Cultivation of hard-to-culture subsurface mercury-resistant bacteria and discovery of new merA gene sequences

Applied and Environmental Microbiology

Volumn 74, Issue 12, 2008, Pages 3795-3803

  Rasmussen, L D ^a,c   Zawadsky, C ^a   Binnerup, S J ^a   Oregaard G ^b,d   Sorensen S J ^b   Kroer, N ^a  

^a NATIONAL ENVIRONMENTAL RESEARCH INSTITUTE   (Denmark)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^d CHR HANSEN A S   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL GEOCHEMISTRY; BACTERIOLOGY; BIOCHEMISTRY; BIOGEOCHEMISTRY; COLLOIDS; ELECTROPHORESIS; GELATION; GENES; MEMBRANES; MOLECULES; NUCLEIC ACIDS; NUMERICAL METHODS; ORGANIC ACIDS; PLATING; POPULATION STATISTICS; SOILS; STANDARDS; WASTEWATER TREATMENT;

16S RRNA; ACTINOBACTERIA; AMERICAN SOCIETY; BETAPROTEOBACTERIA; CULTURABILITY; CULTURE MEDIUM; DENATURING GRADIENT GEL ELECTROPHORESIS (DGGE) ANALYSIS; DIRECT PLATING; FIRMICUTES; GAMMAPROTEOBACTERIA; GENE SEQUENCING; GROWTH SUPPORT; MERCURY REDUCTION; MERCURY(III); MICROBIAL COMMUNITIES; MOLECULAR TECHNIQUES; NATURAL CONDITIONS; NONSTERILE; PCR PRODUCTS; POLYCARBONATE MEMBRANES; PRE INCUBATION; RESISTANT BACTERIA; SOIL SLURRY;

MERCURY (METAL);

MERCURY; POLYCARBONATE; RIBOSOME RNA;

BACTERIUM; BIOGEOCHEMISTRY; GENETIC ANALYSIS; MERCURY (ELEMENT); MICROBIAL COMMUNITY; RED ALGA; SOIL POLLUTION; SPECIES DIVERSITY;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; ARTICLE; BACTERIAL GROWTH; BACTERIUM CULTURE; BACTEROIDETES; BETAPROTEOBACTERIA; BIOGEOCHEMISTRY; COLONY FORMING UNIT; CONTROLLED STUDY; CULTURE MEDIUM; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA DETERMINATION; DNA EXTRACTION; FIRMICUTES; GAMMAPROTEOBACTERIA; GENE SEQUENCE; MERA GENE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; REDUCTION; RNA GENE; SEQUENCE HOMOLOGY;

ANTI-BACTERIAL AGENTS; BACTERIA; BIODIVERSITY; COLONY COUNT, MICROBIAL; DNA FINGERPRINTING; DNA, BACTERIAL; DNA, RIBOSOMAL; DRUG RESISTANCE, BACTERIAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; GENES, BACTERIAL; MERCURY; MOLECULAR SEQUENCE DATA; NUCLEIC ACID DENATURATION; PHYLOGENY; POLYMERASE CHAIN REACTION; RANDOM AMPLIFIED POLYMORPHIC DNA TECHNIQUE; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; SOIL MICROBIOLOGY;

ACTINOBACTERIA; BACTEROIDETES; BETAPROTEOBACTERIA; FIRMICUTES; GAMMAPROTEOBACTERIA;

EID: 45749120833     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.00049-08     Document Type: Article

References (28)

1. Altschul, S. F., T. K. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Barkay, T., N. Kroer, L. D. Rasmussen, and S. J. Sørensen. 1995. Conjugal transfer at natural population densities in a microcosm simulating an estuarine environment. FEMS Microb. Ecol. 16:43-54.
3. Barkay, T., S. M. Miller, and A. O. Summers. 2003. Bacterial mercury resistance from atoms to ecosystems. FEMS Microb. Ecol. 27:355-384.
4. Bollmann, A., K. Lewis, and S. S. Epstein. 2007. Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl. Environ. Microbiol. 73:6386-6390.
5. Clément, P., D. H. Pieper, and B. González. 2001. Molecular characterization of a deletion/duplication rearrangement in tfd genes from Ralstonia eutropha JMP134(pJP4) that improves growth on 3-chlorobenzoic acid but abolishes growth on 2,4-dichlorophenoxyacetic acid. Microbiology 147:2141-2148.
6. Connon, S. A., and S. J. Giovannoni. 2002. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol. 68:3878-3885.
7. Ferrari, B. C., S. J. Binnerup, and M. Gillings. 2005. Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Appl. Environ. Microbiol. 71:8714-8720.
8. Gachhui, R., J. Chaudhuri, S. Ray, K. Pahan, and A. Mandal. 1997. Studies on mercury-detoxicating enzymes from a broad-spectrum mercury-resistant strain of Flavobacterium rigense. Folia Microbiol. 42:337-343.
9. Gans, J., M. Wolinsky, and J. Dunbar. 2005. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387-1390.
10. Hansen, B. M., P. H. Damgaard, J. Eilenberg, and J. C. Pedersen. 1998. Molecular and phenotypic characterization of Bacillus thuringiensis isolated from leaves and insects. J. Invertebr. Pathol. 71:106-114.
11. Janssen, P. H., P. S. Yates, B. E. Grinton, P. M. Taylor, and M. Sait. 2002. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria and Verrucomicrobia. Appl. Environ. Microbiol. 68:2391-2396.
12. Johnsen, A. R., and N. Kroer. 2007. Effects of stress and other environmental factors on horizontal plasmid transfer assessed by direct quantification of discrete transfer events. FEMS Microb. Ecol. 59:718-728.
13. Kaeberlein, T., K. Lewis, and S. S. Epstein. 2002. Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science 296:1127-1129.
14. Kim, E.-H., R. P. Mason, E. T. Porter, and H. L. Soulen. 2006. The impact of resuspension on sediment mercury dynamics, and methylmercury production and fate: a mesocosm study. Mar. Chem. 102:300-315.
15. Kriger, A. A., and R. R. Turner. 1995. Field analysis of mercury in water, sediment and soil using static headspace analysis. Water Air Soil Pollut. 80:1295-1304.
16. Muyzer, G., E. C. de Waal, and A. G. 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.
17. Muyzer, G., A. Teske, C. O. Wirsen, and H. W. Jannasch. 1995. Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 164:165-172.
18. Ní Chadhain, S. M., J. K. Schaefer, S. Crane, G. J. Zylstra, and T. Barkay. 2006. Analysis of mercuric reductase (merA) gene diversity in an anaerobic mercury-contaminated sediment enrichment. Environ. Microbiol. 8:1746-1752.
19. Oregaard, G., and S. J. Sørensen. 2007. High diversity of bacterial mercuric reductase genes from surface and sub-surface floodplain soil (Oak Ridge, USA). ISME J. 1:453-467.
20. Pinhassi, J., J. P. Bowman, O. I. Nedashkovskaya, I. Lekunberri, L. Gomez-Consarnau, and C. Pedros-Alio. 2006. Leeuwenhoekiella blandensis sp. nov., a genome-sequenced marine member of the family Flavobacteriaceae. Int. J. Syst. Evol. Microbiol. 56:1489-1493.
21. Rasmussen, L. D., and S. J. Sørensen. 2001. Effects of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil. FEMS Microbiol. Lett. 36:1-9.
22. Rasmussen, L. D., S. J. Sørensen, R. R. Turner, and T. Barkay. 2000. Application of a mer-lux biosensor for estimating bioavailable mercury in soil. Soil Biol. Biochem. 32:639-646.
23. Sait, M., P. Hugenholtz, and P. H. Janssen. 2002. Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ. Microbiol. 4:654-666.
24. Sørensen, S. J., M. Bailey, L. H. Hansen, N. Kroer, and S. Wuertz. 2005. Studying plasmid horizontal transfer in situ: a critical review. Nat. Rev. Microbiol. 3:700-710.
25. Stevenson, B. S., S. A. Eichorst, J. T. Wertz, T. M. Schmidt, and J. A. Breznak. 2004. New strategies for cultivation and detection of previously uncultured microbes. Appl. Environ. Microbiol. 70:4748-4755.
26. Svenning, M. M., I. Wartiainen, A. G. Hestnes, and S. J. Binnerup. 2003. Isolation of methane oxidizing bacteria from soil by use of a soil substrate membrane system. FEMS Microb. Ecol. 44:347-354.
27. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
28. Vetriani, C., Y. S. Chew, S. M. Miller, J. Yagi, J. Coombs, R. A. Lutz, and T. Barkay. 2005. Mercury adaptation among bacteria from a deep-sea hydrothermal vent. Appl. Environ. Microbiol. 71:220-226.