Metabolic profiling of cold adaptation of a deep-sea psychrotolerant Microbacterium sediminis to prolonged low temperature under high hydrostatic pressure

Metabolic adaptations of Shewanella eurypsychrophilus YLB-09 for survival in the high-pressure environment of the deep sea

Elucidation of the adaptation mechanisms and survival strategies of deep-sea microorganisms to extreme environments could provide a theoretical basis for the industrial development of extreme enzymes. There is currently a lack of understanding of the metabolic adaptation mechanisms of deep-sea microorganisms to high-pressure environments. The objective of this study was to investigate the metabolic regulatory mechanisms enabling a strain of the deep-sea bacterium Shewanella eurypsychrophilus to thrive under high-pressure conditions. To achieve this, we used nuclear magnetic resonance-based metabolomic and RNA sequencing-based transcriptomic analyses of S. eurypsychrophilus strain YLB-09, which was previously isolated by our research group and shown to be capable of tolerating high pressure levels and low temperatures. We found that high-pressure conditions had pronounced impacts on the metabolic pattern of YLB-09, as evidenced by alterations in energy, amino acid, and glycerolipid metabolism, among other processes. YLB-09 adapted to the high-pressure conditions of the deep sea by switching from aerobic intracellular energy metabolism to trimethylamine N-oxide respiration, altering the amino acid profile, and regulating the composition and the fluidity of cell membrane. The findings of our study demonstrate the capacity of microorganisms to alter their metabolism in response to elevated pressure, thereby establishing a foundation for a more profound understanding of the survival mechanisms of life in high-pressure environments.

Characterization and Biosynthetic Regulation of Isoflavone Genistein in Deep-Sea Actinomycetes Microbacterium sp. B1075

Deep-sea environments, as relatively unexplored extremes within the Earth's biosphere, exhibit notable distinctions from terrestrial habitats. To thrive in these extreme conditions, deep-sea actinomycetes have evolved unique biochemical metabolisms and physiological capabilities to ensure their survival in this niche. In this study, five actinomycetes strains were isolated and identified from the Mariana Trench via the culture-dependent method and 16S rRNA sequencing approach. The antimicrobial activity of Microbacterium sp. B1075 was found to be the most potent, and therefore, it was selected as the target strain. Molecular networking analysis via the Global Natural Products Social Molecular Networking (GNPS) platform identified 25 flavonoid compounds as flavonoid secondary metabolites. Among these, genistein was purified and identified as a bioactive compound with significant antibacterial activity. The complete synthesis pathway for genistein was proposed within strain B1075 based on whole-genome sequencing data, with the key gene being CHS (encoding chalcone synthase). The expression of the gene CHS was significantly regulated by high hydrostatic pressure, with a consequent impact on the production of flavonoid compounds in strain B1075, revealing the relationship between actinomycetes' synthesis of flavonoid-like secondary metabolites and their adaptation to high-pressure environments at the molecular level. These results not only expand our understanding of deep-sea microorganisms but also hold promise for providing valuable insights into the development of novel pharmaceuticals in the field of biopharmaceuticals.

Metabolomics and Molecular Networking-Guided Screening of Bacillus-Derived Bioactive Compounds Against a Highly Lethal Vibrio Species

Microorganisms are important sources of bioactive natural products. However, the complexity of microbial metabolites and the low abundance of active compounds render the isolation and purification process laborious and inefficient. During our search for active substances capable of inhibiting the newly discovered highly lethal Vibrio strain vp-HL, we found that the fermentation broth of multiple Bacillus strains exhibited antibacterial activity. However, the substances responsible for the activity remained unclear. Metabolomics, molecular networking (MN), and the Structural similarity Network Annotation Platform for Mass Spectrometry (SNAP-MS) were employed in conjunction with bioactivity screening to predict the antibacterial compounds from Bacillus strains. The analysis of fractions, and their isolation, NMR-based annotation, and bioactivity evaluation of an amicoumacin compound partially confirmed the prediction from these statistical analyses. This work presents the potential of marine Bacillus in producing active substances against Vibrio species. Additionally, it highlighted the significance and feasibility of metabolomics and MN in the dereplication of compounds and the determination of isolation targets.

Metabolic adaptations of Microbacterium sediminis YLB-01 in deep-sea high-pressure environments

The deep-sea environment is an extremely difficult habitat for microorganisms to survive in due to its intense hydrostatic pressure. However, the mechanisms by which these organisms adapt to such extreme conditions remain poorly understood. In this study, we investigated the metabolic adaptations of Microbacterium sediminis YLB-01, a cold and stress-tolerant microorganism isolated from deep-sea sediments, in response to high-pressure conditions. YLB-01 cells were cultured at normal atmospheric pressure and 28 ℃ until they reached the stationary growth phase. Subsequently, the cells were exposed to either normal pressure or high pressure (30 MPa) at 4 ℃ for 7 days. Using NMR-based metabolomic and proteomic analyses of YLB-01 cells exposed to high-pressure conditions, we observed significant metabolic changes in several metabolic pathways, including amino acid, carbohydrate, and lipid metabolism. In particular, the high-pressure treatment stimulates cell division and triggers the accumulation of UDP-glucose, a critical factor in cell wall formation. This finding highlights the adaptive strategies used by YLB-01 cells to survive in the challenging high-pressure environments of the deep sea. Specifically, we discovered that YLB-01 cells regulate amino acid metabolism, promote carbohydrate metabolism, enhance cell wall synthesis, and improve cell membrane fluidity in response to high pressure. These adaptive mechanisms play essential roles in supporting the survival and growth of YLB-01 in high-pressure conditions. Our study offers valuable insights into the molecular mechanisms underlying the metabolic adaptation of deep-sea microorganisms to high-pressure environments. KEY POINTS: • NMR-based metabolomic and proteomic analyses were conducted on Microbacterium sediminis YLB-01 to investigate the significant alterations in several metabolic pathways in response to high-pressure treatment. • YLB-01 cells used adaptive strategies (such as regulated amino acid metabolism, promoted carbohydrate metabolism, enhanced cell wall synthesis, and improved cell membrane fluidity) to survive in the challenging high-pressure environment of the deep sea. • High-pressure treatment stimulated cell division and triggered the accumulation of UDP-glucose, a critical factor in cell wall formation, in Microbacterium sediminis YLB-01 cells.

Insights of microalgal municipal wastewater treatment at low temperatures: Performance, microbiota patterns, and cold-adaptation of tubular and aeration column photobioreactors

In order to refine the treatment of microalgae consortium (MC) for municipal wastewater (MWW) during the winter, this study investigated the effectiveness of tubular and aeration column photobioreactors (TPBR and APBR) in wastewater treatment plant (WWTP) during winter by two start-up modes: microalgae/microalgae-activated sludge (AS). The operation results showed that under 5.7-13.1 °C, TPBR enhanced the assimilation of N and P pollutant by microalgal accumulation, meeting the Chinese discharge standard within 24 h (NH4+-N, TP, and COD ≤8.0, 0.5, and 50 mg·L-1). The microbial community profiles were identified and showed that inoculating AS under low-temperature still promoted bacterial interspecific association, but influenced by the inhibition of microbial diversity by the homogeneous circulation of TPBR, the nitrogen transfer function of MC was lower than that of APBR at low temperatures, except nitrogen fixation (K02588), nitrosification (K10944, K10945, and K10946), assimilatory nitrate reduction (K00366), and ammonification (K01915 and K05601). And the intermittent aeration in the APBR was still beneficial in increasing microbial diversity, which was more beneficial for reducing COD through microbial collaboration. In the treatment, the cryotolerant MGPM were Delftia, Romboutsia, Rhizobiales, and Bacillus, and the cold stress-related genes that were highly up-regulated were defense signaling molecules (K03671 and K00384), cold shock protein gene (K03704), and cellular protector (K01784) were present in both PBRs. This study provided a reference for the feasibility of the low temperature treatment of MC with the different types of PBR, which improved the application of wastewater treatment in more climatic environments.

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.

Revealing the role of microalgae-bacteria niche for boosting wastewater treatment and energy reclamation in response to temperature

Conventional biological treatment usually cannot achieve the same high water quality as advanced treatment when conducted under varied temperatures. Here, satisfactory wastewater treatment efficiency was observed in a microalgae-bacteria consortia (MBC) over a wide temperature range because of the predominance of microalgae. Microalgae contributed more toward wastewater treatment at low temperature because of the unsatisfactory performance of the accompanying bacteria, which experienced cold stress (e.g., bacterial abundance below 3000 sequences) and executed defensive strategies (e.g., enrichment of cold-shock proteins). A low abundance of amoA-C and hao indicated that conventional nitrogen removal was replaced through the involvement of microalgae. Diverse heterotrophic bacteria for nitrogen removal were identified at medium and high temperatures, implying this microbial niche treatment contained diverse flexible consortia with temperature variation. Additionally, pathogenic bacteria were eliminated through microalgal photosynthesis. After fitting the neutral community model and calculating the ecological niche, microalgae achieved a maximum niche breadth of 5.21 and the lowest niche overlap of 0.38, while the accompanying bacterial community in the consortia were shaped through deterministic processes. Finally, the maximum energy yield of 87.4 kJ L^-1 and lipid production of 1.9 g L^-1 were achieved at medium temperature. Altogether, this study demonstrates that advanced treatment and energy reclamation can be achieved through microalgae-bacteria niche strategies.

Transcriptomics and proteomics revealed the psychrotolerant and antibiotic-resistant mechanisms of strain Pseudomonas psychrophila RNC-1 capable of assimilatory nitrate reduction and aerobic denitrification

Aerobic denitrification has been proved to be profoundly affected by temperature and antibiotics, but little is known about how aerobic denitrifiers respond to temperature and antibiotic stress. In this study, the nitrate reduction performance and the intracellular metabolism by a psychrotolerant aerobic denitrifying bacteria, named Pseudomonas psychrophila RNC-1, were systematically investigated at different temperatures (10 °C, 20 °C, 30 °C) and different sulfamethoxazole (SMX) concentrations (0 mg/L, 0.1 mg/L, 0.5 mg/L, 1.0 mg/L, and 5.0 mg/L). The results showed that strain RNC-1 performed satisfactory nitrate removal at 10 °C and 20 °C, but its growth was significantly inhibited at 30 °C. Nitrate removal by strain RNC-1 was slightly promoted in the presence of 0.5 mg/L SMX, whereas it was significantly suppressed with 5.0 mg/L SMX. Nitrogen balance analysis indicated that assimilatory nitrate reduction and dissimilatory aerobic denitrification jointly dominated in the nitrate removal process of strain RNC-1, in which the inhibition effected on assimilation process was much higher than that on the aerobic denitrification process under SMX exposure. Further transcriptomics and proteomics analysis revealed that the psychrotolerant mechanism of strain RNC-1 could be attributed to the up-regulation of RNA translation, energy metabolism, ABC transporters and the over-expression of cold shock proteins, while the down-regulation of oxidative phosphorylation pathway was the primary reason for the deteriorative cell growth at 30 °C. The promotion of nitrate reduction with 0.5 mg/L SMX was related to the up-regulation of amino acid metabolism pathways, while the down-regulation of folate cycle, glycolysis/gluconeogenesis and bacterial chemotaxis pathways were responsible for the inhibition effect at 5.0 mg/L SMX. This work provides a mechanistic understanding of the metabolic adaption of strain RNC-1 under different stress, which is of significance for its application in nitrogen contaminated wastewater treatment processes.

Response of amino acid metabolism to decreased temperatures in anammox consortia: Strong, efficient and flexible

Although amino acid (AA) metabolism is basis of bacterial activities, unique characteristics of its response to decreased temperatures are not fully understood. Achieving nitrogen removal rate of 130-150 mg N/ (L∙d), metabolic differences of anammox consortia between 35 °C and four decreased temperatures (15-30 °C) were revealed respectively. 0-11.4-fold abundance variation of marker metabolites evidenced change of key metabolism (metabolism of AA, lipid and energy production) at decreased temperatures. However, AA metabolism varied more obviously than others, implying stronger response and higher functional potential. Efficiently, network topology confirmed more cellular processes represented by growth metabolism and biofilm formation were influenced by AA metabolism. Flexibly, down-regulated biosynthesis of unfavorable AAs for psychrophilic enzyme differed from enhanced biosynthesis of costly AAs, which only matched partial decreased temperatures to save energy. This work elucidates advantages of AA metabolism over others, exogenous amino acids could significantly promote activity of anammox bacteria at decreased temperatures.

Transcriptomic Analysis Reveals that Changes in Gene Expression Contribute to Microbacterium sediminis YLB-01 Adaptation at Low Temperature Under High Hydrostatic Pressure

Microbes living in extreme environments often adopt strategies for survival, however, only a few studies have examined the adaptive mechanism of deep-sea bacteria in in-situ environments. In this study, transcriptomic data of the deep-sea piezotolerant and psychrotolerant actinomycete Microbacterium sediminis YLB-01 under the conditions of NPNT (normal temperature and pressure: 28 °C, 0.1 MPa), HPNT (normal temperature and high pressure: 28 °C, 30 MPa), NPLT (low temperature and atmospheric pressure: 4 °C, 0.1 MPa) and HPLT (low temperature and high pressure: 4 °C, 30 MPa) were examined and compared. Transcriptome results showed that M. sediminis YLB-01 responds to deep-sea low temperature under high-pressure environments by upregulating the ABC transport system, DNA damage repair response, pentose phosphate pathway, amino acid metabolism and fatty acid metabolism, while down-regulating division, oxidative phosphorylation, the TCA cycle, pyruvate metabolism, ion transport and peptidoglycan biosynthesis. Seven key genes specifically expressed under HPLT conditions were screened, and these genes are present in many strains that are tolerant to low temperatures and high pressures. This study provides transcription level insights into the tolerance mechanisms of M. sediminis YLB-01 in a simulated deep-sea in situ environment.

Effect of exogenous N-acyl-homoserine lactones on the anammox process at 15 ℃: Nitrogen removal performance, gene expression and metagenomics analysis

In this study, C6-HSL and C8-HSL were separately introduced into anammox biofilm reactors to facilitate the anammox performance at 15 ℃. After operation 138 d, total nitrogen removal efficiencies in reactors with amendment C6-HSL or C8-HSL at 15 ℃ reached 76.2% and 74.6%, respectively. Content of extracellular polymeric substances increased by 19.8%, 67.7% and 121.2% in control group, C6-HSL and C8-HSL addition group, respectively. Genes associated with nitrogen removal (i.e., hzo, hzsB, nirS, and ccsB) showed higher expression level at amendment C6-HSL or C8-HSL group. Metagenomics analysis found that amendment of C6-HSL or C8-HL resulted in an increased abundance of genes related to the tricarboxylic acid cycle, amino sugar and nucleotide sugar metabolism, and also genes associated with amino acid biosynthesis pathways. Overall, amendment C6-HSL or C8-HSL had been confirmed as the effective method to improve the performance of anammox bioreactor at 15 ℃.

The cold adaption profiles of Pseudoalteromonas shioyasakiensis D1497 from Yap trench to cope with cold

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P. shioyasakiensis D1497converted more substrate into biomass at low temperature.

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P. shioyasakiensis D1497 prefered to use codons with A/T in the third position.

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The energy metabolism related genes were down regulated in cold environment.

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P. shioyasakiensis D1497 presented an energy saving metabolism strategy to cope with cold.

Genome sequencing of Pseudoalteromonas shioyasakiensis D1497, a psychrophile from the Yap trench, revealed that it contained a circle chromosome of 3,631,285 bp with 40.94% GC content and prefered to use codons with A/T in the third position. Additionally, the relative synonymous codon usage (RSCU) values indicated the codons with A and T in the third position were always the most used. Cultivation of P. shioyasakiensis D1497 presented lower substrate consumption rate, higher ATP pool and higher conversion rate of biomass per unit substrate consumed at low temperature (15 °C) than that of the room temperature (25 °C) culture. Comparative transcriptomic analysis revealed that the mRNA abundance of energy metabolism related genes was decreased in 15 °C culture compared with that of 25 °C culture. In addition to its codon usage biases profile, P. shioyasakiensis D1497 presented an energy saving metabolism strategy to cope with cold, converting more carbon source into biomass in cold environment.

Carbon Dots as New Generation Materials for Nanothermometer: Review

Highly sensitive non-contact mode temperature sensing is substantial for studying fundamental chemical reactions, biological processes, and applications in medical diagnostics. Nanoscale-based thermometers are guaranteeing non-invasive probes for sensitive and precise temperature sensing with subcellular resolution. Fluorescence-based temperature sensors have shown great capacity since they operate as "non-contact" mode and offer the dual functions of cellular imaging and sensing the temperature at the molecular level. Advancements in nanomaterials and nanotechnology have led to the development of novel sensors, such as nanothermometers (novel temperature-sensing materials with a high spatial resolution at the nanoscale). Such nanothermometers have been developed using different platforms such as fluorescent proteins, organic compounds, metal nanoparticles, rare-earth-doped nanoparticles, and semiconductor quantum dots. Carbon dots (CDs) have attracted interest in many research fields because of outstanding properties such as strong fluorescence, photobleaching resistance, chemical stability, low-cost precursors, low toxicity, and biocompatibility. Recent reports showed the thermal-sensing behavior of some CDs that make them an alternative to other nanomaterials-based thermometers. This kind of luminescent-based thermometer is promising for nanocavity temperature sensing and thermal mapping to grasp a better understanding of biological processes. With CDs still in its early stages as nanoscale-based material for thermal sensing, in this review, we provide a comprehensive understanding of this novel nanothermometer, methods of functionalization to enhance thermal sensitivity and resolution, and mechanism of the thermal sensing behavior.