Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07.

Gillian Li Yin Lee,Siti Aisyah Alias,Noor Azmi Shaharuddin,Peter Convey,Azham Zulkharnain,Gerardo González-Rocha,Nur Nadhirah Zakaria,Kenshi Suzuki,Khalilah Abdul Khalil,Siti Aqlima Ahmad,Hiroyuki Futamata

doi:10.3390/ijms21249363

Abstract

Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bacterium Rhodococcus sp. strain AQ5-07, originally isolated from soil from King George Island (South Shetland Islands, maritime Antarctic), was found to be capable of utilizing phenol as sole carbon and energy source. The bacterium achieved 92.91% degradation of 0.5 g/L phenol under conditions predicted by response surface methodology (RSM) within 84 h at 14.8 °C, pH 7.05, and 0.41 g/L ammonium sulphate. The assembled draft genome sequence (6.75 Mbp) of strain AQ5-07 was obtained through whole genome sequencing (WGS) using the Illumina Hiseq platform. The genome analysis identified a complete gene cluster containing catA, catB, catC, catR, pheR, pheA2, and pheA1. The genome harbours the complete enzyme systems required for phenol and catechol degradation while suggesting phenol degradation occurs via the β-ketoadipate pathway. Enzymatic assay using cell-free crude extract revealed catechol 1,2-dioxygenase activity while no catechol 2,3-dioxygenase activity was detected, supporting this suggestion. The genomic sequence data provide information on gene candidates responsible for phenol and catechol degradation by indigenous Antarctic bacteria and contribute to knowledge of microbial aromatic metabolism and genetic biodiversity in Antarctica.

Highlights

The last largely pristine and remote wilderness on Earth, Antarctica is facing a variety of anthropogenic impacts associated with rapidly increasing human activities
We report that the optimum temperature predicted by response surface methodology (RSM) was in the range of optimum temperature revealed by one-factor-at-a-time (OFAT) analysis
The optimum temperature predicted by RSM was in the range of optimum temperature revealed by OFAT

Summary

Introduction

The last largely pristine and remote wilderness on Earth, Antarctica is facing a variety of anthropogenic impacts associated with rapidly increasing human activities. Of all “local” impacts within Antarctica, oil spills have been considered amongst the most damaging through the persistence of petroleum products in this cold environment [5,6]. Due to the chronically low temperatures and dry or frozen conditions across much of Antarctica, the continent’s ecosystems are very sensitive to even small environmental changes, and aromatic hydrocarbon products such as phenol and phenolic compounds (PCs) can have considerable detrimental impacts on terrestrial and aquatic life [10,11,12]

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