Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica

Abstract

Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis—the paradigm of mesophilic hydrocarbonoclastic bacteria—O. antarctica has a larger genome that has witnessed massive gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants, siderophores and micronutrient-scavenging pathways. We also show that at low temperatures, the main protein-folding machine Cpn60 functions as a single heptameric barrel that uses larger proteins as substrates compared with the classical double-barrel structure observed at higher temperatures. With 11 protein crystal structures, we further report the largest set of structures from one psychrotolerant organism. The most common structural feature is an increased content of surface-exposed negatively charged residues compared to their mesophilic counterparts. Our findings are relevant in the context of microbial cold-adaptation mechanisms and the development of strategies for oil-spill mitigation in cold environments.

Latitude-dependent underestimation of microbial extracellular enzyme activity in soils

“…Protease and glucosidase activities from E. coli showed peaks of maximum activity at 45 and 50°C, respectively (Fig. 1g, h) which corresponded to the expected results according to previous reports (Burton et al 2002;Kube et al 2013;Madigan et al 2003;Tang et al 2010). Thermophilic isolates showed peaks of maximum glucosidase activity at 75 and 60°C for strains 10 and 12, respectively (Fig.…”

“…2010; Conant et al 2011;Craine et al 2010;Fierer et al 2006). Generally, enzymatic activity shows maxima at a temperature slightly higher than the optimum for growth of a microorganism (Burton et al 2002;Kube et al 2013;Madigan et al 2003;Tang et al 2010). However, enzymatic activity sharply decreases at increasing temperatures beyond its optimum (Ise and Moorcroft 2006;Madigan et al 2003).…”

Ecosystem function and services provided by the deep sea

“…A variety of biotic processes can detoxify "waste" or potential pollutants contributing to the regulating service of biological waste remediation in the deep sea. A recent example of this occurred during the 2010 Macondo oil spill (also known as the Deepwater Horizon Spill) where members of the deepsea microbial community in the Gulf of Mexico were capable of degrading hydrocarbons and gases released from the well (Valentine et al, 2010;Lu et al, 2012;Crespo-Medina et al, 2014), and recently more bacteria with the potential to oxidize hydrocarbons have been recognized (Kube et al, 2013;Naether et al, 2013).…”

The long-chain alkane metabolism network of Alcanivorax dieselolei

“…Some bacterial species are highly specialized to degrade hydrocarbons and are called hydrocarbonoclastic bacteria 1 , such as Alcanivorax 2 , Thalassolituus 3 , Oleiphilus 4 and Oleispira 5 . They have evolved mechanisms adapted to various marine environments, such as the cold adaptation of Oleispira antarctica 6 and the stress responses (ultraviolet irradiation), osmoregulation and nutrient scavenging of Alcanivorax borkumensis 2,7 , and they play a major role in marine oil pollutant removal 1,[8][9][10] .…”

“…Alcanivorax species are the most important alkanedegrading bacteria in marine environments [6][7][8] . In addition to A. borkumensis, A. dieselolei is another intensively studied bacterium in this genus.…”