Genomic, Molecular, and Phenotypic Characterization of Arthrobacter sp. OVS8, an Endophytic Bacterium Isolated from and Contributing to the Bioactive Compound Content of the Essential Oil of the Medicinal Plant Origanum vulgare L.

Medicinal plants play an important role in the discovery of new bioactive compounds with antimicrobial activity, thanks to their pharmacological properties. However, members of their microbiota can also synthesize bioactive molecules. Among these, strains belonging to the genera Arthrobacter are commonly found associated with the plant's microenvironments, showing plant growth-promoting (PGP) activity and bioremediation properties. However, their role as antimicrobial secondary metabolite producers has not been fully explored. The aim of this work was to characterize the Arthrobacter sp. OVS8 endophytic strain, isolated from the medicinal plant Origanum vulgare L., from molecular and phenotypic viewpoints to evaluate its adaptation and influence on the plant internal microenvironments and its potential as a producer of antibacterial volatile molecules (VOCs). Results obtained from the phenotypic and genomic characterization highlight its ability to produce volatile antimicrobials effective against multidrug-resistant (MDR) human pathogens and its putative PGP role as a producer of siderophores and degrader of organic and inorganic pollutants. The outcomes presented in this work identify Arthrobacter sp. OVS8 as an excellent starting point toward the exploitation of bacterial endophytes as antibiotics sources.

Genome-scale metabolic reconstruction and constraint-based modelling of the Antarctic bacterium Pseudoalteromonas haloplanktis†TAC125.

The Antarctic strain Pseudoalteromonas haloplanktis TAC125 is one of the model organisms of cold-adapted bacteria and is currently exploited as a new alternative expression host for numerous biotechnological applications. Here, we investigated several metabolic features of this strain through in silico modelling and functional integration of -omics data. A genome-scale metabolic model of P. haloplanktis TAC125 was reconstructed, encompassing information on 721 genes, 1133 metabolites and 1322 reactions. The predictive potential of this model was validated against a set of experimentally determined growth rates and a large dataset of growth phenotypic data. Furthermore, evidence synthesis from proteomics, phenomics, physiology and metabolic modelling data revealed possible drawbacks of cold-dependent changes in gene expression on the overall metabolic network of P. haloplanktis TAC125. These included, for example, variations in its central metabolism, amino acid degradation and fatty acid biosynthesis. The genome-scale metabolic model described here is the first one reconstructed so far for an Antarctic microbial strain. It allowed a system-level investigation of variations in cellular metabolic fluxes following a temperature downshift. It represents a valuable platform for further investigations on P. haloplanktis TAC125 cellular functional states and for the design of more focused strategies for its possible biotechnological exploitation.

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach.

We performed a longitudinal study (repeated observations of the same sample over time) to investigate both the composition and structure of temporal changes of bacterial community composition in soil mesocosms, subjected to three different treatments (water and 5 or 25 mg kg(-1) of dried soil Cd(2+)). By analogy with the pan genome concept, we identified a core bacteriome and an accessory bacteriome. Resident taxa were assigned to the core bacteriome, while occasional taxa were assigned to the accessory bacteriome. Core and accessory bacteriome represented roughly 35 and 50 % of the taxa detected, respectively, and were characterized by different taxonomic signatures from phylum to genus level while 15 % of the taxa were found to be unique to a particular sample. In particular, the core bacteriome was characterized by higher abundance of members of Planctomycetes, Actinobacteria, Verrucomicrobia and Acidobacteria, while the accessory bacteriome included more members of Firmicutes, Clamydiae and Proteobacteria, suggesting potentially different responses to environmental changes of members from these phyla. We conclude that the pan-bacteriome model may be a useful approach to gain insight for modeling bacterial community structure and inferring different abilities of bacteria taxa.

DuctApe: a suite for the analysis and correlation of genomic and OmniLog™ Phenotype Microarray data.

Addressing the functionality of genomes is one of the most important and challenging tasks of today's biology. In particular the ability to link genotypes to corresponding phenotypes is of interest in the reconstruction and biotechnological manipulation of metabolic pathways. Over the last years, the OmniLog™ Phenotype Microarray (PM) technology has been used to address many specific issues related to the metabolic functionality of microorganisms. However, computational tools that could directly link PM data with the gene(s) of interest followed by the extraction of information on gene-phenotype correlation are still missing. Here we present DuctApe, a suite that allows the analysis of both genomic sequences and PM data, to find metabolic differences among PM experiments and to correlate them with KEGG pathways and gene presence/absence patterns. As example, an application of the program to four bacterial datasets is presented. The source code and tutorials are available at http://combogenomics.github.io/DuctApe/.

The Great Gobi A Strictly Protected Area: Characterization of Soil Bacterial Communities from Four Oases.

Understanding how microbial communities survive in extreme environmental pressure is critical for interpreting ecological patterns and microbial diversity. Great Gobi A Strictly Protected Area represents an intriguing model for studying the bacterial community since it is a protected and intact wild area of the Mongolian desert. In this work, the composition of a bacterial community of the soil from four oases was characterized by extracting total DNA and sequencing through the Illumina NovaSeq platform. In addition, the soil's chemical and physical properties were determined, and their influence on shaping the microbial communities was evaluated. The results showed a high variability of bacterial composition among oases. Moreover, combining specific chemical and physical parameters significantly shapes the bacterial community among oases. Data obtained suggested that the oases were highly variable in physiochemical parameters and bacterial communities despite the similar extreme climate conditions. Moreover, core functional microbiome were constituted by aerobic chemoheterotrophy and chemoheterotrophy, mainly contributed by the most abundant bacteria, such as Actinobacteriota, Pseudomonadota, and Firmicutes. This result supposes a metabolic flexibility for sustaining life in deserts. Furthermore, as the inhabitants of the extreme regions are likely to produce new chemical compounds, isolation of key taxa is thus encouraged.

Antibacterial activity of Arthrobacter strains isolated from Great Gobi A Strictly Protected Area, Mongolia.

Desert soil hosts many microorganisms, whose activities are essential from an ecological viewpoint. Moreover, they are of great anthropic interest. The knowledge of extreme environments microbiomes may be beneficial for agriculture, technology, and human health. In this study, 11 Arthrobacter strains from topsoil samples collected from the Great Gobi A Strictly Protected Area in the Gobi Desert, were characterized by a combination of different techniques. The phylogenetic analysis, performed using their 16S rDNA sequences and the most similar Arthrobacter sequences found in databases, revealed that most of them were close to A. crystallopoietes, while others joined a sister group to the clade formed by A. humicola, A. pascens, and A. oryzae. The resistance of each strain to different antibiotics, heavy-metals, and NaCl was also tested as well as the inhibitory potential against human pathogens (i.e., Burkholderia ssp., Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus ssp.) via cross-streaking, to check the production of metabolites with antimicrobial activity. Data obtained revealed that all strains were resistant to heavy metals and were able to strongly interfere with the growth of many of the human pathogens tested. The volatile organic compounds (VOCs) profile of the 11 Arthrobacter strains was also analyzed. A total of 16 different metabolites were found, some of which were already known for having an inhibitory action against different Gram-positive and Gram-negative bacteria. Isolate MS-3A13, producing the highest quantity of VOCs, is the most efficient against Burkholderia cepacia complex (Bcc), K. pneumoniae, and coagulase-negative Staphylococci (CoNS) strains. This work highlights the importance of understanding microbial populations' phenotypical characteristics and dynamics in extreme environments to uncover the antimicrobial potential of new species and strains.

Alteration of bacterial communities and organic matter in microbial fuel cells (MFCs) supplied with soil and organic fertilizer.

The alteration of the organic matter (OM) and the composition of bacterial community in microbial fuel cells (MFCs) supplied with soil (S) and a composted organic fertilizer (A) was examined at the beginning and at the end of 3 weeks of incubation under current-producing as well as no-current-producing conditions. Denaturing gradient gel electrophoresis revealed a significant alteration of the microbial community structure in MFCs generating electricity as compared with no-current-producing MFCs. The genetic diversity of cultivable bacterial communities was assessed by random amplified polymorphic DNA (RAPD) analysis of 106 bacterial isolates obtained by using both generic and elective media. Sequencing of the 16S rRNA genes of the more representative RAPD groups indicated that over 50.4% of the isolates from MFCs fed with S were Proteobacteria, 25.1% Firmicutes, and 24.5% Actinobacteria, whereas in MFCs supplied with A 100% of the dominant species belonged to γ-Proteobacteria. The chemical analysis performed by fractioning the OM and using thermal analysis showed that the amount of total organic carbon contained in the soluble phase of the electrochemically active chambers significantly decreased as compared to the no-current-producing systems, whereas the OM of the solid phase became more humified and aromatic along with electricity generation, suggesting a significant stimulation of a humification process of the OM. These findings demonstrated that electroactive bacteria are commonly present in aerobic organic substrates such as soil or a fertilizer and that MFCs could represent a powerful tool for exploring the mineralization and humification processes of the soil OM.

Employing Genome Mining to Unveil a Potential Contribution of Endophytic Bacteria to Antimicrobial Compounds in the Origanum vulgare L. Essential Oil.

Essential oils (EOs) from medicinal plants have long been used in traditional medicine for their widely known antimicrobial properties and represent a promising reservoir of bioactive compounds against multidrug-resistant pathogens. Endophytes may contribute to the yield and composition of EOs, representing a useful tool for biotechnological applications. In this work, we investigated the genomic basis of this potential contribution. The annotated genomes of four endophytic strains isolated from Origanum vulgare L. were used to obtain KEGG ortholog codes, which were used for the annotation of different pathways in KEGG, and to evaluate whether endophytes might harbor the (complete) gene sets for terpene and/or plant hormone biosynthesis. All strains possessed ortholog genes for the mevalonate-independent pathway (MEP/DOXP), allowing for the production of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) precursors. Ortholog genes for the next steps in terpenoid biosynthesis were scarce. All the strains possess potential plant growth promotion (PGP) ability, as shown by the presence of orthologous genes involved in the biosynthesis of indoleacetic acid. The main contribution of endophytes to the yield and composition of O. vulgare EO very likely resides in their PGP activities and in the biosynthesis of precursors of bioactive compounds.

Arable plant communities as a surrogate of crop rhizosphere microbiota.

Soil microbiota is a crucial component of agroecosystem biodiversity, enhancing plant growth and providing important services in agriculture. However, its characterization is demanding and relatively expensive. In this study, we evaluated whether arable plant communities can be used as a surrogate of bacterial and fungal communities of the rhizosphere of Elephant Garlic (Allium ampeloprasum L.), a traditional crop plant of central Italy. We sampled plant, bacterial, and fungal communities, i.e., the groups of such organisms co-existing in space and time, in 24 plots located in eight fields and four farms. At the plot level, no correlations in species richness emerged, while the composition of plant communities was correlated with that of both bacterial and fungal communities. As regards plants and bacteria, such correlation was mainly driven by similar responses to geographic and environmental factors, while fungal communities seemed to be correlated in species composition with both plants and bacteria due to biotic interactions. All the correlations in species composition were unaffected by the number of fertilizer and herbicide applications, i.e., agricultural intensity. Besides correlations, we detected a predictive relationship of plant community composition towards fungal community composition. Our results highlight the potential of arable plant communities to be used as a surrogate of crop rhizosphere microbial communities in agroecosystems.

Safety Level of Microorganism-Bearing Products Applied in Soil-Plant Systems.

The indiscriminate use of chemical fertilizers adversely affects ecological health and soil microbiota provoking loss of soil fertility and greater pathogen and pest presence in soil-plant systems, which further reduce the quality of food and human health. Therefore, the sustainability, circular economy, environmental safety of agricultural production, and health concerns made possible the practical realization of eco-friendly biotechnological approaches like organic matter amendments, biofertilizers, biopesticides, and reuse of agro-industrial wastes by applying novel and traditional methods and processes. However, the advancement in the field of Biotechnology/Agriculture is related to the safety of these microorganism-bearing products. While the existing regulations in this field are well-known and are applied in the preparation and application of waste organic matter and microbial inoculants, more attention should be paid to gene transfer, antibiotic resistance, contamination of the workers and environment in farms and biotech-plants, and microbiome changes. These risks should be carefully assessed, and new analytical tools and regulations should be applied to ensure safe and high-quality food and a healthy environment for people working in the field of bio-based soil amendments.

Fungi, P-Solubilization, and Plant Nutrition.

The application of plant beneficial microorganisms is widely accepted as an efficient alternative to chemical fertilizers and pesticides. It was shown that annually, mycorrhizal fungi and nitrogen-fixing bacteria are responsible for 5 to 80% of all nitrogen, and up to 75% of P plant acquisition. However, while bacteria are the most studied soil microorganisms and most frequently reported in the scientific literature, the role of fungi is relatively understudied, although they are the primary organic matter decomposers and govern soil carbon and other elements, including P-cycling. Many fungi can solubilize insoluble phosphates or facilitate P-acquisition by plants and, therefore, form an important part of the commercial microbial products, with Aspergillus, Penicillium and Trichoderma being the most efficient. In this paper, the role of fungi in P-solubilization and plant nutrition will be presented with a special emphasis on their production and application. Although this topic has been repeatedly reviewed, some recent views questioned the efficacy of the microbial P-solubilizers in soil. Here, we will try to summarize the proven facts but also discuss further lines of research that may clarify our doubts in this field or open new perspectives on using the microbial and particularly fungal P-solubilizing potential in accordance with the principles of the sustainability and circular economy.

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti.

BACKGROUND: Sinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. An extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. AK83 and BL225C are two nodule-isolated strains with diverse symbiotic phenotypes; BL225C is more efficient in promoting growth of the Medicago sativa plants than strain AK83. In order to investigate the genetic determinants of the phenotypic diversification of S. meliloti strains AK83 and BL225C, we sequenced the complete genomes for these two strains. RESULTS: With sizes of 7.14 Mbp and 6.97 Mbp, respectively, the genomes of AK83 and BL225C are larger than the laboratory strain Rm1021. The core genome of Rm1021, AK83, BL225C strains included 5124 orthologous groups, while the accessory genome was composed by 2700 orthologous groups. While Rm1021 and BL225C have only three replicons (Chromosome, pSymA and pSymB), AK83 has also two plasmids, 260 and 70 Kbp long. We found 65 interesting orthologous groups of genes that were present only in the accessory genome, consequently responsible for phenotypic diversity and putatively involved in plant-bacterium interaction. Notably, the symbiosis inefficient AK83 lacked several genes required for microaerophilic growth inside nodules, while several genes for accessory functions related to competition, plant invasion and bacteroid tropism were identified only in AK83 and BL225C strains. Presence and extent of polymorphism in regulons of transcription factors involved in symbiotic interaction were also analyzed. Our results indicate that regulons are flexible, with a large number of accessory genes, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains. CONCLUSIONS: In conclusions, the extended comparative genomics approach revealed a variable subset of genes and regulons that may contribute to the symbiotic diversity.

Current Methods, Common Practices, and Perspectives in Tracking and Monitoring Bioinoculants in Soil.

Microorganisms promised to lead the bio-based revolution for a more sustainable agriculture. Beneficial microorganisms could be a valid alternative to the use of chemical fertilizers or pesticides. However, the increasing use of microbial inoculants is also raising several questions about their efficacy and their effects on the autochthonous soil microorganisms. There are two major issues on the application of bioinoculants to soil: (i) their detection in soil, and the analysis of their persistence and fate; (ii) the monitoring of the impact of the introduced bioinoculant on native soil microbial communities. This review explores the strategies and methods that can be applied to the detection of microbial inoculants and to soil monitoring. The discussion includes a comprehensive critical assessment of the available tools, based on morpho-phenological, molecular, and microscopic analyses. The prospects for future development of protocols for regulatory or commercial purposes are also discussed, underlining the need for a multi-method (polyphasic) approach to ensure the necessary level of discrimination required to track and monitor bioinoculants in soil.

Fermentation Strategies to Improve Soil Bio-Inoculant Production and Quality.

The application of plant beneficial microorganisms has been widely accepted as an efficient alternative to chemical fertilizers and pesticides. Isolation and selection of efficient microorganisms, their characterization and testing in soil-plant systems are well studied. However, the production stage and formulation of the final products are not in the focus of the research, which affects the achievement of stable and consistent results in the field. Recent analysis of the field of plant beneficial microorganisms suggests a more integrated view on soil inoculants with a special emphasis on the inoculant production process, including fermentation, formulation, processes, and additives. This mini-review describes the different groups of fermentation processes and their characteristics, bearing in mind different factors, both nutritional and operational, which affect the biomass/spores yield and microbial metabolite activity. The characteristics of the final products of fermentation process optimization strategies determine further steps of development of the microbial inoculants. Submerged liquid and solid-state fermentation processes, fed-batch operations, immobilized cell systems, and production of arbuscular mycorrhiza are presented and their advantages and disadvantages are discussed. Recommendations for further development of the fermentation strategies for biofertilizer production are also considered.

Metabolic capacity of Sinorhizobium (Ensifer) meliloti strains as determined by phenotype MicroArray analysis.

Sinorhizobium meliloti is a soil bacterium that fixes atmospheric nitrogen in plant roots. The high genetic diversity of its natural populations has been the subject of extensive analysis. Recent genomic studies of several isolates revealed a high content of variable genes, suggesting a correspondingly large phenotypic differentiation among strains of S. meliloti. Here, using the Phenotype MicroArray (PM) system, hundreds of different growth conditions were tested in order to compare the metabolic capabilities of the laboratory reference strain Rm1021 with those of four natural S. meliloti isolates previously analyzed by comparative genomic hybridization (CGH). The results of PM analysis showed that most phenotypic differences involved carbon source utilization and tolerance to osmolytes and pH, while fewer differences were scored for nitrogen, phosphorus, and sulfur source utilization. Only the variability of the tested strain in tolerance to sodium nitrite and ammonium sulfate of pH 8 was hypothesized to be associated with the genetic polymorphisms detected by CGH analysis. Colony and cell morphologies and the ability to nodulate Medicago truncatula plants were also compared, revealing further phenotypic diversity. Overall, our results suggest that the study of functional (phenotypic) variability of S. meliloti populations is an important and complementary step in the investigation of genetic polymorphism of rhizobia and may help to elucidate rhizobial evolutionary dynamics, including adaptation to diverse environments.

Teamwork makes the dream work: Disentangling cross-taxon congruence across soil biota in black pine plantations.

Soil plays a fundamental role in many ecological processes, throughout a complex network of above- and below-ground interactions. This has aroused increasing interest in the use of correlates for biodiversity assessment and has demonstrated their reliability with respect to proxies based on environmental data alone. Although co-variation of species richness and composition in forests has been discussed in the literature, only a few studies have explored these elements in forest plantations, which are generally thought to be poor in biodiversity, being aimed at timber production. Based on this premise our aims were 1) to test if cross-taxon congruence across different groups of organisms (bacteria, vascular plants, mushrooms, ectomycorrhizae, mycelium, carabids, microarthropods, nematodes) is consistent in artificial stands; 2) to evaluate the strength of relationships due to the existing environmental gradients as expressed by abiotic and biotic factors (soil, spatial-topographic, dendrometric variables). Correlations between groups were studied with Mantel and partial Mantel tests, while variance partition analysis was applied to assess the relative effect of environmental variables on the robustness of observed relationships. Significant cross-taxon congruence was observed across almost all taxonomic groups pairs. However, only bacteria/mycelium and mushrooms/mycelium correlations remained significant after removing the environmental effect, suggesting that a strong abiotic influence drives species composition. Considering variation partitioning, the results highlighted the importance of bacteria as a potential indicator: bacteria were the taxonomic group with the highest compositional variance explained by the predictors used; furthermore, they proved to be involved in the only cases where the variance attributed solely to the pure effect of biotic or abiotic predictors was significant. Remarkably, the co-dependent effect of all predictors always explained the highest portion of total variation in all dependent taxa, testifying the intricate and dynamic interplay of environmental factors and biotic interactions in explaining cross-taxon congruence in forest plantations.

Antagonism and antibiotic resistance drive a species-specific plant microbiota differentiation in Echinacea spp.

A key factor in the study of plant-microbes interactions is the composition of plant microbiota, but little is known about the factors determining its functional and taxonomic organization. Here we investigated the possible forces driving the assemblage of bacterial endophytic and rhizospheric communities, isolated from two congeneric medicinal plants, Echinacea purpurea (L.) Moench and Echinacea angustifolia (DC) Heller, grown in the same soil, by analysing bacterial strains (isolated from three different compartments, i.e. rhizospheric soil, roots and stem/leaves) for phenotypic features such as antibiotic resistance, extracellular enzymatic activity, siderophore and indole 3-acetic acid production, as well as cross-antagonistic activities. Data obtained highlighted that bacteria from different plant compartments were characterized by specific antibiotic resistance phenotypes and antibiotic production, suggesting that the bacterial communities themselves could be responsible for structuring their own communities by the production of antimicrobial molecules selecting bacterial-adaptive phenotypes for plant tissue colonization.

Evaluation of dredged sediment co-composted with green waste as plant growing media assessed by eco-toxicological tests, plant growth and microbial community structure.

Dredged sediments have currently no broad reuse options as compared to other wastes due to their peculiar physico-chemical properties, posing problems for the management of the large volumes of sediments dredged worldwide. In this study we evaluated the performance of sediment (S) co-composted with green waste (GW) as growing medium for ornamental plants. Analysis of the microbial community structure, eco-toxicological tests, were conducted on sediments at 1:1 and 3:1S:GW composting ratios. Sediment-based growing media were then reused to growth the ornamental plant Photina x fraseri in a pilot-scale experiment and plants' physiological and chemical parameters were measured. The results showed that co-composting with green waste increased the diversity of bacteria, fungi and archaea as compared to the untreated sediments, and that both the 1:1 and 3:1 S:GW composted sediments had no substantial eco-toxicological impacts, allowing an excellent plant growth. We concluded that co-composted of sediment with green waste produce a growing medium with suitable properties for growing ornamental plants, and represent a sustainable option for beneficial use of dredged sediments.

Preliminary data on antibacterial activity of Echinacea purpurea-associated bacterial communities against Burkholderia cepacia complex strains, opportunistic pathogens of Cystic Fibrosis patients.

Burkholderia cepacia complex bacteria (Bcc) represent a serious threat for immune-compromised patient affected by Cystic Fibrosis (CF) since they are resistant to many substances and to most antibiotics. For this reason, the research of new natural compounds able to inhibit the growth of Bcc strains has raised new interest during the last years. A source of such natural compounds is represented by medicinal plants and, in particular, by bacterial communities associated with these plants able to produce molecules with antimicrobial activity. In this work, a panel of 151 (endophytic) bacteria isolated from three different compartments (rhizospheric soil, roots, and stem/leaves) of the medicinal plant Echinacea purpurea were tested (using the cross-streak method) for their ability to inhibit the growth of 10 Bcc strains. Data obtained revealed that bacteria isolated from the roots of E. purpurea are the most active in the inhibition of Bcc strains, followed by bacteria isolated from the rhizospheric soil, and endophytes from stem/leaf compartment. At the same time, Bcc strains of environmental origin showed a higher resistance toward inhibition than the Bcc strains with clinical (i.e. CF patients) origin. Differences in the inhibition activity of E. purpurea-associated bacteria are mainly linked to the environment -the plant compartment- rather than to their taxonomical position.

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

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