Diversity of ndo Genes in Mangrove Sediments Exposed to Different Sources of Polycyclic Aromatic Hydrocarbon Pollution

Abstract

Polycyclic aromatic hydrocarbon (PAH) pollutants originating from oil spills and wood and fuel combustion are pollutants which are among the major threats to mangrove ecosystems. In this study, the composition and relative abundance in the sediment bacterial communities of naphthalene dioxygenase (ndo) genes which are important for bacterial adaptation to environmental PAH contamination were investigated. Three urban mangrove sites which had characteristic compositions and levels of PAH compounds in the sediments were selected. The diversity and relative abundance of ndo genes in total community DNA were assessed by a newly developed ndo denaturing gradient gel electrophoresis (DGGE) approach and by PCR amplification with primers targeting ndo genes with subsequent Southern blot hybridization analyses. Bacterial populations inhabiting sediments of urban mangroves under the impact of different sources of PAH contamination harbor distinct ndo genotypes. Sequencing of cloned ndo amplicons comigrating with dominant DGGE bands revealed new ndo genotypes. PCR-Southern blot analysis and ndo DGGE showed that the frequently studied nah and phn genotypes were not detected as dominant ndo types in the mangrove sediments. However, ndo genotypes related to nagAc-like genes were detected, but only in oil-contaminated mangrove sediments. The long-term impact of PAH contamination, together with the specific environmental conditions at each site, may have affected the abundance and diversity of ndo genes in sediments of urban mangroves.

Isolation of Surfactant-Resistant Pseudomonads from the Estuarine Surface Microlayer

“…The gene ndo encodes the α subunit of the multicomponent enzyme system naphthalene dioxygenase, involved in aerobic degradation of low molecular weight PAH [23]. All isolates were tested for the presence of the ndo gene by PCR (Multigene TC 9600-G thermocycler; Labnet International) using primers PAH-RHDα GNF (5'-GAGATGCATACCACGTKGGTTGGA-3') and PAH-RHDα GNF (5'-AGCTGTTGTTCGGGAAGAYWG TGCMGTT-3') [11] (IBA GmbH, Germany).…”

“…Screening for genes encoding naphthalene dioxygenase (ndo), the enzyme involved in the first step of the aerobic degradation pathway of naphthalene, was unsuccessful for all isolates. However, the presence of ndo genes or the capacity for naphthalene degradation should not be excluded, because the primers employed do not cover the high diversity of known ndo genes [23] and especially not all the pathways involved in hydrocarbon degradation [44]. Moreover, catabolic genes, like ndo, are frequently found in mobile genetic elements, namely plasmids [62].…”

Diversity, Abundance, and Consistency of Microbial Oxygenase Expression and Biodegradation in a Shallow Contaminated Aquifer

“…4) data. The extent and nature of PCR bias introduced by the highly degenerate Rieske primer set is unknown; however, recent reports by other investigators also suggest that nah genes may occur at low frequency in contaminated soil and sediment habitats (12,18,55). The diversity of novel putative dioxygenase sequences revealed by our survey (Fig.…”

“…Analyses have ranged from metagenomic libraries (62), fluorescence in situ hybridization (56), and functional gene arrays (55) to PCR targeting both DNA (5,9,51) and expressed RNA transcripts (6). The catabolic importance of archetypal NDO systems (encoded by nah genes) in many PAH-contaminated environments has been successfully demonstrated by functional-gene-targeted molecular approaches (6,12,14,18,23,57,63,65). Furthermore, broad-specificity PCR primers have enlarged the target range of molecular methods for environmental gene detection and uncovered previously unknown dioxygenase diversity in environmental samples (42,49,70).…”

Metagenomics in Polluted Aquatic Environments

“…Sediments of three mangrove forests from Guanabara Bay presenting distinct levels of PAH contamination (one of them near a petrochemical refinery) were analyzed regarding the diversity of genes encoding the multicomponent enzyme system naphthalene dioxygenase (NDO) that initiates the degradation metabolism of low molecular weight polycyclic aromatic hydrocarbons (PAH),). They revealed that PAH pollution is capable of shaping NDO gene diversity within these microbial communities (Gomes et al, 2007). Hydrocarbon degrading bacterial communities from Guanabara Bay mangrove sediments were characterized utilizing mesocosm systems by Brito and colleagues in 2006.…”