Ecology of cold environments: new insights of bacterial metabolic adaptation through an integrated genomic-phenomic approach

Abstract

Cold environments dominate Earth’s biosphere, hosting complex microbial communities with the ability to thrive at low temperatures. However, the underlying molecular mechanisms and the metabolic pathways involved in bacterial cold-adaptation mechanisms are still not fully understood. Herein, we assessed the metabolic features of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125), a model organism for cold-adaptation, at both 4 °C and 15 °C, by integrating genomic and phenomic (high-throughput phenotyping) data and comparing the obtained results to the taxonomically related Antarctic bacterium Pseudoalteromonas sp. TB41 (PspTB41). Although the genome size of PspTB41 is considerably larger than PhTAC125, the higher number of genes did not reflect any higher metabolic versatility at 4 °C as compared to PhTAC125. Remarkably, protein S-thiolation regulated by glutathione and glutathionylspermidine appeared to be a new possible mechanism for cold adaptation in PhTAC125. More in general, this study represents an example of how ‘multi-omic’ information might potentially contribute in filling the gap between genotypic and phenotypic features related to cold-adaptation mechanisms in bacteria.

Integrated phenotypic-genotypic approach to understand the influence of ultrasound on metabolic response of Lactobacillus sakei

“…Phenotypic alterations and application of genomic-phenomic approach of a culture subjected to environmental stress e.g. adaption to cold environment has been successfully demonstrated [ 56 ]. Phenotypic variations identified as a result of ultrasound treatment and links associated with the various metabolic pathways demonstrates the relevance of PM technology in providing in-depth analysis of L .…”

Diauxie and co-utilization are not exclusive during growth in nutritionally complex environments

“…The order in which nutrients are used by microbes during the growth depends both on the final biomass and the specific growth rate achievable when grown with amino acids as sole carbon sources. Using available growth phenotypes 21,22 , we show ( Figure 4E) that, on average, amino acids included in cluster 1 permit a higher cell density than those in cluster 2 and so on. Similarly, when focusing on single amino acids and the growth rate measured when using them as unique C source, higher growth rates are obtained with those amino acids that are degraded first in our 19 amino acids growth curve.…”

“…The order in which nutrients are used by microbes during the growth depends both on the final biomass and the specific growth rate achievable when grown with amino acids as sole carbon sources. Using available growth phenotypes 21,22 . We investigated the correlation between amino acids consumption and the achievable biomass amount when the same carbon sources of the 19 AA experiment were used as single carbon and energy sources.…”

One-step formation of three-dimensional macroporous bacterial sponges as a novel approach for the preparation of bioreactors for bioremediation and green treatment of water

“…Adaptation of bacterial cells to their new environment following storage and thawing apparently slows down the metabolic activity of bio-cryogels to degrade phenol at early stages of incubation, without losing their activity completely or their ability to repair the freezing/storage damage as a result of adaptation processes. 46,47 Assuming death of bacteria due to the freezing/thawing cycle, the mixture of bacterial strains showed less activity during the rst week of incubation. During bioremediation the efficiency of the bioremediation process increases.…”