Microbial diversity and anaerobic hydrocarbon degradation potential in an oil-contaminated mangrove sediment

Abstract

BackgroundMangrove forests are coastal wetlands that provide vital ecosystem services and serve as barriers against natural disasters like tsunamis, hurricanes and tropical storms. Mangroves harbour a large diversity of organisms, including microorganisms with important roles in nutrient cycling and availability. Due to tidal influence, mangroves are sites where crude oil from spills farther away can accumulate. The relationship between mangrove bacterial diversity and oil degradation in mangrove sediments remains poorly understood.ResultsMangrove sediment was sampled from 0–5, 15–20 and 35–40 cm depth intervals from the Suruí River mangrove (Rio de Janeiro, Brazil), which has a history of oil contamination. DGGE fingerprinting for bamA, dsr and 16S rRNA encoding fragment genes, and qPCR analysis using dsr and 16S rRNA gene fragment revealed differences with sediment depth.ConclusionsAnalysis of bacterial 16S rRNA gene diversity revealed changes with depth. DGGE for bamA and dsr genes shows that the anaerobic hydrocarbon-degrading community profile also changed between 5 and 15 cm depth, and is similar in the two deeper sediments, indicating that below 15 cm the anaerobic hydrocarbon-degrading community appears to be well established and homogeneous in this mangrove sediment. qPCR analysis revealed differences with sediment depth, with general bacterial abundance in the top layer (0–5 cm) being greater than in both deeper sediment layers (15–20 and 35–40 cm), which were similar to each other.

Screening and Characterization of Aerobic Xylene-Degrading Bacteria from Gasoline Contaminated Soil Sites Around Gas Stations in Northern Jordan

“…Therefore, for successful bioremoval of m-xylene from soil sites, these factors must be taken into consideration during the process of bioremediation under both in situ or ex situ conditions. Globally, it has been documented in literature that variations and changing in the patterns of the microbial populations densities, quantity, microbial activities and heterogeneities have been observed among various petroleum polluted sites due to various physicochemical factors (MacNaughton et al, 1999;Ghazali et al, 2004;Yakimov et al, 2004;Hassanshahian et al, 2010;Das and Chandran, 2011;Staats et al, 2011;Higashioka et al, 2011;Andrade et al, 2012;Alrumman et al, 2015). According to these peer-reviewed articles, these variations in microbial population density and diversity were also affected by the levels of petroleum contamination, suggesting that highly polluted areas appear to have a greater quantity of these microbes.…”

“…Variations could be attributed to adaptation of these bacterial species to utilize and flourish in the presence of crude oil or might be partly due to variations among several physicochemical environmental factors, including differing ambient environmental conditions, soil compositions and organic carbons in the soil. Moreover, the capabilities of degrading aromatic hydrocarbon by bacteria are showed some limitations and hence, no single species of bacteria can degrade all the components of petroleum (Ghazali et al, 2004;Andreoni and Gianfreda, 2007;Das and Chandran, 2011;Andrade et al, 2012;Alrumman et al, 2015). Many different bacterial species are usually needed for complete biodegradation of all the components of petroleum.…”

Functional Gene Markers for Fumarate-Adding and Dearomatizing Key Enzymes in Anaerobic Aromatic Hydrocarbon Degradation in Terrestrial Environments

“…Although this analysis is not a strong diagnostic tool, the identity of distinct terminal restriction fragments can cautiously be elucidated via the cross-referencing of fragment lengths to reference sequences digested in silico, possibly even based on dual digests to increase discriminative confidence [von Netzer et al, 2013]. Similarly, denaturing gradient gel electrophoresis fingerprinting of bamA gene pools has also been applied to analyse the community structure of anaerobic degraders [Andrade et al, 2012;Li et al, 2012].…”

“…For a wide range of bamA/bzdY/oah genes, the forward primer SP9F in combination with the reverse prim-er ASP1R [Kuntze et al, 2008], as well as the slightly modified combination oah_f/oan_r [Staats et al, 2011], has been successfully used in numerous studies, thus demonstrating its applicability for detecting a wide range of anaerobic monoaromatic compound degraders [Andrade et al, 2012;Higashioka et al, 2011;Li et al, 2012;Porter and Young, 2013;Sun et al, 2014a]. Two additional primer sets were designed using the same forward primer SP9F but different reverse primers ASP23R and ASP33R targeting ring-opening hydrolase subclusters, including Gram-positive anaerobic monoaromatic compound degraders, as described above .…”

“…were designed later to recover a wider diversity of degraders, including also Gram-positives . Thus, in the mean- time, the bamA gene was also established as a widely applied biomarker for anaerobic degradation of monocyclic aromatic compounds [Andrade et al, 2012;Li et al, 2012;Young, 2013, 2014;Sun et al, 2014a].…”