38.
23. Rozen S Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. Bioinformatics Methods and Protocols: Methods in Molecular Biology (Krawetz S Misener S, eds), pp. 365 386. Humana Press, Totowa, NJ.
24. Sambrook J, Fritsch EF Maniatis T (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbour Laboratory Press, Cold Spring Harbour, New York.
25. Schloss PD Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71 : 1501 1506.
26. Spanevello MD Patel BKC (2004) The phylogenetic diversity of Thermus and Meiothermus from microbial mats of an Australian subsurface aquifer runoff channel. FEMS Microbiol Ecol 50 : 63 73.
27. Stein JL, Marsh TL, Wu KY, Shizuya H DeLong EF (1996) Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment front a planktonic marine archaeon. J Bacteriol 178 : 591.
28. Torsvik V, Ovreas L Thingstad TF (2002) Prokaryotic diversity - magnitude, dynamics, and controlling factors. Science 296 : 1064 1066.
29. Van de Peer Y De Wachter R (1994) TREECON for windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10 : 569 570.
30. Velasco A, Alonso S, Garcia JL, Perera J Diaz E (1998) Genetic and functional analysis of the styrene catabolic cluster of Pseudomonas sp. strain Y2. J Bacteriol 180 : 1063 1071.
31. Wang Q, Garrity GM, Tiedje JM Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73 : 5261 5267.
32. Wiegand C Pflugmacher S (2005) Ecotoxicological effects of selected cyanobacterial secondary metabolites: a short review. Toxicol Appl Pharmacol 203 : 201 218.
33. Wolfgang L, Strunk O, Klugbauer S et al 1998) Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19 : 554 568.