Endogenous isolation of replicon probes for assessing plasmid ecology of marine sediment microbial communities

Microbiology

Volumn 147, Issue 8, 2001, Pages 2089-2101

  Cook, M A ^a   Osborn, A M ^a   Bettandorff, J ^a   Sobecky, P A ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

DNA; Extrachromasomal elements; Extraction; Marine sediment; Replication origins

Indexed keywords

BACTERIAL DNA; HELICASE;

ARTICLE; CONTROLLED STUDY; ECOLOGY; GENE REPLICATION; GEOGRAPHIC DISTRIBUTION; GRAM NEGATIVE BACTERIUM; HOST; MARINE ENVIRONMENT; MICROBIOLOGY; MOLECULAR BIOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PLASMID; POLYMERASE CHAIN REACTION; POPULATION; PRIORITY JOURNAL; PSEUDOALTEROMONAS; REPLICON; SCREENING; SEASHORE; SEDIMENT; SEQUENCE HOMOLOGY; SHEWANELLA; UNITED STATES; VIBRIO;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PROKARYOTA; PROTEOBACTERIA; PSEUDOALTEROMONAS; SHEWANELLA; SHEWANELLA SP.; VIBRIO; VIBRIO SP.;

EID: 0034858372     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/00221287-147-8-2089     Document Type: Article

References (71)

1. Gapped BLAST and PSIAST: A new generation of protein database search programs
2. The replication of an IncL/M plasmid is subject to antisense control
3. Taxonomy of aerobic marine eubacteria
4. Coincident plasmids and antimicrobial resistance in marine bacteria isolated from polluted and unpolluted Atlantic Ocean samples
5. Occurrence of antibiotic and metal resistance and plasmids in Bacillus strains isolated from marine sediment
6. BRL pUC host: E. coli DH5α™ competent cells
7. The Arcanobacterium (Actinomyces) pyogenes plasmid pAP1 is a member of the pIJ101/pJV1 family of rolling circle replication plasmids
8. A fourth class of theta-replicating plasmids: The pAMβ1 family from Gram-positive bacteria
9. Distribution of bacterial plasmids in clean and polluted sites in a South Wales river
10. Improved oligonucleotide site-directed mutagenesis using M13 vectors
11. Molecular characterization of a plasmid isolated from Riemerella anatipestifer
12. High genetic homology between plasmids of human and animal origins conferring resistance to the aminoglycosides gentamicin and apramycin
13. Identification and classification of bacterial plasmids
14. Conjugative plasmids isolated from bacteria in marine environments show various degrees of homology to each other and are not closely related to well-characterized plasmids
15. Plasmid classification: Incompatibility grouping
16. The use of mini-Gal plasmids for rapid incompatibility grouping of conjugative R plasmids
17. Broad host range DNA cloning system for Gram-negative bacteria: Construction of a gene of Rhizobium meliloti
18. Complete DNA sequence and analysis of an emerging cryptic plasmid isolated from Yersinia pestis
19. Effect of mercury addition on plasmid incidence and gene mobilizing capacity in bulk soil
20. Comparison of the plasmid types obtained by two distantly related recipients in biparental exogenous plasmid isolations from soil
21. Evolution in bacteria and levels of selection
22. Isolation, characterization, and transfer of cryptic gene-mobilizing plasmids in the wheat rhizosphere
23. Plasmid frequency in natural populations of estuarine microorganisms
24. Detection and characterization of broad-host-range plasmids in environmental bacteria by PCR
25. Phylogenetic analysis of the bacterial communities in marine sediments
26. Broad host range conjugative and mobilizable plasmids in Gram-negative bacteria
27. Incidence of plasmids in marine Vibrio spp. isolated from an oil field in the northwestern Gulf of Mexico
28. Frequency of antibiotic and heavy metal resistance, pigmentation and plasmids in bacteria of the marine air-water interface
29. Characterization of plasmid regions of foodborne Yersinia enterocolitica biogroup 1A strains hybridizing to the Yersinia enterocolitica virulence plasmid
30. Functional insights into pG12, a cryptic rolling-circle replicating plasmid from Bacillus thuringiensis
31. Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria
32. Origin and evolution of plasmids
33. Genetic analysis of bacteriophage P4 using P4-plasmid ColE1 hybrids
34. Molecular characterization of the replicon of the Pediococcus pentosaceus 43200 pediocin A plasmid pMD136
35. Complete nucleotide sequence of the Streptomyces lividans plasmid pIJ101 and correlation of the sequence with genetic properties
36. Plasmids isolated from the sugar beet phyllosphere show little or no homology to molecular probes currently available for plasmid typing
37. Bacterial plasmids in Antarctic natural assemblages
38. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses
39. Diversity of mercury resistance plasmids obtained by exogenous isolation from the bacteria of sugar beet in three successive years
40. Plasmid incompatibility
41. Staphylococcal plasmids and their replication
42. Distribution of plasmids in groundwater bacteria
43. The evolution of bacterial plasmids
44. Development and application of molecular tools in the study of IncN-related plasmids from lakewater sediments
45. Complete nucleotide sequence of Birmingham IncPα plasmids. Compilation and comparative analysis
46. Related plasmids found in an English Lake District stream
47. Nucleotide sequence and characterization of a cryptic plasmid from a marine Vibrio sp
48. The plasmid cloning vector pBR325 contains a 482 base-pair-long inverted duplication
49. Characterization of mercury resistance mechanisms in marine sediment microbial communities
50. Genetic characterization of the stabilizing functions of a region of broad-host-range plasmid RK2
51. The neighbor-joining method: A new method for reconstructing phylogenetic trees
52. Comparative analysis of the pC194 group of rolling circle plasmids
53. Plasmids carried by antibiotic-resistant marine bacteria
54. PCR-based detection of mobile genetic elements in total community DNA
55. Self-transmissible mercury resistance plasmids with gene-mobilizing capacity in soil bacterial populations: Influence of wheat roots and mercury addition
56. Plasmids isolated from marine sediment microbial communities contain replication and incompatibility regions unrelated to those of known plasmid groups
57. Isolation of broad-host-range replicons from marine sediment bacteria
58. Replication and control of circular bacterial plasmids
59. Nucleotide sequence of the region of an origin of replication of the antibiotic resistance plasmid R6K
60. Plasmid R6K DNA replication. I. Complete nucleotide sequence of an autonomously replicating segment
61. Retrotransfer or gene capture: A feature of conjugative plasmids, with ecological and evolutionary significance
62. Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and yeast
63. Regions of broad-host-range plasmid RK2 which are essential for replication and maintenance
64. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
65. Rapid method for direct extraction of DNA from soil and sediments
66. Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis
67. Description of a novel plasmid replication origin from a genetically distinct family of conjugative plasmids associated with phytosphere microflora
68. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers
69. 16S ribosomal DNA amplification for phylogenetic study
70. Identification of a virulence-associated protein homolog gene and ISRa1 in a plasmid of Riemerella anatipestifer