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Since nucleic acids and proteins of unicellular prokaryotes are directly exposed to extreme environmental conditions, it is possible to explore the genomic-proteomic compositional determinants of molecular mechanisms of adaptation developed by them in response to harsh environmental conditions. Using a wealth of currently available complete genomes/proteomes we were able to explore signatures of adaptation to three environmental factors, pH, salinity, and temperature, observing major trends in compositions of their nucleic acids and proteins. We derived predictors of thermostability, halophilic, and pH adaptations and complemented them by the principal components analysis. We observed a clear difference between thermophilic and salinity/pH adaptations, whereas latter invoke seemingly overlapping mechanisms. The genome-proteome compositional trade-off reveals an intricate balance between the work of base paring and base stacking in stabilization of coding DNA and r/tRNAs, and, at the same time, universal requirements for the stability and foldability of proteins regardless of the nucleotide biases. Nevertheless, we still found hidden fingerprints of ancient evolutionary connections between the nucleotide and amino acid compositions indicating their emergence, mutual evolution, and adjustment. The evolutionary perspective on the adaptation mechanisms is further studied here by means of the comparative analysis of genomic/proteomic traits of archaeal and bacterial species. The overall picture of genomic/proteomic signals of adaptation obtained here provides a foundation for future engineering and design of functional biomolecules resistant to harsh environments.

[Display omitted] • hTC had higher homogeneous dispersal (92%) than cTC in the thermophilic stage. • hTC enhanced the stability of co-occurrence network. • Low-abundance taxa was important in whole community assembly of hTC. Hyperthermophilic composting (hTC) is a promising technique for solid waste treatment due to its distinctive microbiomes. However, the assembly process of the hTC microbial community remains unclear. We investigated the assembly process of hTC and explored the underlying drivers influencing community assembly in this work by employing conventional thermophilic composting (cTC) as a comparison group. Our results showed that the two composting treatments have different community assembly processes. Especially for the initial and thermophilic phases, hTC is affected by homogeneous dispersal (48%) and homogeneous selection (44%), respectively, while cTC is controlled by undominant (38%) and homogeneous selection (92%), respectively. Furthermore, random forest models and network results suggested that different factors govern the community assembly in these two composting methods. Specifically, the hTC community increases the stability of the thermophilic community via enhancing the interactions of low-abundance taxa with other operational taxonomic units (OTUs) in community assembly. Our results suggested that the distinctive nature of hTC community assembly may be responsible for its adaptation to extreme environments. [ABSTRACT FROM AUTHOR]

Anaerobe fermentation of sugar beet pressed pulp was investigated in pilot-scale digesters. Thermophilic adaptation of mesophilic culture was monitored using chemical analysis and metagenomic characterization of the sludge. Temperature adaptation was achieved by increasing the temperature gradually (2 °C day-1) and by greatly decreasing the OLR. During stable run, the OLR was increased gradually to 11.29 kg VS m-3 d-1 and biogas yield was 5% higher in the thermophilic reactor. VFA levels increased in the thermophilic reactor with increased OLR (acetic acid 646 mg L-1, propionic acid 596 mg L-1), then VFA decreased and the operation was manageable beside the relative high tVFA (1300-2000 mg L-1). The effect of thermophilic adaptation on the microbial communities was studied using a sequencing-based metagenomic approach. Connections between physico-chemical parameters and populations of bacteria and methanogen archaea were revealed. [ABSTRACT FROM AUTHOR]

Abstract: By analyzing the predicted gene expression levels of 33 prokaryotes with living temperature span from <10 °C to >100 °C, a universal positive correlation was found between the percentage of predicted highly expressed genes and the organisms'' optimal growth temperature. A physical interpretation of the correlation revealed that highly expressed genes are statistically more thermostable than lowly expressed genes. These findings show the possibility of the significant contribution of gene expression level to the prokaryotic thermal adaptation and provide evidence for the translational selection pressure on the thermostability of natural proteins during evolution. [Copyright &y& Elsevier]

Abstract: As opposed to mesophilic, thermophilic anaerobic digestion of food waste can increase the biogas output of reactors. To facilitate the transition of anaerobic digesters, this paper investigated the impact of adapting mesophilic sludge to thermophilic conditions. A 5L bench scale reactor was seeded with mesophilic granular sludge obtained from an up-flow anaerobic sludge blanket digester. After 13 days of operation at 35°C, the reactor temperature was instantaneously increased to 55°C and operated at this temperature until day 21. The biomass was then fed food waste on days 21, 42 and 63, each time with an F/M (Food/Microorganism) ratio increasing from 0.12 to 4.43gVS/gVSS. Sludge samples were collected on days 0, 21, 42 and 63 to conduct substrate activity tests, and reactor biogas production was monitored during the full experimental period. The sludge collected on day 21 demonstrated that the abrupt temperature change had no pasteurization effect, but rather lead to a biomass with a fermentative activity of 3.58g Glucose/gVSS/d and a methanogenic activity of 0.47 and 0.26g Substrate/gVSS/d, related respectively, to acetoclastic and hydrogenophilic microorganisms. At 55°C, an ultimate gas production (Go) and a biodegradation potential (Bo) of 0.2–1.4LSTP/gVSfed and of 0.1–0.84LSTP CH4/gVSfed were obtained, respectively. For the treatment of food waste, a fully adapted inoculum was developed by eliminating the initial time-consuming acclimatization stage from mesophilic to thermophilic conditions. The feeding stage was initiated within 20 days, but to increase the population of thermophilic methanogenic microorganisms, a substrate supply program must be carefully observed. [Copyright &y& Elsevier]

Cold shock proteins (Csps) are assumed to play a central role in the regulation of gene expression under cold shock conditions. Acting as single-stranded nucleic acid-binding proteins, they trigger the translation process and are therefore involved in the compensation of the influence of low temperatures (cold shock) upon the cell metabolism. However, it is unknown so far how Csps are switched on and off as a function of temperature. The aim of the present study is the study of possible structural changes responsible for this switching process. 1H-15N HSQC spectra recorded at different temperatures and chemical-shift analysis have indicated subtle conformational changes for the cold-shock protein from the hyperthermophilic bacterium Thermotoga maritima ( TmCsp) when the temperature is elevated from 303 K to its physiological temperature (343 K). The three-dimensional structure of TmCsp was determined by nuclear magnetic resonance (NMR) spectroscopy at 343 K to obtain quantitative information concerning these structural changes. By use of residual dipolar couplings, the loss of NOE information at high temperature could be compensated successfully. Most pronounced conformational changes compared with room-temperature conditions are observed for amino acid residues closely neighbored to two characteristic β-bulges and a well-defined loop region of the protein. Because the residues shown to be responsible for the interaction of TmCsp with single-stranded nucleic acids can almost exclusively be found within these regions, nucleic acid-binding activity might be down-regulated with increasing temperature by the described conformational changes. [ABSTRACT FROM AUTHOR]

Hyperthermophilic organisms optimally grow close to the boiling point of water. As a consequence, their macromolecules must be much more thermostable than those from mesophilic species. Here, proteins from hyperthermophiles and mesophiles are compared with respect to their thermodynamic and kinetic stabilities. The known differences in amino acid sequences and three-dimensional structures between intrinsicallythermostable and thermolabile proteins will be summarized, and the crucial role of electrostatic interactions for protein stability at high temperatures will be highlighted. Successful attempts to increase the thermostability of proteins, which were either based on rational design or on directed evolution, are presented. The relationship between high thermo-stability of enzymes from hyperthermophiles and theirlow catalytic activity at room temperature is discussed. Not all proteins from hyperthermophiles are thermostable enough to retain their structures and functions at the high physiological temperatures. It will be shown how this shortcoming can be surpassed by extrinsic factors such as large molecular chaperones and small compatible solutes. Finally, the potential of thermostable enzymes for biotechnology is discussed. [ABSTRACT FROM AUTHOR]