Reporting Key Features in Cold-Adapted Bacteria

Genomic signatures of cold adaptation in the family Colwelliaceae

Psychrophily is a phenotype describing microbial growth at low temperatures; elucidating the biomolecular and genomic adaptations necessary for survival in the cold is important for understanding life in extreme environments on Earth and in outer space. We used comparative genomics and temperature growth experiments of bacteria from the family Colwelliaceae to identify genomic factors correlated with optimal growth temperature (OGT). A phylogenomic analysis of 67 public and 39 newly sequenced strains revealed three main clades of Colwelliaceae. Temperature growth experiments revealed significant differences in mean OGT by clade, wherein strains of Colwelliaceae had similar growth rates at -1 °C but varied in their ability to tolerate 17 °C. Using amino acid compositional indices, a multiple linear regression model was constructed to predict the OGT of these organisms (RMSE 5.2 °C). Investigation of Colwelliaceae functional genes revealed a putative cold-adaptive gene cassette that was present in psychrophilic strains but absent in a closely related strain with a significantly higher OGT. This study also presents genomic evidence suggesting that the clade of Colwelliaceae containing Colwellia hornerae should be investigated as a new genus. These contributions offer key insights into the psychrophily phenotype and its underlying genomic foundation in the family Colwelliaceae.

From freezing to functioning: cellular strategies of cold-adapted bacteria for surviving in extreme environments

The ability of cold-adapted bacteria to survive in extreme cold and diverse temperatures is due to their unique attributes like cell membrane stability, up-regulation of peptidoglycan biosynthesis, increased production of extracellular polymeric substances, and expansion of membrane pigment. Various cold-adapted proteins, including ice-nucleating proteins (INPs), antifreeze proteins (AFPs), cold shock proteins (Csps), and cold-acclimated proteins (CAPs), help the bacteria to survive in these environments. To sustain cells from extreme cold conditions and maintain stability in temperature fluctuations, survival strategies at the molecular level and their mechanism play significant roles in adaptations in cryospheric conditions. Furthermore, cold shock domains present in the multifunctional cold shock proteins play crucial roles in their adaptation strategies. The considerable contribution of lipopeptides, osmolytes, and membrane pigments plays an integral part in their survival in extreme environments. This review summarizes the evolutionary history of cold-adapted bacteria and their molecular and cellular adaptation strategies to thrive in harsh cold environments. It also discusses the importance of carotenoids produced, lipid composition, cryoprotectants, proteins, and chaperones related to this adaptation. Furthermore, the functions and mechanisms of adaptations within the cell are discussed briefly. One can utilize and explore their potential in various biotechnology applications and their evolutionary journey by knowing the inherent mechanism of their molecular and cellular adaptation to cold climatic conditions. This review will help all branches of the life science community understand the basic microbiology of psychrophiles and their hidden prospect in life science research.

Study on the estradiol degradation gene expression and resistance mechanism of Rhodococcus R-001 under low-temperature stress

Estradiol (E2), an endocrine disruptor, acts by mimicking or interfering with the normal physiological functions of natural hormones within organisms, leading to issues such as endocrine system disruption. Notably, seasonal fluctuations in environmental temperature may influence the degradation speed of estradiol (E2) in the natural environment, intensifying its potential health and ecological risks. Therefore, this study aims to explore how bacteria can degrade E2 under low-temperature conditions, unveiling their resistance mechanisms, with the goal of developing new strategies to mitigate the threat of E2 to health and ecological safety. In this paper, we found that Rhodococcus equi DSSKP-R-001 (R-001) can efficiently degrade E2 at 30 °C and 10 °C. Six genes in R-001 were shown to be involved in E2 degradation by heterologous expression at 30 °C. Among them, 17β-HSD, KstD2, and KstD3, were also involved in E2 degradation at 10 °C; KstD was not previously known to degrade E2. RNA-seq was used to characterize differentially expressed genes (DEGs) to explore the stress response of R-001 to low-temperature environments to elucidate the strain's adaptation mechanism. At the low temperature, R-001 cells changed from a round spherical shape to a long rod or irregular shape with elevated unsaturated fatty acids and were consistent with the corresponding genetic changes. Many differentially expressed genes linked to the cold stress response were observed. R-001 was found to upregulate genes encoding cold shock proteins, fatty acid metabolism proteins, the ABC transport system, DNA damage repair, energy metabolism and transcriptional regulators. In this study, we demonstrated six E2 degradation genes in R-001 and found for the first time that E2 degradation genes have different expression characteristics at 30 °C and 10 °C. Linking R-001 to cold acclimation provides new insights and a mechanistic basis for the simultaneous degradation of E2 under cold stress in Rhodococcus adaptation.

Unveiling microbial guilds and symbiotic relationships in Antarctic sponge microbiomes

Marine sponges host diverse microbial communities. Although we know many of its ecological patterns, a deeper understanding of the polar sponge holobiont is still needed. We combine high-throughput sequencing of ribosomal genes, including the largest taxonomic repertoire of Antarctic sponge species analyzed to date, functional metagenomics, and metagenome-assembled genomes (MAGs). Our findings show that sponges harbor more exclusive bacterial and archaeal communities than seawater, while microbial eukaryotes are mostly shared. Furthermore, bacteria in Antarctic sponge holobionts establish more cooperative interactions than in sponge holobionts from other environments. The bacterial classes that established more positive relations were Bacteroidia, Gamma- and Alphaproteobacteria. Antarctic sponge microbiomes contain microbial guilds that encompass ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and sulfur-oxidizing bacteria. The retrieved MAGs showed a high level of novelty and streamlining signals and belong to the most abundant members of the main microbial guilds in the Antarctic sponge holobiont. Moreover, the genomes of these symbiotic bacteria contain highly abundant functions related to their adaptation to the cold environment, vitamin production, and symbiotic lifestyle, helping the holobiont survive in this extreme environment.

Explorative characterization and taxonomy-aligned comparison of alterations in lipids and other biomolecules in Antarctic bacteria grown at different temperatures

Temperature significantly impacts bacterial physiology, metabolism and cell chemistry. In this study, we analysed lipids and the total cellular biochemical profile of 74 fast-growing Antarctic bacteria grown at different temperatures. Fatty acid diversity and temperature-induced alterations aligned with bacterial classification-Gram-groups, phylum, genus and species. Total lipid content, varied from 4% to 19% of cell dry weight, was genus- and species-specific. Most bacteria increased lipid content at lower temperatures. The effect of temperature on the profile was complex and more species-specific, while some common for all bacteria responses were recorded. Gram-negative bacteria adjusted unsaturation and acyl chain length. Gram-positive bacteria adjusted methyl branching (anteiso-/iso-), chain length and unsaturation. Fourier transform infrared spectroscopy analysis revealed Gram-, genus- and species-specific changes in the total cellular biochemical profile triggered by temperature fluctuations. The most significant temperature-related alterations detected on all taxonomy levels were recorded for mixed region 1500-900 cm-1 , specifically the band at 1083 cm-1 related to phosphodiester groups mainly from phospholipids (for Gram-negative bacteria) and teichoic/lipoteichoic acids (for Gram-positive bacteria). Some changes in protein region were detected for a few genera, while the lipid region remained relatively stable despite the temperature fluctuations.

Molecular Biology Applications of Psychrophilic Enzymes: Adaptations, Advantages, Expression, and Prospective

Psychrophilic enzymes are primarily produced by microorganisms from extremely low-temperature environments which are known as psychrophiles. Their high efficiency at low temperatures and easy heat inactivation property have attracted extensive attention from various food and industrial bioprocesses. However, the application of these enzymes in molecular biology is still limited. In a previous review, the applications of psychrophilic enzymes in industries such as the detergent additives, the food additives, the bioremediation, and the pharmaceutical medicine, and cosmetics have been discussed. In this review, we discuss the main cold adaptation characteristics of psychrophiles and psychrophilic enzymes, as well as the relevant information on different psychrophilic enzymes in molecular biology. We summarize the mining and screening methods of psychrophilic enzymes. We finally recap the expression of psychrophilic enzymes. We aim to provide a reference process for the exploration and expression of new generation of psychrophilic enzymes.

Active microbiota persist in dry permafrost and active layer from Elephant Head, Antarctica

Dry permafrost is a challenging environment for microbial life due to cold, dry, and often oligotrophic conditions. In 2016, Elephant Head, Antarctica, was confirmed as the second site on Earth to contain dry permafrost. It is geographically distinct from the McMurdo Dry Valleys where dry permafrost has been studied previously. Here, we present the first study of the microbial activity, diversity, and functional potential of Elephant Head dry permafrost. Microbial activity was measured using radiorespiration assays with radiolabeled acetate as a carbon source at 5, 0, and -5°C. Low, but detectable, rates of microbial activity were measured in some samples at 0 and -5°C. This is distinct from previous studies of McMurdo Dry Valley dry permafrost which concluded that dry permafrost represents a cold-arid limit to life on the planet. The isolation of cold-adapted organisms from these soils, including one capable of subzero growth, further supports that the Elephant Head dry active layer and dry permafrost harbor viable microbial life, which may be active in situ. Metagenomic, 16S rRNA gene, and internal transcribed spacer and amplicon sequencing identified similar microbial communities to other Antarctic and cold environments. The Elephant Head microbial community appears to be adapted for survival in cold, dry, and oligotrophic conditions based on the presence of cold adaptation and stress response genes in the metagenomes. Together, our results show that dry permafrost environments do not exclude active microbial life at subzero temperatures, suggesting that the cold, dry soils of Mars may also not be as inhospitable as previously thought.

Lichen-associated microbial members are prevalent in the snow microbiome of a sub-arctic alpine tundra

Snow is the largest component of the cryosphere, with its cover and distribution rapidly decreasing over the last decade due to climate warming. It is imperative to characterize the snow (nival) microbial communities to better understand the role of microorganisms inhabiting these rapidly changing environments. Here, we investigated the core nival microbiome, the cultivable microbial members, and the microbial functional diversity of the remote Uapishka mountain range, a massif of alpine sub-arctic tundra and boreal forest. Snow samples were taken over a two-month interval along an altitude gradient with varying degree of anthropogenic traffic and vegetation cover. The core snow alpine tundra/boreal microbiome, which was present across all samples, constituted of Acetobacterales, Rhizobiales and Acidobacteriales bacterial orders, and of Mycosphaerellales and Lecanorales fungal orders, with the dominant fungal taxa being associated with lichens. The snow samples had low active functional diversity, with Richness values ranging from 0 to 19.5. The culture-based viable microbial enumeration ranged from 0 to 8.05 × 103 CFUs/mL. We isolated and whole-genome sequenced five microorganisms which included three fungi, one alga, and one potentially novel bacterium of the Lichenihabitans genus; all of which appear to be part of lichen-associated taxonomic clades.

Cold adapted Pseudomonas: ecology to biotechnology

The cold adapted microorganisms, psychrophiles/psychrotolerants, go through several modifications at cellular and biochemical levels to alleviate the influence of low temperature stress conditions. The low temperature environments depend on these cold adapted microorganisms for various ecological processes. The ability of the microorganisms to function in cold environments depends on the strategies directly associated with cell metabolism, physicochemical constrains, and stress factors. Pseudomonas is one among such group of microorganisms which is predominant in cold environments with a wide range of ecological and biotechnological applications. Bioformulations of Pseudomonas spp., possessing plant growth promotion and biocontrol abilities for application under low temperature environments, are well documented. Further, recent advances in high throughput sequencing provide essential information regarding the prevalence of Pseudomonas in rhizospheres and their role in plant health. Cold adapted species of Pseudomonas are also getting recognition for their potential in biodegradation and bioremediation of environmental contaminants. Production of enzymes and bioactive compounds (primarily as an adaptation mechanism) gives way to their applications in various industries. Exopolysaccharides and various biotechnologically important enzymes, produced by cold adapted species of Pseudomonas, are making their way in food, textiles, and pharmaceuticals. The present review, therefore, aims to summarize the functional versatility of Pseudomonas with particular reference to its peculiarities along with the ecological and biotechnological applications.

Mining of key genes for cold adaptation from Pseudomonas fragi D12 and analysis of its cold-adaptation mechanism

The psychrotroph Pseudomonas fragi D12, which grew strongly under low temperatures, was screened from tundra soil collected from the permanent alpine zone on Changbai Mountain. To mine the genes critical for cold tolerance and to investigate the cold-adaptation mechanism, whole-genome sequencing, comparative genomic analysis, and transcriptome analysis were performed with P. fragi. A total of 124 potential cold adaptation genes were identified, including nineteen unique cold-adaptive genes were detected in the genome of P. fragi D12. Three unique genes associated with pili protein were significantly upregulated at different degrees of low temperature, which may be the key to the strong low-temperature adaptability of P. fragi D12. Meanwhile, we were pleasantly surprised to find that Pseudomonas fragi D12 exhibited different cold-adaptation mechanisms under different temperature changes. When the temperature declined from 30°C to 15°C, the response included maintenance of the fluidity of cell membranes, increased production of extracellular polymers, elevation in the content of compatibility solutes, and reduction in the content of reactive oxygen species, thereby providing a stable metabolic environment. When the temperature decreased from 15°C to 4°C, the response mainly included increases in the expression of molecular chaperones and transcription factors, enabling the bacteria to restore normal transcription and translation. The response mechanism of P. fragi D12 to low-temperature exposure is discussed. The results provide new ideas for the cold-adaptation mechanism of cold-tolerant microorganisms.

In situ Nanopore sequencing reveals metabolic characteristics of the Qilian glacier meltwater microbiome

Nanopore metagenomic sequencing enables rapid annotating microbiological ecosystems, and the previous glacier-related sequencing applications (e.g., targeted ice sheets, ice lake, and cryoconite holes) inspire us to explore high-altitude glacier meltwater at Qilian Mountain, China (3000 to 4000 m above sea level, MASL). Our findings suggest that (1) despite only several hundred meters apart, the microbial communities and functionalities are quite different among vertical alpine distributions; (2) the high-altitude Qilian meltwater microbiome serve several main metabolic functions, including sulfur oxidation, selenite decomposing, photosynthesis, energy production, enzymic, and UV tolerant activities. Meanwhile, our Nanopore metagenomic results indicate that the microbial classifications and functionalities (e.g., chaperones, cold-shock, specific tRNA species, oxidative stress, and resistance to toxic compounds) of Qilian meltwater are highly consistent with the other glacial microbiome, emphasizing that only certain microbial species can survive in the cold environment and the molecular adaptions and lifestyles remain stable all over the world. Besides, we have shown Nanopore metagenomic sequencing can provide reliable prokaryotic classifications within or among studies, which therefore can encourage more applications in the field given faster turnaround time. However, we recommend accumulating at least 400 ng nucleic acids (after extraction) and maximizing Nanopore library preparation efficiency before on-site sequencing to obtain better resolutions.

The Microbiome of Things: Appliances, Machines, and Devices Hosting Artificial Niche-Adapted Microbial Communities

As it is the case with natural substrates, artificial surfaces of man-made devices are home to a myriad of microbial species. Artificial products are not necessarily characterized by human-associated microbiomes; instead, they can present original microbial populations shaped by specific environmental-often extreme-selection pressures. This review provides a detailed insight into the microbial ecology of a range of artificial devices, machines, and appliances, which we argue are specific microbial niches that do not necessarily fit in the "build environment" microbiome definition. Instead, we propose here the Microbiome of Things (MoT) concept analogous to the Internet of Things (IoT) because we believe it may be useful to shed light on human-made, but not necessarily human-related, unexplored microbial niches.

Microbial responses to soil cooling might explain increases in microbial biomass in winter

In temperate, boreal and arctic soil systems, microbial biomass often increases during winter and decreases again in spring. This build-up and release of microbial carbon could potentially lead to a stabilization of soil carbon during winter times. Whether this increase is caused by changes in microbial physiology, in community composition, or by changed substrate allocation within microbes or communities is unclear. In a laboratory incubation study, we looked into microbial respiration and growth, as well as microbial glucose uptake and carbon resource partitioning in response to cooling. Soils taken from a temperate beech forest and temperate cropland system in October 2020, were cooled down from field temperature of 11 °C to 1 °C. We determined microbial growth using 18O-incorporation into DNA after the first two days of cooling and after an acclimation phase of 9 days; in addition, we traced 13C-labelled glucose into microbial biomass, CO2 respired from the soil, and into microbial phospholipid fatty acids (PLFAs). Our results show that the studied soil microbial communities responded strongly to soil cooling. The 18O data showed that growth and cell division were reduced when soils were cooled from 11 to 1 °C. Total respiration was also reduced but glucose uptake and glucose-derived respiration were unchanged. We found that microbes increased the investment of glucose-derived carbon in unsaturated phospholipid fatty acids at colder temperatures. Since unsaturated fatty acids retain fluidity at lower temperatures compared to saturated fatty acids, this could be interpreted as a precaution to reduced temperatures. Together with the maintained glucose uptake and reduced cell division, our findings show an immediate response of soil microorganisms to soil cooling, potentially to prepare for freezing events. The discrepancy between C uptake and cell division could explain previously observed high microbial biomass carbon in temperate soils in winter.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10533-023-01050-x.

Metabolically versatile psychrotolerant Antarctic bacterium Pseudomonas sp. ANT_H12B is an efficient producer of siderophores and accompanying metabolites (SAM) useful for agricultural purposes

BACKGROUND

Bacterial siderophores are chelating compounds with the potential of application in agriculture, due to their plant growth-promoting (PGP) properties, however, high production and purification costs are limiting factors for their wider application. Cost-efficiency of the production could be increased by omitting purification processes, especially since siderophores accompanying metabolites (SAM) often also possess PGP traits. In this study, the metabolism versatility of Pseudomonas sp. ANT_H12B was used for the optimization of siderophores production and the potential of these metabolites and SAM was characterized in the context of PGP properties.

RESULTS

The metabolic diversity of ANT_H12B was examined through genomic analysis and phenotype microarrays. The strain was found to be able to use numerous C, N, P, and S sources, which allowed for the design of novel media suitable for efficient production of siderophores in the form of pyoverdine (223.50-512.60 μM). Moreover, depending on the culture medium, the pH of the siderophores and SAM solutions varied from acidic (pH < 5) to alkaline (pH > 8). In a germination test, siderophores and SAM were shown to have a positive effect on plants, with a significant increase in germination percentage observed in beetroot, pea, and tobacco. The PGP potential of SAM was further elucidated through GC/MS analysis, which revealed other compounds with PGP potential, such as indolic acetic acids, organic acids, fatty acids, sugars and alcohols. These compounds not only improved seed germination but could also potentially be beneficial for plant fitness and soil quality.

CONCLUSIONS

Pseudomonas sp. ANT_H12B was presented as an efficient producer of siderophores and SAM which exhibit PGP potential. It was also shown that omitting downstream processes could not only limit the costs of siderophores production but also improve their agricultural potential.

Pseudomonas petrae sp. nov. isolated from regolith samples in Antarctica

A polyphasic taxonomic approach was used to characterize the four strains P2653^T, P2652, P2498, and P2647, isolated from Antarctic regolith samples. Initial genotype screening performed by PCR fingerprinting based on repetitive sequences showed that the isolates studied formed a coherent cluster separated from the other Pseudomonas species. Identification results based on 16S rRNA gene sequences showed the highest sequence similarity with Pseudomonas graminis (99.7%), which was confirmed by multilocus sequence analysis using the rpoB, rpoD, and gyrB genes. Genome sequence comparison of P2653^T with the most related P. graminis type strain DSM 11363^T revealed an average nucleotide identity of 92.1% and a digital DNA-DNA hybridization value of 46.6%. The major fatty acids for all Antarctic strains were C_16:0, Summed Feature 3 (C_16:1ω7c/C_16:1ω6c) and Summed Feature 8 (C_18:1ω7c/C_18:1ω6c). The predominant respiratory quinone was Q-9, and the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol. The regolith strains could be differentiated from related species by the absence of arginine dihydrolase, ornithine and lysine decarboxylase and by negative tyrosine hydrolysis. The results of this polyphasic study allowed the genotypic and phenotypic differentiation of four analysed strains from the closest related species, which confirmed that the strains represent a novel species within the genus Pseudomonas, for which the name Pseudomonas petrae sp. nov. is proposed with P2653^T (CCM 8850^T = DSM 112068^T = LMG 30619^T) as the type strain.

Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies

Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH &lt; 3), and eurypsychrophiles that grow at low temperatures down to approximately 4°C but have an optimum temperature for growth above 15°C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, “Ferrovum myxofaciens,” and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of “omics” techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15°C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.

Marine enzymes: Classification and application in various industries

Oceans are regarded as a plentiful and sustainable source of biological compounds. Enzymes are a group of marine biomaterials that have recently drawn more attention because they are produced in harsh environmental conditions such as high salinity, extensive pH, a wide temperature range, and high pressure. Hence, marine-derived enzymes are capable of exhibiting remarkable properties due to their unique composition. In this review, we overviewed and discussed characteristics of marine enzymes as well as the sources of marine enzymes, ranging from primitive organisms to vertebrates, and presented the importance, advantages, and challenges of using marine enzymes with a summary of their applications in a variety of industries. Current biotechnological advancements need the study of novel marine enzymes that could be applied in a variety of ways. Resources of marine enzyme can benefit greatly for biotechnological applications duo to their biocompatible, ecofriendly and high effectiveness. It is beneficial to use the unique characteristics offered by marine enzymes to either develop new processes and products or improve existing ones. As a result, marine-derived enzymes have promising potential and are an excellent candidate for a variety of biotechnology applications and a future rise in the use of marine enzymes is to be anticipated.

Discrimination of psychrophilic enzymes using machine learning algorithms with amino acid composition descriptor

Introduction

Psychrophilic enzymes are a class of macromolecules with high catalytic activity at low temperatures. Cold-active enzymes possessing eco-friendly and cost-effective properties, are of huge potential application in detergent, textiles, environmental remediation, pharmaceutical as well as food industry. Compared with the time-consuming and labor-intensive experiments, computational modeling especially the machine learning (ML) algorithm is a high-throughput screening tool to identify psychrophilic enzymes efficiently.

Methods

In this study, the influence of 4 ML methods (support vector machines, K-nearest neighbor, random forest, and naïve Bayes), and three descriptors, i.e., amino acid composition (AAC), dipeptide combinations (DPC), and AAC + DPC on the model performance were systematically analyzed.

Results and discussion

Among the 4 ML methods, the support vector machine model based on the AAC descriptor using 5-fold cross-validation achieved the best prediction accuracy with 80.6%. The AAC outperformed than the DPC and AAC + DPC descriptors regardless of the ML methods used. In addition, amino acid frequencies between psychrophilic and non-psychrophilic proteins revealed that higher frequencies of Ala, Gly, Ser, and Thr, and lower frequencies of Glu, Lys, Arg, Ile,Val, and Leu could be related to the protein psychrophilicity. Further, ternary models were also developed that could classify psychrophilic, mesophilic, and thermophilic proteins effectively. The predictive accuracy of the ternary classification model using AAC descriptor via the support vector machine algorithm was 75.8%. These findings would enhance our insight into the cold-adaption mechanisms of psychrophilic proteins and aid in the design of engineered cold-active enzymes. Moreover, the proposed model could be used as a screening tool to identify novel cold-adapted proteins.

Credibility assessment of cold adaptive Pseudomonas jesenni MP1 and P. palleroniana N26 on growth, rhizosphere dynamics, nutrient status, and yield of the kidney bean cultivated in Indian Central Himalaya

Kidney bean (Phaseolus vulgaris) productivity and nutritional quality are declining due to less nutrient accessibility, poor soil health, and indigent agronomic practices in hilly regions, which collectively led to a fall in farmer's income, and to malnutrition in consumers. Addressing such issues, the present investigation was designed to assess the impact of Pseudomonas jesenii MP1 and Pseudomonas palleroniana N26 treatment on soil health, microbial shift, yield, and nutrient status of the kidney bean in the Harsil and Chakrata locations of Indian Central Himalaya. P. jesenii MP1 and P. palleroniana N26 were characterized as cold adaptive PGPR as they possessed remarkable in vitro plant growth promoting traits. Further, field trial study with PGPR treatments demonstrated remarkable and prolific influence of both strains on yield, kidney bean nutrient status, and soil health at both geographical locations, which was indicated with improved grain yield (11.61%-23.78%), protein (6.13%-24.46%), and zinc content (21.86%-61.17%) over control. The metagenomic study revealed that use of bioinoculants also concentrated the nutrient mobilizing and plant beneficial microorganisms in the rhizosphere of the kidney bean. Moreover, correlation analysis also confirmed that the plant growth-promoting traits of P. jesenii MP1 and P. palleroniana N26 are the basis for improved yield and nutrient status of the kidney bean. Further, cluster and principal component analysis revealed that both P. jesenii MP1 and P. palleroniana N26 exhibited pronounced influence on yield attributes of the kidney bean at both the locations. At the Harsil location, the P. jesenii MP1-treated seed demonstrated highest grain yield over other treatments, whereas at Chakarata, P. jesenii MP1, and P. palleroniana N26 treatment showed almost equal enhancement (~23%) in grain yield over control. The above results revealed that these bioinoculants are efficient plant growth promoters and nutrient mobilizers; they could be used as green technology to improve human health and farmer's income by enhancing soil health, yield, and nutrient status of the kidney bean at hilly regions.

Proteomic and in silico analyses of dextran synthesis influence on Leuconostoc lactis AV1n adaptation to temperature change

Leuconostoc lactis is found in vegetables, fruits, and meat and is used by the food industry in the preparation of dairy products, wines, and sugars. We have previously demonstrated that the dextransucrase of Lc. lactis (DsrLL) AV1n produces a high-molecular-weight dextran from sucrose, indicating its potential use as a dextran-forming starter culture. We have also shown that this bacterium was able to produce 10-fold higher levels of dextran at 20°C than at 37°C, at the former temperature accompanied by an increase in dsrLL gene expression. However, the general physiological response of Lc. lactis AV1n to cold temperature in the presence of sucrose, leading to increased production of dextran, has not been yet investigated. Therefore, we have used a quantitative proteomics approach to investigate the cold temperature-induced changes in the proteomic profile of this strain in comparison to its proteomic response at 37°C. In total, 337 proteins were found to be differentially expressed at the applied significance criteria (adjusted p-value ≤ 0.05, FDR 5%, and with a fold-change ≥ 1.5 or ≤ 0.67) with 204 proteins overexpressed, among which 13% were involved in protein as well as cell wall, and envelope component biosynthesis including DsrLL. Proteins implicated in cold stress were expressed at a high level at 20°C and possibly play a role in the upregulation of DsrLL, allowing the efficient synthesis of the protein essential for its adaptation to cold. Post-transcriptional regulation of DsrLL expression also seems to take place through the interplay of exonucleases and endonucleases overexpressed at 20°C, which would influence the half-life of the dsrLL transcript. Furthermore, the mechanism of cold resistance of Lc. lactis AV1n seems to be also based on energy saving through a decrease in growth rate mediated by a decrease in carbohydrate metabolism and its orientation toward the production pathways for storage molecules. Thus, this better understanding of the responses to low temperature and mechanisms for environmental adaptation of Lc. lactis could be exploited for industrial use of strains belonging to this species.

Heterologous production and characterization of a pyomelanin of Antarctic Pseudomonas sp. ANT_H4: a metabolite protecting against UV and free radicals, interacting with iron from minerals and exhibiting priming properties toward plant hairy roots

BACKGROUND

Antarctica has one of the most extreme environments in the world. This region is inhabited by specifically adapted microorganisms that produce various unique secondary metabolites (e.g. pigments) enabling their survival under the harsh environmental conditions. It was already shown that these natural, biologically active molecules may find application in various fields of biotechnology.

RESULTS

In this study, a cold-active brown-pigment-producing Pseudomonas sp. ANT_H4 strain was characterized. In-depth genomic analysis combined with the application of a fosmid expression system revealed two different pathways of melanin-like compounds biosynthesis by the ANT_H4 strain. The chromatographic behavior and Fourier-transform infrared spectroscopic analyses allowed for the identification of the extracted melanin-like compound as a pyomelanin. Furthermore, optimization of the production and thorough functional analyses of the pyomelanin were performed to test its usability in biotechnology. It was confirmed that ANT_H4-derived pyomelanin increases the sun protection factor, enables scavenging of free radicals, and interacts with the iron from minerals. Moreover, it was shown for the first time that pyomelanin exhibits priming properties toward Calendula officinalis hairy roots in in vitro cultures.

CONCLUSIONS

Results of the study indicate the significant biotechnological potential of ANT_H4-derived pyomelanin and open opportunities for future applications. Taking into account protective features of analyzed pyomelanin it may be potentially used in medical biotechnology and cosmetology. Especially interesting was showing that pyomelanin exhibits priming properties toward hairy roots, which creates a perspective for its usage for the development of novel and sustainable agrotechnical solutions.

A Review on Psychrophilic β-D-Galactosidases and Their Potential Applications

The majority of the Earth's ecosystem is frigid and frozen, which permits a vast range of microbial life forms to thrive by triggering physiological responses that allow them to survive in cold and frozen settings. The apparent biotechnology value of these cold-adapted enzymes has been targeted. Enzymes' market size was around USD 6.3 billion in 2017 and will witness growth at around 6.8% CAGR up to 2024 owing to shifting consumer preferences towards packaged and processed foods due to the rising awareness pertaining to food safety and security reported by Global Market Insights (Report ID-GMI 743). Various firms are looking for innovative psychrophilic enzymes in order to construct more effective biochemical pathways with shorter reaction times, use less energy, and are ecologically acceptable. D-Galactosidase catalyzes the hydrolysis of the glycosidic oxygen link between the terminal non-reducing D-galactoside unit and the glycoside molecule. At refrigerated temperature, the stable structure of psychrophile enzymes adjusts for the reduced kinetic energy. It may be beneficial in a wide variety of activities such as pasteurization of food, conversion of biomass, biological role of biomolecules, ambient biosensors, and phytoremediation. Recently, psychrophile enzymes are also used in claning the contact lens. β-D-Galactosidases have been identified and extracted from yeasts, fungi, bacteria, and plants. Conventional (hydrolyzing activity) and nonconventional (non-hydrolytic activity) applications are available for these enzymes due to its transgalactosylation activity which produce high value-added oligosaccharides. This review content will offer new perspectives on cold-active β-galactosidases, their source, structure, stability, and application.

Isolation of novel cold-tolerance genes from rhizosphere microorganisms of Antarctic plants by functional metagenomics

The microorganisms that thrive in Antarctica, one of the coldest environments on the planet, have developed diverse adaptation mechanisms to survive in these extreme conditions. Through functional metagenomics, in this work, 29 new genes related to cold tolerance have been isolated and characterized from metagenomic libraries of microorganisms from the rhizosphere of two Antarctic plants. Both libraries were hosted in two cold-sensitive strains of Escherichia coli: DH10B ΔcsdA and DH10B ΔcsdA Δrnr. The csdA gene encodes a DEAD-box RNA helicase and rnr gene encodes an exoribonuclease, both essential for cold-adaptation. Cold-tolerance tests have been carried out in solid and liquid media at 15°C. Among the cold-tolerance genes identified, 12 encode hypothetical and unknown proteins, and 17 encode a wide variety of different proteins previously related to other well-characterized ones involved in metabolism reactions, transport and membrane processes, or genetic information processes. Most of them have been connected to cold-tolerance mechanisms. Interestingly, 13 genes had no homologs in E. coli, thus potentially providing entirely new adaptation strategies for this bacterium. Moreover, ten genes also conferred resistance to UV-B radiation, another extreme condition in Antarctica.

Effect of Mineral Carriers on Biofilm Formation and Nitrogen Removal Activity by an Indigenous Anammox Community from Cold Groundwater Ecosystem Alone and Bioaugmented with Biomass from a “Warm” Anammox Reactor

Simple Summary

During more than 50 years of exploitation of the sludge repositories near Chepetsky Mechanical Plant (Glazov, Udmurtia, Russia) containing solid wastes of uranium and processed polymetallic concentrate, the soluble compounds entered the upper aquifer due to infiltration. Nowadays, this has resulted in a high level of pollution of the groundwater with reduced and oxidized nitrogen compounds. In this work, quartz, kaolin, and bentonite clays from various deposits were shown to induce biofilm formation and enhance nitrogen removal by an indigenous microbial community capable of anaerobic ammonium oxidation with nitrite (anammox) at low temperatures. The addition of a “warm” anammox community was also effective in further improving nitrogen removal and expanding the list of mineral carriers most suitable for creating a permeable reactive barrier. It has been suggested that the anammox activity is determined by the presence of essential trace elements in the carrier, the morphology of its surface, and most importantly, competition from rapidly growing microbial groups. Future work was discussed to adapt the “warm” anammox community to cold and provide the anammox community with nitrite through a partial denitrification route within the scope of sustainable anammox-based bioremediation of a nitrogen-polluted cold aquifer. In this unique habitat, novel species of anammox bacteria that are adapted to cold and heavy nitrogen pollution can be discovered.

Abstract

The complex pollution of aquifers by reduced and oxidized nitrogen compounds is currently considered one of the urgent environmental problems that require non-standard solutions. This work was a laboratory-scale trial to show the feasibility of using various mineral carriers to create a permeable in situ barrier in cold (10 °C) aquifers with extremely high nitrogen pollution and inhabited by the Candidatus Scalindua-dominated indigenous anammox community. It has been established that for the removal of ammonium and nitrite in situ due to the predominant contribution of the anammox process, quartz, kaolin clays of the Kantatsky and Kamalinsky deposits, bentonite clay of the Berezovsky deposit, and zeolite of the Kholinsky deposit can be used as components of the permeable barrier. Biofouling of natural loams from a contaminated aquifer can also occur under favorable conditions. It has been suggested that the anammox activity is determined by a number of factors, including the presence of the essential trace elements in the carrier and the surface morphology. However, one of the most important factors is competition with other microbial groups that can develop on the surface of the carrier at a faster rate. For this reason, carriers with a high specific surface area and containing the necessary microelements were overgrown with the most rapidly growing microorganisms. Bioaugmentation with a “warm” anammox community from a laboratory reactor dominated by Ca. Kuenenia improved nitrogen removal rates and biofilm formation on most of the mineral carriers, including bentonite clay of the Dinozavrovoye deposit, as well as loamy rock and zeolite-containing tripoli, in addition to carriers that perform best with the indigenous anammox community. The feasibility of coupled partial denitrification–anammox and the adaptation of a “warm” anammox community to low temperatures and hazardous components contained in polluted groundwater prior to bioaugmentation should be the scope of future research to enhance the anammox process in cold, nitrate-rich aquifers.

Microbiome structure in biofilms from a volcanic island in Maritime Antarctica investigated by genome-centric metagenomics and metatranscriptomics

Antarctica is the coldest and driest continent on Earth, characterized by polyextreme environmental conditions, where species adapted form complex networks of interactions. Microbial communities growing in these harsh environments can form biofilms that help the associated species to survive and thrive. A rich body of knowledge describes environmental biofilm communities; however, most studies have focused on dominant community members rather than functional complexity and metabolic potential. To overcome these limitations, the present study used genome-centric metagenomics to describe two biofilm samples subjected to different temperature collected in Deception Island, Maritime Antarctica. The results unraveled a complex biofilm microbiome represented by 180 metagenome-assembled genomes. The potential metabolic interactions were investigated using metabolic flux balance analysis and revealed that purple bacteria are the community members with the highest correlations with other bacteria. Due to their predicted mixotrophic behavior, they may play a crucial role in the microbiome, likely supporting the heterotrophic species in biofilms. Metatranscriptomics results revealed that the chaperone system and proteins counteracting ROS and toxic compounds have a major role in maintaining bacterial cell homeostasis in sediments of volcanic origin.

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.

Current Advances in the Concept of Quorum Sensing-Based Prevention of Spoilage of Fish Products by Pseudomonads

Microbial spoilage of fish is attributed to quorum sensing (QS)-based activities. QS is a communication process between the cells in which microorganisms secrete and sense the specific chemicals (autoinductors, AIs) that regulate proteolysis, lipolysis, and biofilm formation. These activities change the organoleptic characteristics and reduce the safety of the products. Although the microbial community of fish is diverse and may consist of a range of bacterial strains, the deterioration of fish-based products is attributed to the growth and activity of Pseudomonas spp. This work summarizes recent advancements to assess the influence of QS mechanisms on seafood spoilage by Pseudomonas spp. The quorum sensing inhibition (QSI) in the context of fish preservation has also been discussed. Detailed recognition of this phenomenon is crucial in establishing effective strategies to prevent the premature deterioration of fish-based products.

Cold-adaptive mechanism of psychrophilic bacteria in food and its application

Psychrophilic bacteria are a type of microorganisms that normally grow in low-temperature environments. They are usually found in extremely cold environments. However, as people's demand for low-temperature storage of food becomes higher, psychrophilic bacteria have also begun to appear in cold storage and refrigerators, which has become a food safety hazard. In this paper, the optimal cooling strategies of psychrophilic bacteria are reviewed from the aspects of the cell membrane, psychrophilic enzymes, antifreeze proteins, cold shock proteins, gene regulation, metabolic levels and antifreeze agents, and the principle of psychrophilic mechanism is briefly described. The application of thermophilic bacteria and its products adapted to cold environments in food fields are analyzed. The purpose of this paper is to provide ideas for future research on psychrophilic bacteria based on the mechanism and application of psychrophilic bacteria.

Some Clues about Enzymes from Psychrophilic Microorganisms

Enzymes purified from psychrophilic microorganisms prove to be efficient catalysts at low temperatures and possess a great potential for biotechnological applications. The low-temperature catalytic activity has to come from specific structural fluctuations involving the active site region, however, the relationship between protein conformational stability and enzymatic activity is subtle. We provide a survey of the thermodynamic stability of globular proteins and their rationalization grounded in a theoretical approach devised by one of us. Furthermore, we provide a link between marginal conformational stability and protein flexibility grounded in the harmonic approximation of the vibrational degrees of freedom, emphasizing the occurrence of long-wavelength and excited vibrations in all globular proteins. Finally, we offer a close view of three enzymes: chloride-dependent α-amylase, citrate synthase, and β-galactosidase.

The microbiome of cryospheric ecosystems

The melting of the cryosphere is among the most conspicuous consequences of climate change, with impacts on microbial life and related biogeochemistry. However, we are missing a systematic understanding of microbiome structure and function across cryospheric ecosystems. Here, we present a global inventory of the microbiome from snow, ice, permafrost soils, and both coastal and freshwater ecosystems under glacier influence. Combining phylogenetic and taxonomic approaches, we find that these cryospheric ecosystems, despite their particularities, share a microbiome with representatives across the bacterial tree of life and apparent signatures of early and constrained radiation. In addition, we use metagenomic analyses to define the genetic repertoire of cryospheric bacteria. Our work provides a reference resource for future studies on climate change microbiology.

The cryosphere includes those parts of Earth where water or soil is frozen, such as snow, ice, glaciers and permafrost soils. Here, the authors present a global inventory of cryospheric microbial communities and their genetic repertoires.

Signatures of selection in core and accessory genomes indicate different ecological drivers of diversification among Bacillus cereus clades

Bacterial clades are often ecologically distinct, despite extensive horizontal gene transfer (HGT). How selection works on different parts of bacterial pan‐genomes to drive and maintain the emergence of clades is unclear. Focusing on the three largest clades in the diverse and well‐studied Bacillus cereus sensu lato group, we identified clade‐specific core genes (present in all clade members) and then used clade‐specific allelic diversity to identify genes under purifying and diversifying selection. Clade‐specific accessory genes (present in a subset of strains within a clade) were characterized as being under selection using presence/absence in specific clades. Gene ontology analyses of genes under selection revealed that different gene functions were enriched in different clades. Furthermore, some gene functions were enriched only amongst clade‐specific core or accessory genomes. Genes under purifying selection were often clade‐specific, while genes under diversifying selection showed signs of frequent HGT. These patterns are consistent with different selection pressures acting on both the core and the accessory genomes of different clades and can lead to ecological divergence in both cases. Examining variation in allelic diversity allows us to uncover genes under clade‐specific selection, allowing ready identification of strains and their ecological niche.

Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams

In glacier-fed streams, ecological windows of opportunity allow complex microbial biofilms to develop and transiently form the basis of the food web, thereby controlling key ecosystem processes. Using metagenome-assembled genomes, we unravel strategies that allow biofilms to seize this opportunity in an ecosystem otherwise characterized by harsh environmental conditions. We observe a diverse microbiome spanning the entire tree of life including a rich virome. Various co-existing energy acquisition pathways point to diverse niches and the exploitation of available resources, likely fostering the establishment of complex biofilms during windows of opportunity. The wide occurrence of rhodopsins, besides chlorophyll, highlights the role of solar energy capture in these biofilms while internal carbon and nutrient cycling between photoautotrophs and heterotrophs may help overcome constraints imposed by oligotrophy in these habitats. Mechanisms potentially protecting bacteria against low temperatures and high UV-radiation are also revealed and the selective pressure of this environment is further highlighted by a phylogenomic analysis differentiating important components of the glacier-fed stream microbiome from other ecosystems. Our findings reveal key genomic underpinnings of adaptive traits contributing to the success of complex biofilms to exploit environmental opportunities in glacier-fed streams, which are now rapidly changing owing to global warming.

Physiology of anammox adaptation to low temperatures and promising biomarkers: A review

The adaptation of bacteria involved in the anaerobic ammonium oxidation (anammox) to low temperatures in the mainstream of WWTP will unlock substantial treatment savings. However, their adaptation mechanisms have begun to be revealed only very recently. This study reviewed the state-of-the-art knowledge on these mechanisms from -omics studies, crucially including metaproteomics and metabolomics. Anammox bacteria adapt to low temperatures by synthesizing both chaperones of RNA and proteins and chemical chaperones. Furthermore, they preserve energy for the core metabolism by reducing biosynthesis in general. Thus, in this study, a number of biomarkers are proposed to help practitioners assess the extent of anammox bacteria adaptation and predict the decomposition of biofilms/granules or slower growth. The promising biomarkers also include unique ladderane lipids. Further proteomic and metabolomic studies are necessary for a more detailed understanding of anammox low-temperature adaptation, thus easing the transition to more cost-effective and sustainable wastewater treatment.

Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation

Exploring the molecular mechanisms behind bacterial adaptation to extreme temperatures has potential biotechnological applications. In the present study, Pseudomonas sp. Lz4W, a Gram-negative psychrophilic bacterium adapted to survive in Antarctica, was selected to decipher the molecular mechanism underlying the cold adaptation. Proteome analysis of the isolates grown at 4°C was performed to identify the proteins and pathways that are responsible for the adaptation. However, many proteins from the expressed proteome were found to be hypothetical proteins (HPs), whose function is unknown. Investigating the functional roles of these proteins may provide additional information in the biological understanding of the bacterial cold adaptation. Thus, our study aimed to assign functions to these HPs and understand their role at the molecular level. We used a structured insilico workflow combining different bioinformatics tools and databases for functional annotation. Pseudomonas sp. Lz4W genome (CP017432, version 1) contains 4493 genes and 4412 coding sequences (CDS), of which 743 CDS were annotated as HPs. Of these, from the proteome analysis, 61 HPs were found to be expressed consistently at the protein level. The amino acid sequences of these 61 HPs were submitted to our workflow and we could successfully assign a function to 18 HPs. Most of these proteins were predicted to be involved in biological mechanisms of cold adaptations such as peptidoglycan metabolism, cell wall organization, ATP hydrolysis, outer membrane fluidity, catalysis, and others. This study provided a better understanding of the functional significance of HPs in cold adaptation of Pseudomonas sp. Lz4W. Our approach emphasizes the importance of addressing the “hypothetical protein problem” for a thorough understanding of mechanisms at the cellular level, as well as, provided the assessment of integrating proteomics methods with various annotation and curation approaches to characterize hypothetical or uncharacterized protein data. The MS proteomics data generated from this study has been deposited to the ProteomeXchange through PRIDE with the dataset identifier–PXD029741.

Life from a Snowflake: Diversity and Adaptation of Cold-Loving Bacteria among Ice Crystals

Incredible as it is, researchers have now the awareness that even the most extreme environment includes special habitats that host several forms of life. Cold environments cover different compartments of the cryosphere, as sea and freshwater ice, glaciers, snow, and permafrost. Although these are very particular environmental compartments in which various stressors coexist (i.e., freeze–thaw cycles, scarce water availability, irradiance conditions, and poorness of nutrients), diverse specialized microbial communities are harbored. This raises many intriguing questions, many of which are still unresolved. For instance, a challenging focus is to understand if microorganisms survive trapped frozen among ice crystals for long periods of time or if they indeed remain metabolically active. Likewise, a look at their site-specific diversity and at their putative geochemical activity is demanded, as well as at the equally interesting microbial activity at subzero temperatures. The production of special molecules such as strategy of adaptations, cryoprotectants, and ice crystal-controlling molecules is even more intriguing. This paper aims at reviewing all these aspects with the intent of providing a thorough overview of the main contributors in investigating the microbial life in the cryosphere, touching on the themes of diversity, adaptation, and metabolic potential.

Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice

The anthropogenic release of oil hydrocarbons into the cold marine environment is an increasing concern due to the elevated usage of sea routes and the exploration of new oil drilling sites in Arctic areas. The aim of this study was to evaluate prokaryotic community structures and the genetic potential of hydrocarbon degradation in the metagenomes of seawater, sea ice, and crude oil encapsulating the sea ice of the Norwegian fjord, Ofotfjorden. Although the results indicated substantial differences between the structure of prokaryotic communities in seawater and sea ice, the crude oil encapsulating sea ice (SIO) showed increased abundances of many genera-containing hydrocarbon-degrading organisms, including Bermanella, Colwellia, and Glaciecola. Although the metagenome of seawater was rich in a variety of hydrocarbon degradation-related functional genes (HDGs) associated with the metabolism of n-alkanes, and mono- and polyaromatic hydrocarbons, most of the normalized gene counts were highest in the clean sea ice metagenome, whereas in SIO, these counts were the lowest. The long-chain alkane degradation gene almA was detected from all the studied metagenomes and its counts exceeded ladA and alkB counts in both sea ice metagenomes. In addition, almA was related to the most diverse group of prokaryotic genera. Almost all 18 good- and high-quality metagenome-assembled genomes (MAGs) had diverse HDGs profiles. The MAGs recovered from the SIO metagenome belonged to the abundant taxa, such as Glaciecola, Bermanella, and Rhodobacteracea, in this environment. The genera associated with HDGs were often previously known as hydrocarbon-degrading genera. However, a substantial number of new associations, either between already known hydrocarbon-degrading genera and new HDGs or between genera not known to contain hydrocarbon degraders and multiple HDGs, were found. The superimposition of the results of comparing HDG associations with taxonomy, the HDG profiles of MAGs, and the full genomes of organisms in the KEGG database suggest that the found relationships need further investigation and verification.

Microbial adaptation to different environmental conditions: molecular perspective of evolved genetic and cellular systems

Microorganisms are ubiquitous on Earth and can inhabit almost every environment. In a complex heterogeneous environment or in face of ecological disturbance, the microbes adjust to fluctuating environmental conditions through a cascade of cellular and molecular systems. Their habitats differ from cold microcosms of Antarctica to the geothermal volcanic areas, terrestrial to marine, highly alkaline zones to the extremely acidic areas and freshwater to brackish water sources. The diverse ecological microbial niches are attributed to the versatile, adaptable nature under fluctuating temperature, nutrient availability and pH of the microorganisms. These organisms have developed a series of mechanisms to face the environmental changes and thereby keep their role in mediate important ecosystem functions. The underlying mechanisms of adaptable microbial nature are thoroughly investigated at the cellular, genetic and molecular levels. The adaptation is mediated by a spectrum of processes like natural selection, genetic recombination, horizontal gene transfer, DNA damage repair and pleiotropy-like events. This review paper provides the fundamentals insight into the microbial adaptability besides highlighting the molecular network of microbial adaptation under different environmental conditions.

Soil microbial trait-based strategies drive metabolic efficiency along an altitude gradient

Trait-based approaches provide a candidate framework for linking soil microbial community to ecosystem processes, yet how the trade-offs in different microbial traits regulate the community-level metabolic efficiency remains unknown. Herein we assessed the roles of the microbial taxa with particular trait strategies in mediating soil microbial metabolic efficiency along an altitude gradient on the Tibetan Plateau. Results showed that soil microbial metabolic efficiency declined with increasing altitude, as indicated by the increasing metabolic quotient (microbial respiration per unit biomass, qCO2) and decreasing carbon use efficiency (CUE). Both qCO2 and CUE were predominantly predicted by microbial physiological and taxonomic attributes after considering key environmental factors including soil pH, substrate quantity and quality. Specifically, the reduced metabolic efficiency was associated with higher investment into nutrient (particularly for phosphorus) acquisitions via enzymes. Furthermore, we identified key microbial assemblies selected by harsh environments (low substrate quality and temperature) as important predictors of metabolic efficiency. These results suggest that particular microbial assemblies adapted to nutrient limited and cold habitats, but at the expense of lower metabolic efficient at higher altitude. Our findings provide a candidate mechanism underlying community-level metabolic efficiency, which has important implications for microbial-mediated processes such as carbon dynamics under global climate changes.

Regulated strategies of cold-adapted microorganisms in response to cold: a review

There are a large number of active cold-adapted microorganisms in the perennial cold environment. Due to their high-efficiency and energy-saving catalytic properties, cold-adapted microorganisms have become valuable natural resources with potential in various biological fields. In this study, a series of cold response strategies for microorganisms were summarized. This mainly involves the regulation of cell membrane fluidity, synthesis of cold adaptation proteins, regulators and metabolic changes, energy supply, and reactive oxygen species. Also, the potential of biocatalysts produced by cold-adapted microorganisms including cold-active enzymes, ice-binding proteins, polyhydroxyalkanoates, and surfactants was introduced, which provided a guidance for expanding its application values. Overall, new insights were obtained on response strategies of microorganisms to cold environments in this review. This will deepen the understanding of the cold tolerance mechanism of cold-adapted microorganisms, thus promoting the establishment and application of low-temperature biotechnology.

Cold-Active Shewanella glacialimarina TZS-4T nov. Features a Temperature-Dependent Fatty Acid Profile and Putative Sialic Acid Metabolism

Species of genus Shewanella are among the most frequently identified psychrotrophic bacteria. Here, we have studied the cellular properties, growth dynamics, and stress conditions of cold-active Shewanella strain #4, which was previously isolated from Baltic Sea ice. The cells are rod-shaped of ~2μm in length and 0.5μm in diameter, and they grow between 0 and 25°C, with an optimum at 15°C. The bacterium grows at a wide range of conditions, including 0.5–5.5% w/v NaCl (optimum 0.5–2% w/v NaCl), pH 5.5–10 (optimum pH 7.0), and up to 1mM hydrogen peroxide. In keeping with its adaptation to cold habitats, some polyunsaturated fatty acids, such as stearidonic acid (18:4n-3), eicosatetraenoic acid (20:4n-3), and eicosapentaenoic acid (20:5n-3), are produced at a higher level at low temperature. The genome is 4,456kb in size and has a GC content of 41.12%. Uniquely, strain #4 possesses genes for sialic acid metabolism and utilizes N-acetyl neuraminic acid as a carbon source. Interestingly, it also encodes for cytochrome c3 genes, which are known to facilitate environmental adaptation, including elevated temperatures and exposure to UV radiation. Phylogenetic analysis based on a consensus sequence of the seven 16S rRNA genes indicated that strain #4 belongs to genus Shewanella, closely associated with Shewanella aestuarii with a ~97% similarity, but with a low DNA–DNA hybridization (DDH) level of ~21%. However, average nucleotide identity (ANI) analysis defines strain #4 as a separate Shewanella species (ANI score=76). Further phylogenetic analysis based on the 92 most conserved genes places Shewanella strain #4 into a distinct phylogenetic clade with other cold-active marine Shewanella species. Considering the phylogenetic, phenotypic, and molecular characterization, we conclude that Shewanella strain #4 is a novel species and name it Shewanella glacialimarina sp. nov. TZS-4_T, where glacialimarina means sea ice. Consequently, S. glacialimarina TZS-4_T constitutes a promising model for studying transcriptional and translational regulation of cold-active metabolism.

Cold Regulation of Genes Encoding Ion Transport Systems in the Oligotrophic Bacterium Caulobacter crescentus

In this study, we characterize the response of the free-living oligotrophic alphaproteobacterium Caulobacter crescentus to low temperatures by global transcriptomic analysis. Our results showed that 656 genes were upregulated and 619 were downregulated at least 2-fold after a temperature downshift. The identified differentially expressed genes (DEG) belong to several functional categories, notably inorganic ion transport and metabolism, and a subset of these genes had their expression confirmed by reverse transcription quantitative real-time PCR (RT-qPCR). Several genes belonging to the ferric uptake regulator (Fur) regulon were downregulated, indicating that iron homeostasis is relevant for adaptation to cold. Several upregulated genes encode proteins that interact with nucleic acids, particularly RNA: cspA, cspB, and the DEAD box RNA helicases rhlE, dbpA, and rhlB. Moreover, 31 small regulatory RNAs (sRNAs), including the cell cycle-regulated noncoding RNA (ncRNA) CcnA, were upregulated, indicating that posttranscriptional regulation is important for the cold stress response. Interestingly, several genes related to transport were upregulated under cold stress, including three AcrB-like cation/multidrug efflux pumps, the nitrate/nitrite transport system, and the potassium transport genes kdpFABC. Further characterization showed that kdpA is upregulated in a potassium-limited medium and at a low temperature in a SigT-independent way. kdpA mRNA is less stable in rho and rhlE mutant strains, but while the expression is positively regulated by RhlE, it is negatively regulated by Rho. A kdpA-deleted strain was generated, and its viability in response to osmotic, acidic, or cold stresses was determined. The implications of such variation in the gene expression for cold adaptation are discussed. IMPORTANCE Low-temperature stress is an important factor for nucleic acid stability and must be circumvented in order to maintain the basic cell processes, such as transcription and translation. The oligotrophic lifestyle presents further challenges to ensure the proper nutrient uptake and osmotic balance in an environment of slow nutrient flow. Here, we show that in Caulobacter crescentus, the expression of the genes involved in cation transport and homeostasis is altered in response to cold, which could lead to a decrease in iron uptake and an increase in nitrogen and high-affinity potassium transport by the Kdp system. This previously uncharacterized regulation of the Kdp transporter has revealed a new mechanism for adaptation to low temperatures that may be relevant for oligotrophic bacteria.

Ecogenomics and Adaptation Strategies of Southern Ocean Viral Communities

The Southern Ocean (SO) represents up to one-fifth of the total carbon drawdown worldwide. Intense selective pressures (low temperature, high UV radiation, and strong seasonality) and physical isolation characterize the SO, serving as a "natural" laboratory for the study of ecogenomics and unique adaptations of endemic viral populations. Here, we report 2,416 novel viral genomes from the SO, obtained from newly sequenced viral metagenomes in combination with mining of publicly available data sets, which represents a 25% increase in the SO viral genomes reported to date. They comprised 567 viral clusters (defined as approximately genus-level groups), with 186 genera endemic to the SO, demonstrating that the SO viral community is predominantly constituted by a large pool of genetically divergent viral species from widespread viral families. The predicted proteome from SO viruses revealed that several protein clusters related to cold-shock-event responses and quorum-sensing mechanisms involved in the lysogenic-lytic cycle shift decision were under positive selection, which is ultimately important for fine adaptation of viral populations in response to the strong selective pressures of the SO. Finally, changes in the hydrophobicity patterns and amino acid frequencies suggested marked temperature-driven genetic selection of the SO viral proteome. Our data provide valuable insights into how viruses adapt and remain successful in this extreme polar marine environment. IMPORTANCE Viruses are the most abundant biologic entities in marine systems and strongly influence the microbial community composition and diversity. However, little is known about viral communities' adaptation and diversification in the ocean. In this work, we take advantage of the geographical isolation and the intense selective pressures of the SO, to which viruses are exposed, to identify potential viral adaptations due to positive environmental selection and dispersal limitation. To that end, we recovered more than two thousand novel viral genomes, revealing a high degree of divergence in these SO endemic communities. Furthermore, we describe remarkable viral adaptations in amino acid frequencies and accessory proteins related to cold shock response and quorum sensing that allow them to thrive at lower temperatures. Consequently, our work greatly expands the understanding of the diversification of the viral communities of the SO and their particular adaptations to low temperatures.

Sea-Ice Bacteria Halomonas sp. Strain 363 and Paracoccus sp. Strain 392 Produce Multiple Types of Poly-3-Hydroxyalkaonoic Acid (PHA) Storage Polymers at Low Temperature

Poly-3-hydroxyalkanoic acids (PHAs) are bacterial storage polymers commonly used in bioplastic production. Halophilic bacteria are industrially interesting organisms, as their salinity tolerance and psychrophilic nature lowers sterility requirements and subsequent production costs. We investigated PHA synthesis in two bacterial strains, Halomonas sp. 363 and Paracoccus sp. 392, isolated from Southern Ocean sea ice and elucidated the related PHA biopolymer accumulation and composition with various approaches, such as transcriptomics, microscopy, and chromatography. We show that both bacterial strains produce PHAs at 4°C when the availability of nitrogen and/or oxygen limited growth. The genome of Halomonas sp. 363 carries three phaC synthase genes and transcribes genes along three PHA pathways (I to III), whereas Paracoccus sp. 392 carries only one phaC gene and transcribes genes along one pathway (I). Thus, Halomonas sp. 363 has a versatile repertoire of phaC genes and pathways enabling production of both short- and medium-chain-length PHA products. IMPORTANCE Plastic pollution is one of the most topical threats to the health of the oceans and seas. One recognized way to alleviate the problem is to use degradable bioplastic materials in high-risk applications. PHA is a promising bioplastic material as it is nontoxic and fully produced and degraded by bacteria. Sea ice is an interesting environment for prospecting novel PHA-producing organisms, since traits advantageous to lower production costs, such as tolerance for high salinities and low temperatures, are common. We show that two sea-ice bacteria, Halomonas sp. 363 and Paracoccus sp. 392, are able to produce various types of PHA from inexpensive carbon sources. Halomonas sp. 363 is an especially interesting PHA-producing organism, since it has three different synthesis pathways to produce both short- and medium-chain-length PHAs.

Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines

Subzero hypersaline brines are liquid microbial habitats within otherwise frozen environments, where concentrated dissolved salts prevent freezing. Such extreme conditions presumably require unique microbial adaptations, and possibly altered ecologies, but specific strategies remain largely unknown. Here we examined prokaryotic taxonomic and functional diversity in two seawater-derived subzero hypersaline brines: first-year sea ice, subject to seasonally fluctuating conditions; and ancient cryopeg, under relatively stable conditions geophysically isolated in permafrost. Overall, both taxonomic composition and functional potential were starkly different. Taxonomically, sea-ice brine communities (∼10⁵ cells mL^–1) had greater richness, more diversity and were dominated by bacterial genera, including Polaribacter, Paraglaciecola, Colwellia, and Glaciecola, whereas the more densely inhabited cryopeg brines (∼10⁸ cells mL^–1) lacked these genera and instead were dominated by Marinobacter. Functionally, however, sea ice encoded fewer accessory traits and lower average genomic copy numbers for shared traits, though DNA replication and repair were elevated; in contrast, microbes in cryopeg brines had greater genetic versatility with elevated abundances of accessory traits involved in sensing, responding to environmental cues, transport, mobile elements (transposases and plasmids), toxin-antitoxin systems, and type VI secretion systems. Together these genomic features suggest adaptations and capabilities of sea-ice communities manifesting at the community level through seasonal ecological succession, whereas the denser cryopeg communities appear adapted to intense bacterial competition, leaving fewer genera to dominate with brine-specific adaptations and social interactions that sacrifice some members for the benefit of others. Such cryopeg genomic traits provide insight into how long-term environmental stability may enable life to survive extreme conditions.

Eight metagenome-assembled genomes provide evidence for microbial adaptation in 20,000 to 1,000,000-year-old Siberian permafrost

Permafrost microbes may be metabolically active in microscopic layers of liquid brines, even in ancient soil. Metagenomics can help discern whether permafrost microbes show adaptations to this environment. Thirty-three metagenome-assembled genomes (MAGs) were obtained from six depths (3.5 m to 20 m) of freshly-cored permafrost from the Siberia Kolyma-Indigirka Lowland region. These soils have been continuously frozen for ∼20,000 to 1,000,000 years. Eight of these MAGs were ≥80% complete with <10% contamination and were taxonomically identified as Aminicenantes, Atribacteria, Chloroflexi, and Actinobacteria within bacteria and Thermoprofundales within archaea. MAGs from these taxa have previously been obtained from non-permafrost environments and have been suggested to show adaptations to long-term energy-starvation, but they have never been explored in ancient permafrost. The permafrost MAGs had higher proportions of clusters of orthologous genes (COGs) from 'Energy production and conversion' and 'Carbohydrate transport and metabolism' than their non-permafrost counterparts. They also contained genes for trehalose synthesis, thymine metabolism, mevalonate biosynthesis and cellulose degradation that were less prevalent in non-permafrost genomes. Many of these genes are involved in membrane stabilization and osmotic stress responses, consistent with adaptation to the anoxic, high ionic strength, cold environments of permafrost brine films. Our results suggest that this ancient permafrost contains DNA in high enough quality to assemble MAGs from microorganisms with adaptations to subsist long-term freezing in this extreme environment. Importance Permafrost around the world is thawing rapidly. Many scientists from a variety of disciplines have shown the importance of understanding what will happen to our ecosystem, commerce, and climate when permafrost thaws. The fate of permafrost microorganisms is connected to these predicted rapid environmental changes. Studying ancient permafrost with culture independent techniques can give a glimpse into how these microorganisms function in these extreme low temperature and energy conditions. This will aid understanding of how they will change with the environment. This study presents genomic data from this unique environment aged ∼20,000 to 1,000,000-years-old.

The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study

Previous reports have shown that environmental temperature impacts proteome evolution in Bacteria and Archaea. However, it is unknown whether thermoadaptation mainly occurs via the sequential accumulation of substitutions, massive horizontal gene transfers, or both. Measuring the real contribution of amino acid substitution to thermoadaptation is challenging, because of confounding environmental and genetic factors (e.g., pH, salinity, genomic G + C content) that also affect proteome evolution. Here, using Methanococcales, a major archaeal lineage, as a study model, we show that optimal growth temperature is the major factor affecting variations in amino acid frequencies of proteomes. By combining phylogenomic and ancestral sequence reconstruction approaches, we disclose a sequential substitutional scheme in which lysine plays a central role by fine tuning the pool of arginine, serine, threonine, glutamine, and asparagine, whose frequencies are strongly correlated with optimal growth temperature. Finally, we show that colonization to new thermal niches is not associated with high amounts of horizontal gene transfers. Altogether, although the acquisition of a few key proteins through horizontal gene transfer may have favored thermoadaptation in Methanococcales, our findings support sequential amino acid substitutions as the main factor driving thermoadaptation.

Molecular cloning and biochemical characterization of a NAD-dependent sorbitol dehydrogenase from cold-adapted Pseudomonas mandelii

Sugar alcohols (polyols) have important roles as nutrients, anti-freezing agents and scavengers of free radicals in cold-adapted bacteria, but the characteristics of polyol dehydrogenases in cold-adapted bacteria remain largely unknown. In this study, based on the observation that a cold-adapted bacterium Pseudomonas mandelii JR-1 predominantly utilized d-sorbitol as its carbon source, among the four polyols examined (d-galactitol, d-mannitol, d-sorbitol and d-xylitol), we cloned and characterized a sorbitol dehydrogenase (SDH, EC 1.1.1.14) belonging to the short-chain dehydrogenase/reductase family from this bacterium (the SDH hereafter referred to as PmSDH). PmSDH contained Asn111, Ser140, Tyr153 and Lys157 as catalytic active site residues and existed as an ∼67-kDa dimer in size-exclusion chromatography. PmSDH converted d-sorbitol to d-fructose using nicotinamide adenine dinucleotide (NAD+) as a cofactor and, vice versa, d-fructose to d-sorbitol using nicotinamide adenine dinucleotide reduced (NADH) as a cofactor. PmSDH maintained its conformational flexibility, secondary and tertiary structures, and thermal stability at 4-25°C. These results indicate that PmSDH, which has a flexible structure and a high catalytic activity at colder temperatures, is well suited to sorbitol utilization in the cold-adapted bacterium P. mandelii JR-1.

Response of Lactiplantibacillus plantarum NMGL2 to Combinational Cold and Acid Stresses during Storage of Fermented Milk as Analyzed by Data-Independent Acquisition Proteomics

To understand the mechanism of tolerance of lactic acid bacteria (LAB) during cold storage of fermented milk, 31 LAB strains were isolated from traditional fermented products, and Lactiplantibacillus plantarum NMGL2 was identified with good tolerance to both cold and acid stresses. Data-independent acquisition proteomics method was employed to analyze the response of Lpb. plantarum NMGL2 to the combinational cold and acid stresses during storage of the fermented milk made with the strain at 4 °C for 21 days. Among the differentially expressed proteins identified, 20 low temperature-resistant proteins and 10 acid-resistant proteins were found. Protein interaction analysis showed that the low temperature-resistant proteins associated with acid-resistant proteins were Hsp1, Hsp2, Hsp3, CspC, MurA1, MurC, MurD, MurE1, and MurI, while the acid-resistant proteins associated with low temperature-resistant proteins were DnaA, DnaK, GrpE, GroEL, and RbfA. The overall metabolic pathways of Lpb. plantarum NMGL2 in response to the stresses were determined including increased cell wall component biosynthesis, extracellular production of abundant glycolipids and glycoproteins, increased expression of F₁F_o-ATPase, activation of glutamate deacidification system, enhanced expression of proteins and chaperones associated with cell repairing caused by the acidic and cold environment into the correct proteins. The present study for the first time provides further understanding of the proteomic pattern and metabolic changes of Lpb. plantarum in response to combinational cold and acid stresses in fermented milk, which facilitates potential application of Lpb. plantarum in fermented foods with enhanced survivability.

Taxonomic Characterization and Microbial Activity Determination of Cold-Adapted Microbial Communities in Lava Tube Ice Caves from Lava Beds National Monument, a High-Fidelity Mars Analogue Environment

Martian lava tube caves resulting from a time when the planet was still volcanically active are proposed to contain deposits of water ice, a feature that may increase microbial habitability. In this study, we taxonomically characterized and directly measured metabolic activity of the microbial communities that inhabit lava tube ice from Lava Beds National Monument, an analogue environment to martian lava tubes. We investigated whether this environment was habitable to microorganisms by determining their taxonomic diversity, metabolic activity, and viability using both culture-dependent and culture-independent techniques. With 16S rRNA gene sequencing, we recovered 27 distinct phyla from both ice and ice-rock interface samples, primarily consisting of Actinobacteria, Proteobacteria, Bacteroidetes, Firmicutes, and Chloroflexi. Radiorespiration and Biolog EcoPlate assays found these microbial communities to be metabolically active at both 5°C and -5°C and able to metabolize diverse sets of heterotrophic carbon substrates at each temperature. Viable cells were predominantly cold adapted and capable of growth at 5°C (1.3 × 10⁴ to 2.9 × 10⁷ cells/mL), and 24 of 38 cultured isolates were capable of growth at -5°C. Furthermore, 14 of these cultured isolates, and 16 of the 20 most numerous amplicon sequences we recovered were most closely related to isolates and sequences obtained from other cryophilic environments. Given these results, lava tube ice appears to be a habitable environment, and considering the protections martian lava tubes offer to microbial communities from harsh surface conditions, similar martian caves containing ice may be capable of supporting extant, active microbial communities.