Bioremediation Methods and Protocols
Since its first systematic application during the 1970s, bioremediation, or the exploitation of a biological system’s degradative potential to combat toxic pollutants such as heavy metals, polyaromatic hydrocarbons (PAH), cyanides, and radioactive materia
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1. Introduction It has been widely recognised that the environment has been polluted by a number of synthetic compounds in the past century, especially after industrialisation. The past few decades have witnessed an increasing interest in bioremediation where living organisms (mainly microorganisms) are used to break down these pollutants in the environment to environmental-friendly compounds. To evaluate the role of microorganisms in the metabolism of certain pollutants in the environment, many techniques need to be employed, including biological and analytical methods, of which stable isotope probing (SIP) is of particular interest (Table 9.1). Stable isotope probing (SIP) relies on the incorporation of stable isotopes (13 C, 15 N) into DNA (1), RNA (2) or phospholipid fatty acid (PLFA) (3–4). Subsequent separation and identification of labelled DNA, RNA or PLFAs offer S.P. Cummings (ed.), Bioremediation, Methods in Molecular Biology 599, DOI 10.1007/978-1-60761-439-5 9, © Humana Press, a part of Springer Science+Business Media, LLC 2010
129
C6 -benzene
C-acetate + perchloroethene
-polychlorinated biphenyls
C-phenanthrene,13 C-pyrene
C-labelled 2,4dichlorophenoxyacetic acid
C-pyrene
C6 -benzene
C6 salicylate; C naphthalene phenanthrene
C-labelled naphthalene and glucose
13
13
13
13
13
13
13
12
13
13
PAH-contaminated soil
C-pyrene
13
Soil
Bioreactor treating PAH-contaminated soil
Gasoline-contaminated groundwater
Bioreactor-treated soil
Agriculture soil
PAH-contaminated soil
Pine tree soil
Pristine river sediment
Coal gasification soil
Habitat
Substrate Acti-
Acidovorax; rangium
Pseudomonas;
Intraspo-
Acidovorax.; Pseudomonas; Ralstonia
16S rRNA
16S rRNA
16S rRNA
16S rRNA
Sphingomonas; uncultivated - and ␥Proteobacteria Azoarcus
16S rRNA
β-Proteobacteria related to Ramlibacter (Comamonadaceae)
16S rRNA; ARHDs1 16S rRNA
Nocar-
16S rRNA
16S rRNA
Acidovorax
Pseudonocardia; Kribbella; dioides; Sphingomonas
Dehalococcoides
Clostridia;
16S rRNA
Uncultivated ␥-Proteobacteria Deltaproteobacteria; nobacteria
Marker genes
Phylogenetic groups identified
Table 9.1 Recent studies using DNA/RNA-SIP for identifying active microorganisms for bioremediation
(continued)
(35)
(34)
(33)
(32)
(31)
(30)
(20)
(29)
(28)
(27)
Reference
130 Chen et al.
C-phenol
C-pentachlorophenol
C-phenol
CH3 Cl CH3 Br
C6 -benzene; 13 C7 -toluene
C-benzoic acid
13
13
13
13
13
13
Agriculture soil
Garden soil
Soil Soil
Agriculture soil
Pristine grassland soil
Activated sludge
Marine sediment or contaminated sediment
Habitat
1 Aromatic ring hydroxylating dioxygenase – Not available
13
C7 -benzoate
13
Substrate
Table 9.1 (Continued)
Burkholderia;
Sphin-
Burkholderia
Arthrobacter; Hydrogenophaga; Pseudomonas; Rhodococcus
Hyphomicrobium; Aminobacter Burkholderia
Kocuria; Staphylococcus; Pseudomonas
Pseudomonas; gomonas
Acidovorax
–
Phylogenetic groups identified
16S rRNA
16S rRNA; bphA; todC
cmuA 16S rRNA; cmuA
16S rRNA
16S rRNA
16S rRNA
nosZ
Ma
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