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Chapter 5.1.2 : Biodegradation of Organochlorine Pesticides

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Abstract:

The widespread use of organochlorine pesticides (OCPs), mainly in the past, has caused serious environmental problems. Many OCPs were recently categorized as persistent organic pollutants (POPs) that should be controlled as toxic environmental contaminants. On the other hand, many bacterial strains and consortia have been identified that can degrade OCPs, including man-made ones, and various pathways for the biodegradation of OCPs have been clarified. Especially, aerobic OCP-degrading bacteria have been analyzed in detail as an excellent model for studying the bacterial adaptation and evolution in the environment. In fact, most such degradation pathways are thought to be established by the assembly of preexisting and newly evolved pathways, involving enzymes whose functions are thought to have evolved during relatively short period. Furthermore, a large amount of bacterial genomic information is now available, and the appearance and evolution of bacteria capable of degrading man-made OCPs can be discussed on the basis of such genomic information and mobile genetic elements. These accumulating knowledge on the biodegradation of OCPs will also be useful for practical bioremediation.

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
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Image of FIGURE 1
FIGURE 1

Degradation pathway of OCPs (2,4-D, 2,4,5-T, PCP, γ-HCH, and linuron) in aerobic bacteria. Reactions catalyzed by dehalogenases ( Table 2 ) are shown in bold. See text for detail. doi:10.1128/9781555818821.ch5.1.2.f1

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
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Image of FIGURE 2
FIGURE 2

Degradation pathway of atrazine by aerobic bacteria. See text for details. doi:10.1128/9781555818821.ch5.1.2.f2

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
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Image of FIGURE 3
FIGURE 3

Degradation pathway of DDT in the environmant. DDT is converted to DDE and DDD by microbial activities, chemical reactions, or phytochemical reactions. Aerobic DDT-degrading bacteria hydroxylate one of the aromatic rings in DDT, and furthre convert into 4-chlorobenzoate. See text for details. doi:10.1128/9781555818821.ch5.1.2.f3

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
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Image of FIGURE 4
FIGURE 4

Structures of other OCPs described in this chapter. doi:10.1128/9781555818821.ch5.1.2.f4

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
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Image of FIGURE 5
FIGURE 5

Three main replicons of UT26. Replicons are drawn in circular. Note that the size scale depends on the replicons. The top positions of the three replicons have been defined as putative replication origins (position 1). Positions of the genes, IS, and bacterial essential genes proposed by Gil et al. are marked with red, blue, and back bars, respectively. Results of GC skew and GC content are shown inside of the black scale circles: GC skew (inside), the parts higher and lower than zero were colored with cyan and magenta, respectively; GC content (outside), the parts higher and lower than average of each replicon were colored with green and red, respectively. Result of a BLASTN search of each region of the UT26 genome toward genome sequences of seven other non-γ-HCH-degrading sphingomonad strains, L-1, sp. SKA58, sp. SYK-6, RW1, RB2256, DSM 12444, and sp. PP1Y were shown outside of the black scale circles in this order. The region whose homologous sequence was found in the other strains (L-1, SKA58, SYK-6, RW1, RB2256, DSM 12444, and PP1Y from inside to outside) was colored in the gradient depending on the level of similarity as shown in explanatory note. Result of the BLASTN search of each region of the UT26 genome toward draft genome sequences of γ-HCH-degrading sphingomonad strains, B90A, sp. TKS, sp. MI1205, and sp. MM-1 were shown outside of the circle for the positions of IS in this order. See text for details. This figure was drawn by ArcWithColor (http://www.ige.tohoku.ac.jp/joho/gmProject/gmdownload.html). doi:10.1128/9781555818821.ch5.1.2.f5

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
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Image of FIGURE 6
FIGURE 6

Neighbor-joining phylogenetic tree of 16S rRNA genes of sphingomonad strains. Neighbor-joining phylogenetic tree of the conserved sites (1,385 nucleotides) in 16S rRNA genes of 13 sphingomonad strains, UT26S (UT26_1, SJA_C1-r0010; UT26_2, SJA_C2-r0010; UT26_3, SJA_C2-r0040), B90A (B90A, NR_042943), Sp+ (Sp+, NR_042944), sp. TKS (TKS_1, TKS_2, and TKS_3: unpublished data), L-1 (L-1_1, Sphch_R0043; L-2_2, Sphch_R0058; L-1_3, Sphch_R0067), sp. SKA58 (SKA58_1, SKA58_r00366; SKA58_2, SKA58_r18278), sp. MI1205 (MI1205_1 and MI1205_2: unpublished data), sp. SYK-6 (SYK6_1, SLG_r0030; SYK6_2, SLG_r0060), RW1 (RW1_1, Swit_R0031; RW1_2, Swit_R0040), sp. MM-1 (MM-1_1, G432_r19183; MM-1_2, G432_r19185), RB2256 (RB2256, Sala_R0048), DSM 12444 (DSM_1, Saro_R0065; DSM_2, Saro_R0059; DSM_3, Saro_R0053), and sp. PP1Y (PPY_1, PP1Y_AR03; PPY_2, PP1Y_AR23; PPY_3, PP1Y_AR65) was constructed using MAFFT program (http://mafft.cbrc.jp/alignment/software/) and visualized by Njplot software. 16S rRNA gene (: gene ID 7437018) of strain K-12 substr. W3110 () was used as an out-of-group sequence. Bootstrap values calculated from 1,000 resampling using neighbor joining are shown at the respective nodes. Length of lines reflects relative evolutionary distances among the sequences. sp. SKA58 should be sp. SKA58 on the basis of comprehensive 16S rDNA analysis. However, we used for the strain according to the database to avoid confusion. γ-HCH degraders are boldface. Strains having IS are marked with black circles, and copy number of IS in each strain is shown in parentheses after the circle. doi:10.1128/9781555818821.ch5.1.2.f6

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
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Image of FIGURE 7
FIGURE 7

Proposed model for the appearance and evolution of γ-HCH degraders. See text for details. doi:10.1128/9781555818821.ch5.1.2.f7

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
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