Cold adaptive traits revealed by comparative genomic analysis of the eurypsychrophileRhodococcussp. JG3 isolated from high elevation McMurdo Dry Valley permafrost, Antarctica

Abstract

The permafrost soils of the high elevation McMurdo Dry Valleys are the most cold, desiccating and oligotrophic on Earth. Rhodococcus sp. JG3 is one of very few bacterial isolates from Antarctic Dry Valley permafrost, and displays subzero growth down to -5°C. To understand how Rhodococcus sp. JG3 is able to survive extreme permafrost conditions and be metabolically active at subzero temperatures, we sequenced its genome and compared it to the genomes of 14 mesophilic rhodococci. Rhodococcus sp. JG3 possessed a higher copy number of genes for general stress response, UV protection and protection from cold shock, osmotic stress and oxidative stress. We characterized genome wide molecular adaptations to cold, and identified genes that had amino acid compositions favourable for increased flexibility and functionality at low temperatures. Rhodococcus sp. JG3 possesses multiple complimentary strategies which may enable its survival in some of the harshest permafrost on Earth.

Insights into the Identification of the Specific Spoilage Organisms in Chicken Meat

“…Therefore, to address this goal, it is important to design bacterial culture media that are able to select psychrotrophic bacteria with large genomes. Extensive genome size allows microorganisms to succeed in cold and oligotrophic environments [47][48][49]. Based on this information, an oligotrophic medium was designed and used to recover psychrotrophic and slow-growing bacteria (∼96 h incubation).…”

Whole Genome Sequence of Dermacoccus abyssi MT1.1 Isolated from the Challenger Deep of the Mariana Trench Reveals Phenazine Biosynthesis Locus and Environmental Adaptation Factors

“…In high pressure environments, the transport of compounds such as amino acid is reduced, leading to upregulation of certain transporters to counteract significant inhibition of amino acids uptake into cells at high pressure [30]. Different types of ABC transporter permeases were detected in the D. abyssi MT1.1 T genome including ABC transporter permease, an amino acid ABC transporter permease, and a branched-chain amino acid ABC transporter permease that is up-regulated at high pressure to compensate for the reduction of transportation functionality [31]. Another significant group of proteins involved in protein export across the outer membrane are the export proteins SecD and SecF.…”

“…Another significant group of proteins involved in protein export across the outer membrane are the export proteins SecD and SecF. Strains lacking these proteins have been shown to be cold and high pressure-sensitive [31].…”

“…The D. abyssi MT1.1 T genome contained copies of antioxidant enzyme-encoding genes that counteract the effect of reactive oxygen species (ROS) generated at low temperatures, such as superoxide dismutase, catalase, thioredoxin, thioredoxin-disulfide reductase, peroxiredoxin, peroxiredoxin (OsmC family), NAD(P)H-quinone oxidoreductase, alkyl hydroperoxide reductase, glutathione S-transferase (family protein), arsenate reductase, and glutaredoxin (family proteins), all of which have the ability to repair damage caused to proteins and other cell components by ROS [31] (Table S2).…”

“…The genome of the D. abyssi MT1.1 T exhibited the presence of genes encoding the carbon starvation protein A CstA, in addition to the glycogen synthesis protein GlgA, the glycogen debranching enzyme GlgX, and glycogen/starch/alpha-glucan phosphorylase, which is responsible for the breakdown of these storage molecules. The genome also included multiple copies of genes encoding for carbon-nitrogen hydrolase and carbonic anhydrase proteins essential for efficient CO 2 fixation [31,37,38] (Table S3).…”