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PMID: 14597712 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 100 ·No. 23 ·2003-11-11 ·Pages 13591-6

Jeon CO, Park W, Padmanabhan P, DeRito C, Snape JR, Madsen EL

Abstract

Microorganisms maintain the biosphere by catalyzing biogeochemical processes, including biodegradation of organic chemical pollutants. Yet seldom have the responsible agents and their respective genes been identified. Here we used field-based stable isotopic probing (SIP) to discover a group of bacteria responsible for in situ metabolism of an environmental pollutant, naphthalene. We released 13C-labeled naphthalene in a contaminated study site to trace the flow of pollutant carbon into the naturally occurring microbial community. Using GC/MS, molecular biology, and classical microbiological techniques we documented 13CO2 evolution (2.3% of the dose in 8 h), created a library of 16S rRNA gene clones from 13C labeled sediment DNA, identified a taxonomic cluster (92 of 95 clones) from the microbial community involved in metabolism of the added naphthalene, and isolated a previously undescribed bacterium (strain CJ2) from site sediment whose 16S rRNA gene matched that of the dominant member (48%) of the clone library. Strain CJ2 is a beta proteobacterium closely related to Polaromonas vacuolata. Moreover, strain CJ2 hosts the sequence of a naphthalene dioxygenase gene, prevalent in site sediment, detected before only in environmental DNA. This investigative strategy may have general application for elucidating the bases of many biogeochemical processes, hence for advancing knowledge and management of ecological and industrial systems that rely on microorganisms.

MeSH Terms
Bacteria/classification,metabolism Biodegradation, Environmental Carbon Dioxide/metabolism Cesium/pharmacology Chlorides/pharmacology Cloning, Molecular Cluster Analysis Dioxygenases Gas Chromatography-Mass Spectrometry Molecular Sequence Data Multienzyme Complexes/metabolism Naphthalenes/metabolism Oxygenases/chemistry,metabolism Phylogeny Polymerase Chain Reaction RNA, Ribosomal/metabolism RNA, Ribosomal, 16S/metabolism Soil Microbiology Time Factors
Chemicals
Chlorides Multienzyme Complexes Naphthalenes RNA, Ribosomal RNA, Ribosomal, 16S Carbon Dioxide Cesium naphthalene Oxygenases Dioxygenases naphthalene dioxygenase cesium chloride
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Jeon C O
Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853-8101, USA.
Park W
Padmanabhan P
DeRito C
Snape J R
Madsen E L
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.1735529100
Published
2003-11-11
Epub
2003-00-03
Pages
13591-6
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC263858
Subset
IM
Databases
GENBANK
AY166684, AY194928, AY194929, AY194930, AY194931, AY194932, AY250090, AY250091, AY250092, AY250093, AY250094, AY250095, AY250096, AY250097, AY250098, AY250099, AY250100, AY250101, AY250102, AY250103, AY250104, AY250105, AY250106, AY250107, AY250108, AY250109, AY250110, AY250111, AY250112, AY250113, AY250114
External Links
PubMed source DOI: 10.1073/pnas.1735529100 PMC Full Text View journal details
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