Species and Metabolic Pathways Involved in Bioremediation of Vietnamese Soil From Bien Hoa Airbase Contaminated With Herbicides

Abstract

Four bacterial strains were isolated from enrichment cultures inoculated with soil from Bien Hoa military base in Vietnam contaminated with the herbicides 2,4-dichlorophenoxyacetate (2,4-D) and 2,4,5-trichlorophenoxyacetate (2,4,5-T). They were classified as Pseudomonas aeruginosa BT1 2.2, Sphingomonas histidinilytica BT1 5.2, Bordetella petrii BT1 9.2, and Achromobacter xylosoxidans BT1 10.2. All four were able to degrade 2,4-D and 2,4,5-T, but only the last three species used them as the sole sources of carbon and energy. Mass balance analyses suggest that between 33 and 46% of the carbon in the herbicides is incorporated into dry weight (DW). We obtained insight into their degradation pathways by the genomic analysis of these strains. A tfdCDEF gene cluster was found in A. xylosoxidans BT1 10.2 with amino acid sequences of their gene products showing high identity to those in B. petrii DSM12804. Bordetella petrii BT1 9.2 has a full complement of the tfdABCDEF genes. Surprisingly, the gene organization along with the amino acid sequences of the gene products are virtually identical to those of Cupriavidus pinatubonensis JMP134, referred to as type I tfd genes, and different from those of A. xylosoxidans BT1 10.2 and B. petrii DSM12804. We hypothesize that some of the genetic potential to degrade the herbicides has been recruited in recent mating events between these species and other members of the proteobacteria. This is the first report showing that B. petrii BT1 9.2 emerges as a key player in the degradation of 2,4-D.

Evolution End Classification of tfd Gene Clusters Mediating Bacterial Degradation of 2,4-Dichlorophenoxyacetic Acid (2,4-D)

“…A blastn-search revealed seventeen (excluding canonical tfd I ) gene clusters which had an over 90% match with the tfdB I F I E I D I C I T structure of the tfd I gene cluster. They were designated as tfdT1T2CD (unpublished), tfdCDEF or tfdT-CDEF [ 35 , 45 ], tfdCDEF [ 58 ], tfdFEDCT [ 43 ], tfdB I F I E I D I C I T [ 44 ], tfdBFEDC , tfdBFET [ 5 ], tfdBFEDCS [ 7 ] or not annotated (CP016005, CP026110) ( Table S1 ). Fourteen of those seventeen tfd I gene clusters were located on plasmids in species belonging to the Burkholderiaceae family.…”

“…This group combines non-traditional clusters that have variable gene structures and significantly differ from the canonical tfd gene clusters of the I and II types. The published clusters were annotated as dccEA I D I , dccA II D II , dccEA I D I [ 62 ], tfdC2E2 , tfdC2E2F2 , tfdDRFCE , tfdDRF [ 38 , 63 ], cnbCDEF [ 64 ], tfdBCDEFKR [ 41 ], tfdEC , tfdCE [ 7 ], tfdBaFRDEC [ 10 ], tfdEICIFIRDI , K , BI and tfdDII , FIIEIICII , BII [ 46 ]. Nevertheless, comparative genomic analysis showed that the genetic structure of this tfd IV type cluster could be divided into three main subtypes—A, B and C ( Figure 2 a) (details of the new classification and nomenclature are described in the Section 3 and Section 4 .…”

“…They encode for enzymes involved in the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) which has human health and ecological risks [ 1 , 2 ], but is still used worldwide as an herbicide in agriculture [ 3 ]. Continued exploration of microbial 2,4-D degradation in various environments in China [ 4 , 5 ], Brazil [ 6 ], Vietnam [ 7 , 8 ], Russia [ 9 ] and Japan [ 10 ] suggests that this problem is still in the spotlight.…”

“…In the past three decades, all explorations of tfd gene clusters, from a comparative genomic point of view, have been focused primarily on their tandem matching with the canonical gene structure of tfd I and tfd II gene clusters. Many of both canonical and non-canonical clusters have been identified, amongst them: tfdT-CDEF [ 35 ], tfdDRCEBKAF [ 36 ], tfdCDEF and tfdC II E II BKA ( Delftia acidovorans P4a), tfdRCEBKA [ 37 ], tfdC2E2F2 and tfdDRFCE [ 38 ], tfdAKBECR [ 39 ], tfdRDCEFBKA [ 40 ], tfdBCDEFKR [ 41 ], tfdFAKB I E I C I D I R I and tfdC II E II B II [ 42 ], tfdFEDCT [ 43 ], tfdB I F I E I D I C I T and variations of the tfdKB II FE II C II D II R cluster with deletions [ 44 ], tfdBFET , tfdAKBFECDR and tfdBFEDC [ 5 ], tfdBFEDCS , tfdFE(tctC)DCS [ 7 ], tfdBaFRDEC [ 10 ], tfdCDEF [ 45 ], tfdEICIFIRDI , K , BI , tfdDII , FIIEIICII , BII [ 46 ] and other cluster structures. Amongst the clusters related to tcb and clc , the following have been identified: tetRtetCDEF [ 47 ], mocpDCBAR [ 39 ], cbnR-ABCD [ 48 , 49 ], clcRABCD [ 50 ], clcRABCDE [ 51 ], clcr1a1b1d1e1 [ 52 ], dccEDCBAR [ 53 ] and others.…”

Correlating biodegradation kinetics of 2,3,7,8-tetrachlorodibenzo-p-dioxin to the dynamics of microbial communities originating from soil in Vietnam contaminated with herbicides and dioxins

“…Although there is no direct evidence for the involvement of Bordetella and Sphingomonas in the degradation of 2,3,7,8-TCDD, the fact that they are relatively dominant in these 2 types of culture makes it a likely assumption. It has been shown earlier that species from the genera Bordetella and Sphingomonas have the genes encoding the enzymes degrading 2,4-D and 2,4,5-T, and indeed use that potential to degrade these herbicides ( Nguyen et al, 2021a , b ). We suggest that the presence of the herbicides 2,4-D and 2,4,5-T in the soil has contributed to the bioremediation results.…”