Bacterial life at low temperature: physiological aspects and biotechnological implications

Cold-active microbial enzymes and their biotechnological applications

Microorganisms known as psychrophiles/psychrotrophs, which survive in cold climates, constitute majority of the biosphere on Earth. Their capability to produce cold-active enzymes along with other distinguishing characteristics allows them to survive in the cold environments. Due to the relative ease of large-scale production compared to enzymes from plants and animals, commercial uses of microbial enzyme are alluring. The ocean depths, polar, and alpine regions, which make up over 85% of the planet, are inhabited to cold ecosystems. Microbes living in these regions are important for their metabolic contribution to the ecosphere as well as for their enzymes, which may have potential industrial applications. Cold-adapted microorganisms are a possible source of cold-active enzymes that have high catalytic efficacy at low and moderate temperatures at which homologous mesophilic enzymes are not active. Cold-active enzymes can be used in a variety of biotechnological processes, including food processing, additives in the detergent and food industries, textile industry, waste-water treatment, biopulping, environmental bioremediation in cold climates, biotransformation, and molecular biology applications with great potential for energy savings. Genetically manipulated strains that are suitable for producing a particular cold-active enzyme would be crucial in a variety of industrial and biotechnological applications. The potential advantage of cold-adapted enzymes will probably lead to a greater annual market than for thermo-stable enzymes in the near future. This review includes latest updates on various microbial source of cold-active enzymes and their biotechnological applications.

Cold-Adapted Proteases: An Efficient and Energy-Saving Biocatalyst

The modern biotechnology industry has a demand for macromolecules that can function in extreme environments. One example is cold-adapted proteases, possessing advantages such as maintaining high catalytic efficiency at low temperature and low energy input during production and inactivation. Meanwhile, cold-adapted proteases are characterised by sustainability, environmental protection, and energy conservation; therefore, they hold significant economic and ecological value regarding resource utilisation and the global biogeochemical cycle. Recently, the development and application of cold-adapted proteases have gained gaining increasing attention; however, their applications potential has not yet been fully developed, which has seriously restricted the promotion and application of cold-adapted proteases in the industry. This article introduces the source, related enzymology characteristics, cold resistance mechanism, and the structure-function relationship of cold-adapted proteases in detail. This is in addition to discussing related biotechnologies to improve stability, emphasise application potential in clinical medical research, and the constraints of the further developing of cold-adapted proteases. This article provides a reference for future research and the development of cold-adapted proteases.

Thermal acclimation of methanotrophs from the genus Methylobacter

Methanotrophs oxidize most of the methane (CH4) produced in natural and anthropogenic ecosystems. Often living close to soil surfaces, these microorganisms must frequently adjust to temperature change. While many environmental studies have addressed temperature effects on CH4 oxidation and methanotrophic communities, there is little knowledge about the physiological adjustments that underlie these effects. We have studied thermal acclimation in Methylobacter, a widespread, abundant, and environmentally important methanotrophic genus. Comparisons of growth and CH4 oxidation kinetics at different temperatures in three members of the genus demonstrate that temperature has a strong influence on how much CH4 is consumed to support growth at different CH4 concentrations. However, the temperature effect varies considerably between species, suggesting that how a methanotrophic community is composed influences the temperature effect on CH4 uptake. To understand thermal acclimation mechanisms widely we carried out a transcriptomics experiment with Methylobacter tundripaludum SV96T. We observed, at different temperatures, how varying abundances of transcripts for glycogen and protein biosynthesis relate to cellular glycogen and ribosome concentrations. Our data also demonstrated transcriptional adjustment of CH4 oxidation, oxidative phosphorylation, membrane fatty acid saturation, cell wall composition, and exopolysaccharides between temperatures. In addition, we observed differences in M. tundripaludum SV96T cell sizes at different temperatures. We conclude that thermal acclimation in Methylobacter results from transcriptional adjustment of central metabolism, protein biosynthesis, cell walls and storage. Acclimation leads to large shifts in CH4 consumption and growth efficiency, but with major differences between species. Thus, our study demonstrates that physiological adjustments to temperature change can substantially influence environmental CH4 uptake rates and that consideration of methanotroph physiology might be vital for accurate predictions of warming effects on CH4 emissions.

Comparative transcriptomic and lipidomic analyses indicate that cold stress enhanced the production of the long C18–C22 polyunsaturated fatty acids in Aurantiochytrium sp

Aurantiochytrium sp. belonging to Thraustochytrids are known for their capacity to produce long-chain polyunsaturated fatty acids (PUFAs). However, effects of cold stress accompanied with staged-temperature control on the fatty acid metabolism in Aurantiochytrium sp. were rarely studied. In this study, cold stress (15°C, 5°C) was applied for Aurantiochytrium sp., with the physiological responses (morphology, growth, fatty acid profiling) and gene expression related FA synthesis, lipid metabolism, and regulatory processes was observed. Results showed that there is a significant change for the lipid types under 5°C (251 species) and 15°C (97 species) treatment. The 5°C treatment was benefit for the C18–C22 PUFAs with the yield of docosahexaenoic acid (DHA) increased to 1.25 times. After incubation at 15°C, the accumulation of eicosadienoic acid (EA) (20:2) was increased to 2.00-fold. Based on transcriptomic and qPCR analysis, an increase in genes involved in fatty acid synthase (FAS) and polyketide synthase (PKS) pathways was observed under low-temperature treatment. With upregulation of 3-ketoacyl-CoA synthase (2.44-fold), ketoreductase (2.50-fold), and dTDP-glucose 4,6-Dehydratase (rfbB) (2.31-fold) involved in PKS pathway, the accumulation of DHA was enhanced under 5°C. While, FAS and fatty elongase 3 (ELO) involved in the FAS pathway were upregulated (1.55-fold and 2.45-fold, respectively) to accumulate PUFAs at 15°C. Additionally, glycerol-3-phosphate acyltransferase (GPAT), lysophospholipid acyltransferase (LPAT), phosphatidic acid phosphatase (PAP), phosphatidylserine synthase (PSS), and phosphatidylserine decarboxylase (PSD) involved in glycerophospholipid biosynthesis were upregulated at 5°C increasing the accumulation of phosphatidic acid (PA), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and phosphatidylinositol (PI). However, glycolysis and the TCA cycle were inhibited under 5°C. This study provides a contribution to the application of two-staged temperature control in the Aurantiochytrium sp. fermentation for producing cold stress-enhancing PUFAs, in order to better understand the function of the key genes for future genetic engineering.

Cold-Active Enzymes and Their Potential Industrial Applications-A Review

More than 70% of our planet is covered by extremely cold environments, nourishing a broad diversity of microbial life. Temperature is the most significant parameter that plays a key role in the distribution of microorganisms on our planet. Psychrophilic microorganisms are the most prominent inhabitants of the cold ecosystems, and they possess potential cold-active enzymes with diverse uses in the research and commercial sectors. Psychrophiles are modified to nurture, replicate, and retain their active metabolic activities in low temperatures. Their enzymes possess characteristics of maximal activity at low to adequate temperatures; this feature makes them more appealing and attractive in biotechnology. The high enzymatic activity of psychrozymes at low temperatures implies an important feature for energy saving. These enzymes have proven more advantageous than their mesophilic and thermophilic counterparts. Therefore, it is very important to explore the efficiency and utility of different psychrozymes in food processing, pharmaceuticals, brewing, bioremediation, and molecular biology. In this review, we focused on the properties of cold-active enzymes and their diverse uses in different industries and research areas. This review will provide insight into the areas and characteristics to be improved in cold-active enzymes so that potential and desired enzymes can be made available for commercial purposes.

Effects of hot water spray and sub-zero saline chilling on bacterial decontamination of broiler carcasses

Reduction of Salmonella on poultry carcasses is one way to prevent salmonellosis. The purpose of this research was to evaluate the effects of subzero saline chilling (SSC) with/without hot water spray (HWS) on broiler carcasses prior to chilling for bacterial reduction. Eviscerated broiler carcasses were subjected to water immersion chilling (WIC, 0% NaCl/0.5°C) or SSC (4% NaCl/-2.41°C) with/without prior HWS at 71°C for 1 min. Broiler carcasses in SSC were chilled faster than those in WIC, regardless of HWS. The combination of HWS and SSC resulted in the best reduction of mesophilic aerobic bacteria, Escherichia coli, and total coliforms on the carcasses over the WIC, SSC, and HWS/WIC. No Salmonella was detected on the carcasses in SSC and HWS/SSC while Salmonella positive was observed on the carcasses chilled in WIC and HWS/WIC. A trace of Gram-negative genus was detected on carcasses in HWS/SSC while many other microbiomes were observed on those in WIC, SSC, and HWS/WIC when quantitative microbiota profiles of 16S rRNA gene sequences were evaluated. Based on these results, chilling of broiler carcasses in 4% NaCl/-2.41°C after HWS at 71°C for 1 min significantly reduced carcass chilling time and bacterial contamination over the control chilling.

Pigment production by cold-adapted bacteria and fungi: colorful tale of cryosphere with wide range applications

Pigments are an essential part of everyday life on Earth with rapidly growing industrial and biomedical applications. Synthetic pigments account for a major portion of these pigments that in turn have deleterious effects on public health and environment. Such drawbacks of synthetic pigments have shifted the trend to use natural pigments that are considered as the best alternative to synthetic pigments due to their significant properties. Natural pigments from microorganisms are of great interest due to their broader applications in the pharmaceutical, food, and textile industry with increasing demand among the consumers opting for natural pigments. To fulfill the market demand of natural pigments new sources should be explored. Cold-adapted bacteria and fungi in the cryosphere produce a variety of pigments as a protective strategy against ecological stresses such as low temperature, oxidative stresses, and ultraviolet radiation making them a potential source for natural pigment production. This review highlights the protective strategies and pigment production by cold-adapted bacteria and fungi, their industrial and biomedical applications, condition optimization for maximum pigment extraction as well as the challenges facing in the exploitation of cryospheric microorganisms for pigment extraction that hopefully will provide valuable information, direction, and progress in forthcoming studies.

Investigation on the Cultivation Conditions of a Newly Isolated Fusarium Fungal Strain for Enhanced Lipid Production

Fusarium equiseti UMN-1 fungal strain isolated from soybean is selected as a potential oleaginous fungal strain for biodiesel generation. It possesses desirable features, such as high lipid content (up to 56%) and high fatty acid methyl ester (FAME) content (more than 98%) in total lipids, and also has the capability to produce cellulase. This research focused on the investigation of the characteristics of this strain and optimization of culture conditions to enhance lipid production. Impact of temperature, agitation, C/N ratio, medium composition, and carbon and nitrogen sources has been observed, and central composite design (CCD) has been applied to improve the lipid accumulation. The optimum range for temperature, agitation, C/N ratio, and carbon and nitrogen concentrations was discovered, and the CCD model with the optimized growth medium and growth conditions achieved a maximum lipid production of 3.89 g/L. This research on F. equiseti UMN-1 fungal strain is expected to improve the feasibility of using microbial lipids of F. equiseti UMN-1 strains as the source of biofuels.

Genomic and physiological characterization and description of Marinobacter gelidimuriae sp. nov., a psychrophilic, moderate halophile from Blood Falls, an antarctic subglacial brine

Antarctic subice environments are diverse, underexplored microbial habitats. Here, we describe the ecophysiology and annotated genome of a Marinobacter strain isolated from a cold, saline, iron-rich subglacial outflow of the Taylor Glacier, Antarctica. This strain (BF04_CF4) grows fastest at neutral pH (range 6-10), is psychrophilic (range: 0°C-20°C), moderately halophilic (range: 0.8%-15% NaCl) and hosts genes encoding potential low temperature and high salt adaptations. The predicted proteome suggests it utilizes fewer charged amino acids than a mesophilic Marinobacter strain. BF04_CF4 has increased concentrations of membrane unsaturated fatty acids including palmitoleic (33%) and oleic (27.5%) acids that may help maintain cell membrane fluidity at low temperatures. The genome encodes proteins for compatible solute biosynthesis and transport, which are known to be important for growth in saline environments. Physiological verification of predicted metabolic functions demonstrate BF04_CF4 is capable of denitrification and may facilitate iron oxidation. Our data indicate that strain BF04_CF4 represents a new Marinobacter species, Marinobacter gelidimuriae sp. nov., that appears well suited for the subglacial environment it was isolated from. Marinobacter species have been isolated from other cold, saline environments in the McMurdo Dry Valleys and permanently cold environments globally suggesting that this lineage is cosmopolitan and ecologically relevant in icy brines.

Competitive Traits Are More Important than Stress-Tolerance Traits in a Cadmium-Contaminated Rhizosphere: A Role for Trait Theory in Microbial Ecology

Understanding how biotic and abiotic factors govern the assembly of rhizosphere-microbial communities is a long-standing goal in microbial ecology. In phytoremediation research, where plants are used to remediate heavy metal-contaminated soils, a deeper understanding of rhizosphere-microbial ecology is needed to fully exploit the potential of microbial-assisted phytoremediation. This study investigated whether Grime's competitor/stress-tolerator/ruderal (CSR) theory could be used to describe the impact of cadmium (Cd) and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the assembly of soil-bacterial communities using Illumina 16S rRNA profiling and the predictive metagenomic-profiling program, PICRUSt. Using predictions based on CSR theory, we hypothesized that Cd and the presence of a rhizosphere would affect community assembly. We predicted that the additional resource availability in the rhizosphere would enrich for competitive life strategists, while the presence of Cd would select for stress-tolerators. Traits identified as competitive followed CSR predictions, discriminating between rhizosphere and bulk-soil communities whilst stress-tolerance traits increased with Cd dose, but only in bulk-soil communities. These findings suggest that a bacterium's competitive attributes are critical to its ability to occupy and proliferate in a Cd-contaminated rhizosphere. Ruderal traits, which relate to community re-colonization potential, were synergistically decreased by the presence of the rhizosphere and Cd dose. Taken together this microcosm study suggests that the CSR theory is broadly applicable to microbial communities. Further work toward developing a simplified and robust strategy for microbial CSR classification will provide an ecologically meaningful framework to interpret community-level changes across a range of biomes.

Abiotic and Biotic Factors Regulating Inter-Kingdom Engagement between Insects and Microbe Activity on Vertebrate Remains

Abstract: A number of abiotic and biotic factors are known to regulate arthropod attraction, colonization, and utilization of decomposing vertebrate remains. Such information is critical when assessing arthropod evidence associated with said remains in terms of forensic relevance. Interactions are not limited to just between the resource and arthropods. There is another biotic factor that has been historically overlooked; however, with the advent of high-throughput sequencing, and other molecular techniques, the curtain has been pulled back to reveal a microscopic world that is playing a major role with regards to carrion decomposition patterns in association with arthropods. The objective of this publication is to review many of these factors and draw attention to their impact on microbial, specifically bacteria, activity associated with these remains as it is our contention that microbes serve as a primary mechanism regulating associated arthropod behavior.

Cloning and Characterization of Cold-Adapted α-Amylase from Antarctic Arthrobacter agilis

In this study, the gene encoding an α-amylase from a psychrophilic Arthrobacter agilis PAMC 27388 strain was cloned into a pET-28a(+) vector and heterologously expressed in Escherichia coli BL21(DE3). The recombinant α-amylase with a molecular mass of about 80 kDa was purified by using Ni²⁺-NTA affinity chromatography. This recombinant α-amylase exhibited optimal activity at pH 3.0 and 30 °C and was highly stable at varying temperatures (30-60 °C) and within the pH range of 4.0-8.0. Furthermore, α-amylase activity was enhanced in the presence of FeCl₃ (1 mM) and β-mercaptoethanol (5 mM), while CoCl₂ (1 mM), ammonium persulfate (5 mM), SDS (10 %), Triton X-100 (10 %), and urea (1 %) inhibited the enzymatic activity. Importantly, the presence of Ca²⁺ ions and phenylmethylsulfonyl fluoride (PMSF) did not affect enzymatic activity. Thin layer chromatography (TLC) analysis showed that recombinant A. agilis α-amylase hydrolyzed starch, maltotetraose, and maltotriose, producing maltose as the major end product. These results make recombinant A. agilis α-amylase an attractive potential candidate for industrial applications in the textile, paper, detergent, and pharmaceutical industries.

Metal removal and reduction potential of an exopolysaccharide produced by Arctic psychrotrophic bacterium Pseudomonas sp. PAMC 28620

Metal reducing potential of an exopolysaccharide (EPS) produced by Arctic glacier soil bacteriumPseudomonassp. PAMC 28620.

Transcriptome and gene expression analysis of DHA producer Aurantiochytrium under low temperature conditions

Aurantiochytrium is a promising docosahexaenoic acid (DHA) production candidate due to its fast growth rate and high proportions of lipid and DHA content. In this study, high-throughput RNA sequencing technology was employed to explore the acclimatization of this DHA producer under cold stress at the transcriptional level. The overall de novo assembly of the cDNA sequence data generated 29,783 unigenes, with an average length of 1,200 bp. In total, 13,245 unigenes were annotated in at least one database. A comparative genomic analysis between normal conditions and cold stress revealed that 2,013 genes were differentially expressed during the growth stage, while 2,071 genes were differentially expressed during the lipid accumulation stage. Further functional categorization and analyses showed some differentially expressed genes were involved in processes crucial to cold acclimation, such as signal transduction, cellular component biogenesis, and carbohydrate and lipid metabolism. A brief survey of the transcripts obtained in response to cold stress underlines the survival strategy of Aurantiochytrium; of these transcripts, many directly or indirectly influence the lipid composition. This is the first study to perform a transcriptomic analysis of the Aurantiochytrium under low temperature conditions. Our results will help to enhance DHA production by Aurantiochytrium in the future.

The diversity of bacteria isolated from antarctic freshwater reservoirs possessing the ability to produce polyhydroxyalkanoates

The diversity of polyhydroxyalkanoates-producing bacteria in freshwater reservoirs in the Ecology Glacier foreland, Antarctica, was examined by a cultivation-dependent method. Isolated strains were analyzed phylogenetically by 16S rRNA gene sequencing, and classified as members of Alpha-, Beta-, or Gammaproteobacteria classes. Polymerase chain reaction was used to detect PHA synthase genes. Potential polyhydroxyalkanoates (PHAs) producers belonging mainly to Pseudomonas sp., and Janthinobacterium sp. were isolated from all five sampling sites, suggesting that PHA synthesis is a common bacterial feature at pioneer sites. All Pseudomonas strains had the genetic potential to synthesize medium-chain-length PHAs, whereas some isolated Janthinobacterium strains might produce short-chain-length PHAs or medium-chain-length PHAs. It is the first report revealing that Janthinobacterium species could have the potential to produce medium-chain-length PHAs.

Biotechnology of cold-active proteases

The bulk of Earth's biosphere is cold (<5 °C) and inhabited by psychrophiles. Biocatalysts from psychrophilic organisms (psychrozymes) have attracted attention because of their application in the ongoing efforts to decrease energy consumption. Proteinases as a class represent the largest category of industrial enzymes. There has been an emphasis on employing cold-active proteases in detergents because this allows laundry operations at ambient temperatures. Proteases have been used in environmental bioremediation, food industry and molecular biology. In view of the present limited understanding and availability of cold-active proteases with diverse characteristics, it is essential to explore Earth's surface more in search of an ideal cold-active protease. The understanding of molecular and mechanistic details of these proteases will open up new avenues to tailor proteases with the desired properties. A detailed account of the developments in the production and applications of cold-active proteases is presented in this review.

Discrimination between mesophilic and psychrotolerant strains in the Bacillus cereus group based on the PstI digestion of the pycA gene

A simple and rapid assay for the detection of Bacillus weihenstephanensis isolates and other psychrotolerant strains in the Bacillus cereus group was developed. It is based on the presence of a nucleotide substitution at position 795 on the housekeeping pycA gene in all B. weihenstephanensis strains. This mutation creates a PstI recognition site. It is absent in mesophilic strains in the B. cereus group. The pycA gene is amplified by PCR and the amplicons submitted to PstI digestions. In mesophilic strains, a single band of 1,718 bp in length is visualised on an agarose gel. In B. weihenstephanensis strains and in all other psychrotolerant strains from the B. cereus group, the amplicons are cleaved and two bands of 1,175 and 543 bp, respectively, are visualised. This method could be used for the screening of B. cereus collections and for the identification of psychrotolerant and mesophilic isolates from different environments.

Genome sequence of Exiguobacterium antarcticum B7, isolated from a biofilm in Ginger Lake, King George Island, Antarctica

Exiguobacterium antarcticum is a psychotropic bacterium isolated for the first time from microbial mats of Lake Fryxell in Antarctica. Many organisms of the genus Exiguobacterium are extremophiles and have properties of biotechnological interest, e.g., the capacity to adapt to cold, which make this genus a target for discovering new enzymes, such as lipases and proteases, in addition to improving our understanding of the mechanisms of adaptation and survival at low temperatures. This study presents the genome of E. antarcticum B7, isolated from a biofilm sample of Ginger Lake on King George Island, Antarctic peninsula.

Psychrophilic enzymes: from folding to function and biotechnology

Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.

Efficiency of indigenous and inoculated cold-adapted soil microorganisms for biodegradation of diesel oil in alpine soils

Biodegradation of diesel oil (5 g(middot)kg [soil dry weight](sup-1)) was investigated in five alpine subsoils, differing in soil type and bedrock, in laboratory experiments during 20 days at 10(deg)C. The biodegradation activities of the indigenous soil microorganisms and of a psychrotrophic diesel oil-degrading inoculum and the effect of biostimulation by inorganic fertilization (C/N/P ratio = 100:10:2) were determined. Fertilization significantly enhanced diesel oil biodegradation activity of the indigenous soil microorganisms. Biostimulation by fertilization enhanced diesel oil biodegradation to a significantly greater degree than bioaugmentation with the psychrotrophic inoculum. In none of the five soils did fertilization plus inoculation result in a higher decontamination than fertilization alone. A total of 16 to 23% of the added diesel oil contamination was lost by abiotic processes. Total decontamination without and with fertilization was in the range of 16 to 31 and 27 to 53%, respectively.

Cold-active extracellular alkaline protease from an alkaliphilicStenotrophomonas maltophilia: production of enzyme and its industrial applications

A novel psychro-tolerant bacterium Stenotrophomonas maltophilia (MTCC 7528) with an ability to produce extracellular, cold-active, alkaline, and detergent-stable protease was isolated from soil samples obtained from Gangotri glacier, Western Himalaya, India. The culture conditions for higher protease production were optimized with respect to incubation time, agitation, substrate, pH, and temperature. Maximum protease production of 56.2 U·mL–1was achieved in the medium at 20 °C and pH 9.0 after 120 h incubation. The protease was partially purified by ion-exchange chromatography and approximately 55-fold purification was achieved. The purified enzyme was a 75 kDa protease with maximum activity and stability at pH 10 and 20 °C. The activity of enzyme is stimulated by Mn2+and inhibited completely by metalloprotease inhibitors, indicating that it is a metalloprotease. The protease showed excellent stability and compatibility with commercial detergents and exhibited high efficiency for the removal of different types of protein-containing stains at low temperature. The wash performance analysis of blood and grass stains on cotton fabric showed an increase in reflectance by 26% and 23%, respectively, after treatment with enzyme in comparison to detergent only. These results indicate that it may be a potential component to use as a detergent additive for cold washing and in environmental bioremediation in cold regions.

A cold-active extracellular metalloprotease from Curtobacterium luteum (MTCC 7529): enzyme production and characterization

A novel psychro-tolerant bacterium, Curtobacterium luteum, secreting an extracellular protease was isolated from the soil of Gangotri glacier, Western Himalaya. Maximum enzyme production was achieved when the strain was grown in a pH-neutral medium containing skim milk at 15 degrees C over 120 h. The metal ions such as Zn(2+) and Cr(2+) enhanced enzyme production. The specific activity of purified enzyme was 8,090 units/mg after 34.1-fold purification. The 115 kDa enzyme was a metalloprotease (activity inhibited by EDTA and EGTA) and showed maximum activity at 20 degrees C and pH 7. The enzyme was active over a broad pH range and retained 84% of its original activity between pH 6 and 8. There was no loss in enzyme activity when exposed for 3 h at 4-20 degrees C. However, the enzyme lost 65% of activity at 30 degrees C, and was almost inactivated at 50 degrees C, but was resistant to repeated freezing and thawing. The enzyme activity was stimulated by manganese ions; however, it was inactivated by copper ions.

Exploration of Csp genes from temperate and glacier soils of the Indian Himalayas and in silico analysis of encoding proteins

The metagenomic Csp library was constructed from the temperate and glacier soils of central Himalaya, India followed by polymerase chain reaction (PCR) amplification. The library was further screened for low-temperature adaptation, and the positive recombinants were sorted out by determining changes in the melting temperature (Tm). A homology search of cloned sequence showed their identity with the Csp genes of Pseudomonas fluorescens, Psychrobacter cryohalolentis K5, and Shewanella spp MR-4. Amino acid sequence analysis annotated the presence of conserved aromatic and basic amino acids as well as RNA binding motifs from the cold shock domain. Furthermore, a PROSITE scan showed a moderate identity of less than 60% with the known cold shock-inducible proteins (ribosomal proteins, rbfA, DEAD-box helicases), cold acclimation protein, and temperature-induced protein (SRP1/TIP1). This study highlighted the prevalence of Csp genes from cold Himalayan environments that can be explored for tailor-made crop constructions in future.

Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach

BACKGROUND

Many microorganisms have a wide temperature growth range and versatility to tolerate large thermal fluctuations in diverse environments, however not many have been fully explored over their entire growth temperature range through a holistic view of its physiology, genome, and transcriptome. We used Exiguobacterium sibiricum strain 255-15, a psychrotrophic bacterium from 3 million year old Siberian permafrost that grows from -5 degrees C to 39 degrees C to study its thermal adaptation.

RESULTS

The E. sibiricum genome has one chromosome and two small plasmids with a total of 3,015 protein-encoding genes (CDS), and a GC content of 47.7%. The genome and transcriptome analysis along with the organism's known physiology was used to better understand its thermal adaptation. A total of 27%, 3.2%, and 5.2% of E. sibiricum CDS spotted on the DNA microarray detected differentially expressed genes in cells grown at -2.5 degrees C, 10 degrees C, and 39 degrees C, respectively, when compared to cells grown at 28 degrees C. The hypothetical and unknown genes represented 10.6%, 0.89%, and 2.3% of the CDS differentially expressed when grown at -2.5 degrees C, 10 degrees C, and 39 degrees C versus 28 degrees C, respectively.

CONCLUSION

The results show that E. sibiricum is constitutively adapted to cold temperatures stressful to mesophiles since little differential gene expression was observed between 4 degrees C and 28 degrees C, but at the extremities of its Arrhenius growth profile, namely -2.5 degrees C and 39 degrees C, several physiological and metabolic adaptations associated with stress responses were observed.

Isolation and identification of a psychrotrophic Acinetobacter sp. CR9 and characterization of its alkaline lipase

Forty three psychrotrophic bacteria were isolated from soil samples collected from Chandra river in sub-alpine region of western Himalaya, India. Among these, 11 isolates were found positive for lipase production at low temperature. Of 11 isolates, CR9 produced largest zone of clearance on plate assay and was able to produce lipase under wide range of pH. The isolate CR9 was identified as Acinetobacter sp. based on morphological and physiochemical characterization and 16S rRNA gene sequencing analysis. According to 16S rRNA gene sequencing data the closest phylogenetic neighbor for strain CR9 was Acinetobacter lwoffii (98.9%). The partially purified lipase from strain CR9 exhibited maximum activity at temperature 40 degrees C and pH optima at 8.0. Cu(2+), Mo(2+), Mg(2+), Zn(2+), phenylmethanesulfonyl fluoride (PMSF), dithiothreitol (DTT) and beta-mercaptoethanol (2-ME) enhanced the enzyme activity, whereas Ca(2+) and ethylenediaminetetraacetic acid (EDTA) had inhibitory effect. Lipase hydrolyzed wide range of short chain fatty acid esters of p-nitrophenyl. The organism CR9 also hydrolyzed tributyrin, Tween 80, soybean oil, mustard oil and olive oil. The results highlight the relevance of unexplored microbes from cold environments of western Himalaya for the isolation of novel lipase producing bacteria.

Biodegradation of polychlorinated biphenyls in Aroclor 1232 and production of metabolites from 2,4,4'-trichlorobiphenyl at low temperature by psychrotolerant Hydrogenophaga sp. strain IA3-A

AIMS

To determine the extent and pattern of degradation of polychlorinated biphenyls (PCBs) in Aroclor 1232 at 5 degrees C by a psychrotolerant bacterium, and to confirm the formation of intermediates of PCB metabolism at low temperature using 2,4,4'-trichlorobiphenyl (2,4,4'-TCB).

METHODS AND RESULTS

10 ppm of Aroclor 1232 or 100 micromol l(-1) 2,4,4'-TCB was incubated with biphenyl-grown cells at 5 degrees C or 30 degrees C for 48 or 72 h. Degradation of PCBs and the products of metabolism of 2,4,4'-TCB were confirmed by gas chromatography and mass spectrometry. Extents of degradation of many of the PCBs were similar at 5 degrees C and 30 degrees C. The extent of biodegradation of PCBs in Aroclor 1232 at 5 degrees C was dependent on chlorination pattern. The 14 chlorine-containing intermediates of 2,4,4'-TCB metabolism, which were detected, include several isomers of dihydrodiols, dihydroxy compounds and meta-cleavage compounds.

CONCLUSIONS

The bacterium will be useful for bioremediation of PCB-contaminated sites in cold climates; however, knowledge of the products of PCB metabolism is necessary, as they could be more toxic than the parent compounds.

SIGNIFICANCE AND IMPACT OF THE STUDY

Substantial degradation of some PCBs in Aroclor 1232 was demonstrated at low temperature within 48 h. The detection of several isomeric intermediates suggests that multiple pathways are used to transform PCBs in this strain. For the first time, formation of metabolic products from 2,4,4'-TCB at low temperature is confirmed.

Biodegradative potential and characterization of psychrotolerant polychlorinated biphenyl-degrading marine bacteria isolated from a coastal station in the Terra Nova Bay (Ross Sea, Antarctica)

Antarctic marine bacteria were screened for their ability to degrade polychlorinated biphenyls (PCB) as the sole carbon and energy source at both 4 degrees C and 15 degrees C. PCB-degrading isolates (7.1%) were identified by sequencing their 16S rDNA as Pseudoalteromonas, Psychrobacter and Arthrobacter members. One representative isolate per genera was selected for evaluating the biodegradative potential under laboratory scale and phenotypically characterized. Removal of individual PCB congeners was between 35.6% and 79.8% at 4 degrees C and between 0.4% and 82.8% at 15 degrees C. Differences in the removal patterns of PCB congeners were observed in relation to the phylogenetic affiliation: Arthrobacter isolate showed similar biodegradation efficiencies when growing at 4 degrees C and 15 degrees C, while Pseudoalteromonas better degraded PCBs at 15 degrees C. No biodegradation was detected for Psychrobacter isolate at 4 degrees C. Results obtained highlight the occurrence of PCB-degrading bacteria in Antarctic seawater and suggest the potential exploitation of autochthonous bacteria for PCB bioremediation in cold marine environments.

Biphenyl uptake by psychrotolerant Pseudomonas sp. strain Cam-1 and mesophilic Burkholderia sp. strain LB400

We investigated the uptake of biphenyl by the psychrotolerant, polychlorinated biphenyl (PCB)-degrader, Pseudomonas sp. strain Cam-1 and the mesophilic PCB-degrader, Burkholderia sp. strain LB400. The effects of growth substrates, metabolic inhibitors, and temperature on [14C]biphenyl uptake were studied. Biphenyl uptake by both strains was induced by growth on biphenyl, and was inhibited by dinitrophenol (DNP) and carbonyl cyanide m-chlorophenylhydrazone (CCCP), which are metabolic uncouplers. The Vmax and Km for biphenyl uptake by Cam-1 at 22 degrees C were 5.4 +/- 1.7 nmol x min(-1) x (mg of cell protein)(-1) and 83.1 +/- 15.9 micromol x L(-1), respectively. The Vmax and Km for biphenyl uptake by LB400 at 22 degrees C were 3.2 +/- 0.3 nmol x min(-1) x (mg of cell protein(-1)) and 51.5 +/- 9.6 micromol x L(-1), respectively. At 15 degrees C, the maximum rate for biphenyl uptake by Cam-1 and LB400 was 3.1 +/- 0.3 nmol x min(-1) x (mg of cell protein)(-1) and 0.89 +/- 0.1 nmol x min(-1) x (mg of cell protein)(-1), respectively. Thus, the maximum rate for biphenyl uptake by Cam-1 at 15 degrees C was more than 3 times higher than that for LB400.

Cell division theory and individual-based modeling of microbial lag: part II. Modeling lag phenomena induced by temperature shifts

This paper is the second in a series of two, and studies microbial lag in cell number and/or biomass measurements caused by temperature changes with an individual-based modeling approach. For this purpose, the theory of cell division, as discussed in the first part of this series of research papers, was implemented in the individual-based modeling framework BacSim. Simulations of this model are compared with experimental data of Escherichia coli, growing in an aerated, glucose-rich medium and subjected to sudden temperature shifts. The premise of a constant cell volume under changing temperature conditions predicts no lag in cell numbers after the shift, in contrast to the experimental observations. Based on literature research, two biological mechanisms that could be responsible for the observed lag phenomena are proposed. The first assumes that the average cell volume depends on temperature while the second assumes that a lag in biomass growth occurs after the temperature shift. For a lag in cell number caused by an increased average cell volume, the cell biomass always increases at the maximal rate. Therefore, cells are evidently not stressed and do not have to adapt to the new conditions, as opposed to a lag in biomass growth. Implementation and simulation of both mechanisms are found to describe the experimental observations equally well. Therefore, further research is needed to distinguish between the two mechanisms. This can be done by observing, in addition to cell numbers, a measure for the average cell volumes. In conclusion, the individual-based modeling approach is a good methodology to investigate and test biological theories and assumptions. Also, based on the simulations, suggestions for further experimental observations can be made.

RecD plays an essential function during growth at low temperature in the antarctic bacterium Pseudomonas syringae Lz4W

The Antarctic psychrotrophic bacterium Pseudomonas syringae Lz4W has been used as a model system to identify genes that are required for growth at low temperature. Transposon mutagenesis was carried out to isolate mutant(s) of the bacterium that are defective for growth at 4 degrees but normal at 22 degrees . In one such cold-sensitive mutant (CS1), the transposon-disrupted gene was identified to be a homolog of the recD gene of several bacteria. Trans-complementation and freshly targeted gene disruption studies reconfirmed that the inactivation of the recD gene leads to a cold-sensitive phenotype. We cloned, sequenced, and analyzed approximately 11.2 kbp of DNA from recD and its flanking region from the bacterium. recD was the last gene of a putative recCBD operon. The RecD ORF was 694 amino acids long and 40% identical (52% similar) to the Escherichia coli protein, and it could complement the E. coli recD mutation. The recD gene of E. coli, however, could not complement the cold-sensitive phenotype of the CS1 mutant. Interestingly, the CS1 strain showed greater sensitivity toward the DNA-damaging agents, mitomycin C and UV. The inactivation of recD in P. syringae also led to cell death and accumulation of DNA fragments of approximately 25-30 kbp in size at low temperature (4 degrees ). We propose that during growth at a very low temperature the Antarctic P. syringae is subjected to DNA damage, which requires direct participation of a unique RecD function. Additional results suggest that a truncated recD encoding the N-terminal segment of (1-576) amino acids is sufficient to support growth of P. syringae at low temperature.

The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure

The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precursors of modern life both stored information and acted as catalysts. For the first time among extensive studies on ribozymes, we have investigated the influence of hydrostatic pressure on the hairpin ribozyme catalytic activity. High pressures are of interest when studying life under extreme conditions and may help to understand the behavior of macromolecules at the origins of life. Kinetic studies of the hairpin ribozyme self-cleavage were performed under high hydrostatic pressure. The activation volume of the reaction (34 +/- 5 ml/mol) calculated from these experiments is of the same order of magnitude as those of common protein enzymes, and reflects an important compaction of the RNA molecule during catalysis, associated to a water release. Kinetic studies were also carried out under osmotic pressure and confirmed this interpretation and the involvement of water movements (78 +/- 4 water molecules per RNA molecule). Taken together, these results are consistent with structural studies indicating that loops A and B of the ribozyme come into close contact during the formation of the transition state. While validating baro-biochemistry as an efficient tool for investigating dynamics at work during RNA catalysis, these results provide a complementary view of ribozyme catalytic mechanisms.

Purification, partial amino acid sequence and mode of action of pediocin PD-1, a bacteriocin produced by Pediococcus damnosus NCFB 1832

Pediocin PD-1 is a ribosomally synthesized antimicrobial peptide produced by Pediococcus damnosus NCFB1832. It inhibits the growth of several food spoilage bacteria, including malolactic bacteria isolated from wine. Pediocin PD-1 is 2866.87+/-0.4 Da in size, has an isoelectric point (pI) of ca. 9.0 and, on amino acid composition, has partial homology to the lantibiotic plantaricin C. The highest activity of pediocin PD-1 against cells of Oenococcus oeni was observed at an external pH of 5.0 and at 25 degrees C. The primary mode of action of pediocin PD-1 is most probably due to pore formation, as indicated by the efflux of K+ from metabolically active cells of O. oeni. In the presence of 10 mM gadolinium (Gd3+), pediocin PD-1 did not affect cells of O. oeni. This suggests that the mode of action of pediocin PD-1 relies on a net negatively charged cell surface. In comparison to nisin, pediocin PD-1 is less active against non-growing cells of O. oeni.

Unifying temperature effects on the growth rate of bacteria and the stability of globular proteins

The specific growth rate constant for bacterial growth does not obey the Arrhenius-type kinetics displayed by simple chemical reactions. Instead, for bacteria, steep convex curves are observed on an Arrhenius plot at the low- and high-temperature ends of the biokinetic range, with a region towards the middle of the growth range loosely approximating linearity. This central region has been considered by microbiologists to be the "normal physiological range" for bacterial growth, a concept whose meaningfulness we now question. We employ a kinetic model incorporating thermodynamic terms for temperature-induced enzyme denaturation, central to which is a term to account for the large positive heat capacity change during unfolding of the proteins within the bacteria. It is now widely believed by biophysicists that denaturation of complex proteins and/or other macromolecules is due to hydrophobic hydration of non-polar compounds. Denaturation is seen as the process by which enthalpic and entropic forces becomes imbalanced both at high and at low temperatures resulting in conformational changes in the enzyme structure that expose hydrophobic amino acid groups to the surrounding water molecules. The "thermodynamic" rate model, incorporating the heat capacity change and its effect on the enthalpy and entropy of the system, fitted 35 sets of data for psychrophilic, psychrotrophic, mesophilic and thermophilic bacteria well, resulting in biologically meaningful estimates for the important thermodynamic parameters. As these results mirror those obtained by biophysicists for globular proteins, it appears that the same or a similar mechanism applies to bacteria as applies to proteins.

Psychrophilic enzymes: hot topics in cold adaptation

More than three-quarters of the Earth's surface is occupied by cold ecosystems, including the ocean depths, and polar and alpine regions. These permanently cold environments have been successfully colonized by a class of extremophilic microorganisms that are known as psychrophiles (which literally means cold-loving). The ability to thrive at temperatures that are close to, or below, the freezing point of water requires a vast array of adaptations to maintain the metabolic rates and sustained growth compatible with life in these severe environmental conditions.

A Novel H-NS-like protein from an antarctic psychrophilic bacterium reveals a crucial role for the N-terminal domain in thermal stability

We describe here new members of the H-NS protein family identified in a psychrotrophic Acinetobacter spp. bacterium collected in Siberia and in a psychrophilic Psychrobacter spp. bacterium collected in Antarctica. Both are phylogenetically closely related to the HvrA and SPB Rhodobacter transcriptional regulators. Their amino acid sequence shares 40% identity, and their predicted secondary structure displays a structural and functional organization in two modules similar to that of H-NS in Escherichia coli. Remarkably, the Acinetobacter protein fully restores to the wild-type H-NS-dependent phenotypes, whereas the Psychrobacter protein is no longer able to reverse the effects of H-NS deficiency in an E. coli mutant strain above 30 degrees C. Moreover, in vitro experiments demonstrate that the ability of the Psychrobacter H-NS protein to bind curved DNA and to form dimers is altered at 37 degrees C. The construction of hybrid proteins containing the N- or the C-terminal part of E. coli H-NS fused to the C- or N-terminal part of the Psychrobacter protein demonstrates the role of the N-terminal domain in this process. Finally, circular dichroism analysis of purified H-NS proteins suggests that, as compared with the E. coli and Acinetobacter proteins, the alpha-helical domain displays weaker intermolecular interactions in the Psychrobacter protein, which may account for the low thermal stability observed at 37 degrees C.

Linking of microorganisms to phenanthrene metabolism in soil by analysis of (13)C-labeled cell lipids

Phenanthrene-metabolizing soil microbial communities were characterized by examining mineralization of [(14)C]phenanthrene, by most-probable-number (MPN) counting, by 16S-23S spacer DNA analysis of the numerically dominant, culturable phenanthrene-degrading isolates, and by examining incorporation of [(13)C]phenanthrene-derived carbon into sterols and polar lipid fatty acids (PLFAs). An unpolluted agricultural soil, a roadside soil diffusely polluted with polycyclic aromatic hydrocarbons (PAHs), and two highly PAH-polluted soils from industrial sites were analyzed. Microbial phenanthrene degraders were not detected by MPN counting in the agricultural soil and the roadside soil. In the industrial soils, phenanthrene degraders constituted 0.04 and 3.6% of the total number of CFU. 16S-23S spacer DNA analysis followed by partial 16S DNA sequencing of representative isolates from one of the industrial soils showed that one-half of the isolates belonged to the genus Sphingomonas and the other half were closely related to an unclassified beta-proteobacterium. The (13)C-PLFA profiles of the two industrial soils were relatively similar and resembled the profiles of phenanthrene-degrading Sphingomonas reference strains and unclassified beta-proteobacterium isolates but did not match the profiles of Pseudomonas, Mycobacterium, or Nocardia reference strains. The (13)C-PLFA profiles of phenanthrene degraders in the agricultural soil and the roadside soil were different from each other and different from the profiles of the highly polluted industrial soils. Only in the roadside soil were 10me/12me18:0 PLFAs enriched in (13)C, suggesting that actinomycetes metabolized phenanthrene in this soil. The (13)C-PLFA profiles of the unpolluted agricultural soil did not resemble the profiles of any of the reference strains. In all of the soils investigated, no excess (13)C was recovered in the 18:2omega6,9 PLFA, suggesting that fungi did not contribute significantly to assimilation of [(13)C]phenanthrene.

Seasonal factors affecting surfactant biodegradation in Antarctic coastal waters: comparison of a polluted and pristine site

This report is the first seasonal study of anthropogenic pollutant biodegradation rates in Antarctic coastal waters. The capacity of surface waters from Rothera Research Station, Adelaide Island, Antarctica, to biodegrade the anionic surfactant sodium dodecyl sulphate (SDS) was quantified in biodegradation tests from April 1988 to January 1999. Large temporal differences in the persistence of SDS were observed. In mid-winter (July), the SDS-biodegradation half life was twice that measured in mid-summer (January), despite small temperature differences (up to 2.45 degrees C). Comparisons between water from a pristine site and a site receiving grey-waste water from the station showed that some acclimation to SDS was occurring in the contaminated water. This resulted in SDS half lives up to to approximately 80 h shorter in the polluted water compared with the pristine site in the summer months when a large population of SDS-degrading bacteria had developed. Biodegradation half lives in Antarctic coastal waters (160-460 h) were generally far higher than those observed in temperate waters.

Cloning, sequencing, and expression of the cold-inducible hutU gene from the antarctic psychrotrophic bacterium Pseudomonas syringae

A promoter-fusion study with a Tn 5-based promoter probe vector had earlier found that the hutU gene which encodes the enzyme urocanase for the histidine utilization pathway is upregulated at a lower temperature (4 degrees C) in the Antarctic psychrotrophic bacterium Pseudomonas syringae. To examine the characteristics of the urocanase gene and its promoter elements from the psychrotroph, the complete hutU and its upstream region from P. syringae were cloned, sequenced, and analyzed in the present study. Northern blot and primer extension analyses suggested that the hutU gene is inducible upon a downshift of temperature (22 to 4 degrees C) and that there is more than one transcription initiation site. One of the initiation sites was specific to the cells grown at 4 degrees C, which was different from the common initiation sites observed at both 4 and 22 degrees C. Although no typical promoter consensus sequences were observed in the flanking region of the transcription initiation sites, there was a characteristic CAAAA sequence at the -10 position of the promoters. Additionally, the location of the transcription and translation initiation sites suggested that the hutU mRNA contains a long 5'-untranslated region, a characteristic feature of many cold-inducible genes of mesophilic bacteria. A comparison of deduced amino acid sequences of urocanase from various bacteria, including the mesophilic and psychrotrophic Pseudomonas spp., suggests that there is a high degree of similarity between the enzymes. The enzyme sequence contains a signature motif (GXGX(2)GX(10)G) of the Rossmann fold for dinucleotide (NAD(+)) binding and two conserved cysteine residues in and around the active site. The psychrotrophic enzyme, however, has an extended N-terminal end.