Bacterial growth at −15 °C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1

Abstract

Planococcus halocryophilus strain Or1, isolated from high Arctic permafrost, grows and divides at À 15 1C, the lowest temperature demonstrated to date, and is metabolically active at À 25 1C in frozen permafrost microcosms. To understand how P. halocryophilus Or1 remains active under the subzero and osmotically dynamic conditions that characterize its native permafrost habitat, we investigated the genome, cell physiology and transcriptomes of growth at À 15 1C and 18% NaCl compared with optimal (25 1C) temperatures. Subzero growth coincides with unusual cell envelope features of encrustations surrounding cells, while the cytoplasmic membrane is significantly remodeled favouring a higher ratio of saturated to branched fatty acids. Analyses of the 3.4 Mbp genome revealed that a suite of cold and osmotic-specific adaptive mechanisms are present as well as an amino acid distribution favouring increased flexibility of proteins. Genomic redundancy within 17% of the genome could enable P. halocryophilus Or1 to exploit isozyme exchange to maintain growth under stress, including multiple copies of osmolyte uptake genes (Opu and Pro genes). Isozyme exchange was observed between the transcriptome data sets, with selective upregulation of multi-copy genes involved in cell division, fatty acid synthesis, solute binding, oxidative stress response and transcriptional regulation. The combination of protein flexibility, resource efficiency, genomic plasticity and synergistic adaptation likely compensate against osmotic and cold stresses. These results suggest that non-spore forming P. halocryophilus Or1 is specifically suited for active growth in its Arctic permafrost habitat (ambient temp. B À 16 1C), indicating that such cryoenvironments harbor a more active microbial ecosystem than previously thought.

Bacterial genome replication at subzero temperatures in permafrost

“…Here, we have demonstrated bacterial growth on 13 C-acetate at temperatures down to À 20 1C. Our findings of subzero DNA synthesis after 6 months are in agreement with earlier reports indicating microbial growth/metabolism in permafrost within 100-160 days at similar temperature (Rivkina et al, 2000), growth of bacterial isolates at À 5 to À 15 1C (Bakermans and Nealson, 2004;Mykytczuk et al, 2012Mykytczuk et al, , 2013 and acetate incorporation into bacterial lipids in permafrost down to À 20 1C (Rivkina et al, 2000). Furthermore, the active bacterial phyla observed in this SIP study (Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes and many Alphaproteobacteria) have also been shown to produce ribo-tags and mRNA in a metatranscriptome study of the active layer of a Svalbard fen (Tveit et al, 2013).…”

“…Increases in both the production of extracellular polymeric substances (acting as cryoprotectants) and in bacterial abundance under similar subzero temperature conditions have been observed in brine channels from sea ice and frost flowers (Krembs et al, 2002;Collins et al, 2008;Meiners et al, 2008;Bowman and Deming 2010;Krembs et al, 2011). This hypothesis is further supported by recent evidence that permafrost isolates have thermohaline-dependent responses for both polysaccharide and fatty acid composition (Ponder et al, 2005) as well as for gene expression patterns (Mykytczuk et al, 2013). Alternatively, the activity of hypo-psychrophilic bacteria may represent a shift in competition for resources, where opportunistic psychrophiles that are adept at garnering nearly all the organic carbon at near freezing temperatures are inactive below À 6 1C.…”

Requirements and limits for life in the context of exoplanets

“…Many organisms can grow and reproduce at temperatures well below the freezing point of pure water because their intracellular material contains salts and other solutes that lower the freezing point of the solution. Recently, Mykytczuk et al (20) reported an isolate from Arctic permafrost that grows and divides at −15°C, the lowest temperature demonstrated to date, and is metabolically active at −25°C in frozen soils. Thin films of water at the interface between ice and soil grains, augmented by any solutes, provide adequate water for life at these low temperatures (20,21).…”

Aerobically respiring prokaryotic strains exhibit a broader temperature–pH–salinity space for cell division than anaerobically respiring and fermentative strains

“…Each group occupied a unique position within the total parameter space for cell division (figures 2 and 3; figure S2 for medians). The lowest minimum temperature within the aerobic respiration group (2158C) corresponded to the bacterium Planococcus halocryophilus [47,48], constituting the lowest temperature within the entire dataset (figures 1 and 2; table 3). By contrast, strains employing organic terminal electron acceptors displayed the highest mean temperature maximum for cell division (x ¼ 77 + 38C s.e.…”