Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data

Abstract

Biostimulation with different nitrogen sources is often regarded as a strategy of choice in combating oil spills in marine environments. Such environments are typically depleted in nitrogen, therefore limiting the balanced microbial utilization of carbon-rich petroleum constituents. It is fundamental, yet only scarcely accounted for, to analyze the catabolic consequences of application of biostimulants. Here, we examined such alterations in enrichment microcosms using sediments from chronically crude oil-contaminated marine sediment at Ancona harbor (Italy) amended with natural fertilizer, uric acid (UA), or ammonium (AMM). We applied the web-based AromaDeg resource using as query Illumina HiSeq meta-sequences (UA: 27,893 open reading frames; AMM: 32,180) to identify potential catabolic differences. A total of 45 (for UA) and 65 (AMM) gene sequences encoding key catabolic enzymes matched AromaDeg, and their participation in aromatic degradation reactions could be unambiguously suggested. Genomic signatures for the degradation of aromatics such as 2-chlorobenzoate, indole-3-acetate, biphenyl, gentisate, quinoline and phenanthrene were common for both microcosms. However, those for the degradation of orcinol, ibuprofen, phenylpropionate, homoprotocatechuate and benzene (in UA) and 4-aminobenzene-sulfonate, p-cumate, dibenzofuran and phthalate (in AMM), were selectively enriched. Experimental validation was conducted and good agreement with predictions was observed. This suggests certain discrepancies in action of these biostimulants on the genomic content of the initial microbial community for the catabolism of petroleum constituents or aromatics pollutants. In both cases, the emerging microbial communities were phylogenetically highly similar and were composed by very same proteobacterial families. However, examination of taxonomic assignments further revealed different catabolic pathway organization at the organismal level, which should be considered for designing oil spill mitigation strategies in the sea.

Bioprospecting Reveals Class III ω-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines

“…They were recovered from clone libraries created from two chronically polluted marine sediment samples, an acidic beach pool, and the P. oleovorans genome (see the legend to Table S1) (16–18). This means a ratio of circa 1 positive result per 50,000 clones tested; note that this ratio is an indicator of the abundance of enzyme activities in metagenomes (5, 19).…”

Hydrocarbon pollutants shape bacterial community assembly of harbor sediments

“…The lack of nitrogen and phosphorus in marine environments is one of the main factors negatively affecting the growth of HC-degrading bacteria in polluted sites. Recently, the use of uric acid as a natural fertilizer for the bioremediation of marine oil pollution has been proposed to overcome this limitation (Ron and Rosenberg, 2014) and a microcosm-scale study showed its rapid conversion to ammonium and a role in the selection of microbial communities encompassing known hydrocarbonoclastic bacteria (Bargiela et al, 2015b;Gertler et al, 2015). Four of the tested isolates (one A. borkumensis and three M. hydrocarbonoclasticus) were capable to degrade uric acid suggesting their potential to be responsive to uric acid amendment in bioremediation trials.…”

Microcosm-based interaction studies between members of two ecophysiological groups of bioemulsifier producer and a hydrocarbon degrader from the Indian intertidal zone

“…Increasing microbial degradation of BTX by bioaugmentation (increasing the number of degraders) and biostimulation (addition of stimulative nutrients) are novel strategies (Bargiela et al 2015). As it was observed that bacteria preferentially attack on simpler carbon sources (hydrocarbons), addition of stimulative/enhancer carbon sources leading to higher degradation seems to be good strategy.…”

“…Nutrient-enhanced bioremediation is effective only up to a point (Singh et al 2015). Bargiela et al (2015) showed the use of nitrogen sources could work as biostimulant and increase the BTX degradation in microcosms. Biostimulants affected the initial microbial communities and re-organized the microbial taxa on the basis of metabolic abilities of both BTX degradation and the biostimulants used.…”

“…Biostimulants affected the initial microbial communities and re-organized the microbial taxa on the basis of metabolic abilities of both BTX degradation and the biostimulants used. These are the factors which need to be considered among the strategies for oil spill mitigation at sea (Bargiela et al 2015). In the marine sediments, the degradation of crude oil was limited by the availability of N and P. But addition of simple empirical estimates of the nutrient proportions may not be sufficient for successful remediation (Singh et al 2015).…”