Alterations in Membrane Phospholipid Fatty Acids of Gram-Positive Piezotolerant Bacterium Sporosarcina sp. DSK25 in Response to Growth Pressure

In Staphylococcus aureus, the acyl-CoA synthetase MbcS supports branched-chain fatty acid synthesis from carboxylic acid and aldehyde precursors

In the human pathogen Staphylococcus aureus, branched-chain fatty acids (BCFAs) are the most abundant fatty acids in membrane phospholipids. Strains deficient for BCFAs synthesis experience auxotrophy in laboratory culture and attenuated virulence during infection. Furthermore, the membrane of S. aureus is among the main targets for antibiotic therapy. Therefore, determining the mechanisms involved in BCFAs synthesis is critical to manage S. aureus infections. Here, we report that the overexpression of SAUSA300_2542 (annotated to encode an acyl-CoA synthetase) restores BCFAs synthesis in strains lacking the canonical biosynthetic pathway catalyzed by the branched-chain α-keto acid dehydrogenase (BKDH) complex. We demonstrate that the acyl-CoA synthetase activity of MbcS activates branched-chain carboxylic acids (BCCAs), and is required by S. aureus to utilize the isoleucine derivative 2-methylbutyraldehyde to restore BCFAs synthesis in S. aureus. Based on the ability of some staphylococci to convert branched-chain aldehydes into their respective BCCAs and our findings demonstrating that branched-chain aldehydes are in fact BCFAs precursors, we propose that MbcS promotes the scavenging of exogenous BCCAs and mediates BCFA synthesis via a de novo alternative pathway.

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.

Microbial membrane lipid adaptations to high hydrostatic pressure in the marine environment

The deep-sea is characterized by extreme conditions, such as high hydrostatic pressure (HHP) and near-freezing temperature. Piezophiles, microorganisms adapted to high pressure, have developed key strategies to maintain the integrity of their lipid membrane at these conditions. The abundance of specific membrane lipids, such as those containing unsaturated and branched-chain fatty acids, rises with increasing HHP. Nevertheless, this strategy is not universal among piezophiles, highlighting the need to further understand the effects of HHP on microbial lipid membranes. Challenges in the study of lipid membrane adaptations by piezophiles also involve methodological developments, cross-adaptation studies, and insight into slow-growing piezophiles. Moreover, the effects of HHP on piezophiles are often difficult to disentangle from effects caused by low temperature that are often characteristic of the deep sea. Here, we review the knowledge of membrane lipid adaptation strategies of piezophiles, and put it into the perspective of marine systems, highlighting the future challenges of research studying the effects of HHP on the microbial lipid composition.

Effects of Pressurized Aeration on the Biodegradation of Short-Chain Chlorinated Paraffins by Escherichia coli Strain 2

Short-chain chlorinated paraffins (SCCPs) were defined as persistent organic pollutants in 2017, and they can migrate and transform in the environment, accumulate in organisms, and amplify through the food chain. Although they pose a serious threat to environmental safety and human health, there are few papers on their removal. The current SCCP removal methods are expensive, require severe operating conditions, involve time-consuming biological treatment, and have poor removal specificities. Therefore, it is important to seek efficient methods to remove SCCPs. In this paper, a pressurized reactor was introduced, and the removal performance of SCCPs by Escherichia coli strain 2 was investigated. The results indicated that moderate pure oxygen pressurization promoted bacterial growth, but when it exceeded 0.15 MPa, the bacterial growth was severely inhibited. When the concentration of SCCPs was 20 mg/L, the removal rate of SCCPs was 85.61% under 0.15 MPa pure oxygen pressurization for 7 days, which was 25% higher than at atmospheric pressure (68.83%). In contrast, the removal rate was only 69.28% under 0.15 MPa air pressure. As the pressure continued to increase, the removal rate of SCCPs decreased significantly. The total amount of extracellular polymeric substances (EPS) increased significantly upon increasing the pressure, and the amount of tightly bound EPS (TB-EPS) was higher than that of loosely bound EPS (LB-EPS). The pressure mainly promoted the secretion of proteins in LB-EPS. Furthermore, an appropriate pure oxygen pressure of 0.15 MPa improved the dehydrogenase activity. The gas chromatography–mass spectrometry (GC–MS) results indicated that the degradation pathway possibly involved the cleavage of the C–Cl bond in SCCPs, which produced Cl⁻, followed by C–C bond breaking. This process degraded long-chain alkanes into short-chain alkanes. Moreover, the main degradation products detected were 2,4-dimethylheptane (C₉H₂₀), 2,5-dimethylheptane (C₉H₂₀), and 3,3-dimethylhexane (C₈H₁₈).

Pre-incubation conditions determine the fermentation pattern and microbial community structure in fermenters at mild hydrostatic pressure

Fermentation at elevated hydrostatic pressure is a novel strategy targeting product selectivity. However, the role of inoculum history and cross-resistance, that is, acquired tolerance from incubation under distinctive environmental stress, remains unclear in high-pressure operation. In our here presented work, we studied fermentation and microbial community responses of halotolerant marine sediment inoculum (MSI) and anaerobic digester inoculum (ADI), pre-incubated in serum bottles at different temperatures and subsequently exposed to mild hydrostatic pressure (MHP; < 10 MPa) in stainless steel reactors. Results showed that MHP effects on microbial growth, activity, and community structure were strongly temperature-dependent. At moderate temperature (20°C), biomass yield and fermentation were not limited by MHP; suggesting a cross-resistance effect from incubation temperature and halotolerance. Low temperatures (10°C) and MHP imposed kinetic and bioenergetic limitations, constraining growth and product formation. Fermentation remained favorable in MSI at 28°C and ADI at 37°C, despite reduced biomass yield resulting from maintenance and decay proportionally increasing with temperature. Microbial community structure was modified by temperature during the enrichment, and slight differences observed after MHP-exposure did not compromise functionality. Results showed that the relation incubation temperature-halotolerance proved to be a modifier of microbial responses to MHP and could be potentially exploited in fermentations to modulate product/biomass ratio.

Scientific and technological progress in the microbial exploration of the hadal zone

The hadal zone is the deepest point in the ocean with a depth that exceeds 6000 m. Exploration of the biological communities in hadal zone began in the 1950s (the first wave of hadal exploration) and substantial advances have been made since the turn of the twenty-first century (the second wave of hadal exploration), resulting in a focus on the hadal sphere as a research hotspot because of its unique physical and chemical conditions. A variety of prokaryotes are found in the hadal zone. The mechanisms used by these prokaryotes to manage the high hydrostatic pressures and acquire energy from the environment are of substantial interest. Moreover, the symbioses between microbes and hadal animals have barely been studied. In addition, equipment has been developed that can now mimic hadal environments in the laboratory and allow cultivation of microbes under simulated in situ pressure. This review provides a brief summary of recent progress in the mechanisms by which microbes adapt to high hydrostatic pressures, manage limited energy resources and coexist with animals in the hadal zone, as well as technical developments in the exploration of hadal microbial life.

Microbial cell surface engineering for high-level synthesis of bio-products

Microbial cell surface layers, which mainly include the cell membrane, cell wall, periplasmic space, outer membrane, capsules, S-layers, pili, and flagella, control material exchange between the cell and the extracellular environment, and have great impact on production titers and yields of various bio-products synthesized by microbes. Recent research work has made exciting achievements in metabolic engineering using microbial cell surface components as novel regulation targets without direct modifications of the metabolic pathways of the desired products. This review article will summarize the accomplishments obtained in this emerging field, and will describe various engineering strategies that have been adopted in bacteria and yeasts for the enhancement of mass transfer across the cell surface, improvement of protein expression and folding, modulation of cell size and shape, and re-direction of cellular resources, all of which contribute to the construction of more efficient microbial cell factories toward the synthesis of a variety of bio-products. The existing problems and possible future directions will also be discussed.

Characterization of two novel psychrophilic and piezotolerant strains, Shewanella psychropiezotolerans sp. nov. and Shewanella eurypsychrophilus sp. nov, adapted to an extreme deep-sea environment

Three marine bacterial strains designated YLB-06^T, YLB-08^T and YLB-09 were isolated under high hydrostatic pressure from deep-sea sediment samples collected from the Southwest Indian Ocean. They were Gram-stain-negative, oxidase- and catalase-positive, facultative anaerobic and motile. In addition, the strains were capable of growing at 0-20 °C (optimum 4-10 °C) and 0.1-40 MPa (optimum 0.1 MPa), were psychrophiles and piezotolerant, and could use trimethylamine N-oxide (TMAO), DMSO, elemental sulfur and insoluble Fe (III) as terminal electron acceptors during anaerobic growth. Strain YLB-06^T could also use nitrate, and strains YLB-08^T and YLB-09 could use nitrite as a terminal electron acceptor. Phylogenetic tree analyses based on 16S rRNA gene sequences and 400 optimized universal marker sequences indicated that the strains belonged to the genus Shewanella. The 16S rRNA gene highest similarity, together with the estimated ANI and DDH values for these strains with their related type strains, were below the respective thresholds for species differentiation. The ANI and DDH values between YLB-08^T and YLB-09 were 99.9% and 91.8%, respectively, implying that they should belong to the same genospecies. The YLB-06^T genome had duplicated genes, and multiple movement modalities, attachment modalities, biofilm synthesis systems, intercellular interactions and a strong antioxidant system, which were all beneficial for survival in an extreme deep-sea environment. The G + C contents of strains YLB-06^T, YLB-08^T and YLB-09 were 45.1, 43.5 and 43.6 mol%, respectively. Based on polyphasic taxonomic properties, two novel psychropiezotolerant species are proposed, Shewanella psychropiezotolerans sp. nov. with YLB-06^T (=MCCC 1A12715^T = KCTC 62907^T) and S. eurypsychrophilus sp. nov with YLB-08^T (=MCCC 1A12718^T = KCTC 62909^T) as type strains.

Cytotoxicity of functionalized CeO2 nanoparticles towards Escherichia coli and adaptive response of membrane properties

The cytotoxicity and mechanisms of cerium oxide nanoparticles (CeO₂-NPs) on organisms have attracted great concerns recently, while that of CeO₂-NPs with functional groups remains unclear. This study investigated cytotoxic effects and mechanisms of CeO₂-NPs with hydroxyl, carboxyl, or amino functional groups towards a strain Escherichia coli (E. Coli). Results showed that CeO₂-NPs produced a stronger cytotoxicity in NaCl medium than in PBS medium at the concentrations of 10-400 mg/L. The toxicity followed the order of CeO₂-COOH > CeO₂-NH₂ > CeO₂-OH. Exposing to CeO₂-NPs increased cell membrane permeability and reduced membrane fluidity. The membrane phospholipid fatty acid compositions also varied greatly as a response to the stress of CeO₂-NPs, with the proportion of unsaturated fatty acids increased and saturated fatty acids decreased. Both intracellular reactive oxygen species (ROS) level and malonaldehyde (MDA) level declined, suggesting the oxidative stress from ROS may be not the primary reason for the membrane damage. Other mechanisms such as direct membrane oxidation by Ce⁴⁺ or physical penetration based on a close contact between nanoparticles and microbes might contribute to the membrane damages and cell viability loss. The present study provides a significant insight into the influence of functionalized CeO₂-NPs on a gram-negative bacterium.

The Polyextremophilic Bacterium Clostridium paradoxum Attains Piezophilic Traits by Modulating Its Energy Metabolism and Cell Membrane Composition

In polyextremophiles, i.e., microorganisms growing preferentially under multiple extremes, synergistic effects may allow growth when application of the same extremes alone would not. High hydrostatic pressure (HP) is rarely considered in studies of polyextremophiles, and its role in potentially enhancing tolerance to other extremes remains unclear. Here, we investigated the HP-temperature response in Clostridium paradoxum, a haloalkaliphilic moderately thermophilic endospore-forming bacterium, in the range of 50 to 70°C and 0.1 to 30 MPa. At ambient pressure, growth limits were extended from the previously reported 63°C to 70°C, defining C. paradoxum as an actual thermophile. Concomitant application of high HP and temperature compared to standard conditions (i.e., ambient pressure and 50°C) remarkably enhanced growth, with an optimum growth rate observed at 22 MPa and 60°C. HP distinctively defined C. paradoxum physiology, as at 22 MPa biomass, production increased by 75% and the release of fermentation products per cell decreased by >50% compared to ambient pressure. This metabolic modulation was apparently linked to an energy-preserving mechanism triggered by HP, involving a shift toward pyruvate as the preferred energy and carbon source. High HPs decreased cell damage, as determined by Syto9 and propidium iodide staining, despite no organic solute being accumulated intracellularly. A distinct reduction in carbon chain length of phospholipid fatty acids (PLFAs) and an increase in the amount of branched-chain PLFAs occurred at high HP. Our results describe a multifaceted, cause-and-effect relationship between HP and cell metabolism, stressing the importance of applying HP to define the boundaries for life under polyextreme conditions.IMPORTANCE Hydrostatic pressure (HP) is a fundamental parameter influencing biochemical reactions and cell physiology; however, it is less frequently applied than other factors, such as pH, temperature, and salinity, when studying polyextremophilic microorganisms. In particular, how HP affects microbial tolerance to other and multiple extremes remains unclear. Here, we show that under polyextreme conditions of high pH and temperature, Clostridium paradoxum demonstrates a moderately piezophilic nature as cultures grow to highest cell densities and most efficiently at a specific combination of temperature and HP. Our results highlight the importance of considering HP when exploring microbial physiology under extreme conditions and thus have implications for defining the limits for microbial life in nature and for optimizing industrial bioprocesses occurring under multiple extremes.

Isolation and characterization of a novel piezotolerant bacterium Lysinibacillus yapensis sp. nov., from deep-sea sediment of the Yap Trench, Pacific Ocean

A Gram-positive, aerobic, rod-shaped, spore-forming bacterium, designated YLB-03^T, with peritrichous flagella was isolated from deep-sea sediment of the Yap Trench at a depth of 4435 m. The bacterium was found to be catalase-positive but oxidase-negative. Growth of this bacterium was observed at 15-50°C (optimum 37°C), pH 5-10.5 (optimum 7), 0-5% NaCl (optimum 1%, w/v) and 0.1-50 MPa (optimum 0.1 MPa). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YLB-03^T was a member of the genus Lysinibacillus. Strain YLB-03^T was closely related to Lysinibacillus sinduriensis BLB-1^T and Lysinibacillus chungkukjangi 2RL3-2^T (98.4%), Lysinibacillus halotolerans LAM-612^T (98.0%), Lysinibacillus telephonicus KT735049^T (97.5%), Lysinibacillus endophyticus C9^T (97.5%), Lysinibacillus composti NCCP-36^T and Lysinibacillus massiliensis 4400831^T (97.3%). The ANI and the GGDC DNA-DNA hybridization estimate values between strain YLB-03^T and closely related type strains were 73.7-76.3% and 34.7-38.7%, respectively. The principal fatty acids were anteiso-C_15:0 and iso-C_15:0. The G+C content of the chromosomal DNA was 39.6 mol%. The respiratory quinone was determined to be MK-7. The diagnostic amino acids in the cell wall peptidoglycan contained Lys-Asp (type A4α) and the cell-wall sugars were glucose and xylose. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid. The combined genotypic and phenotypic data showed that strain YLB-03^T represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus yapensis sp. nov. is proposed, with the type strain YLB-03^T (= MCCC 1A12698^T = JCM 32871^T).

Plasma Unesterified Fatty-Acid Profile Is Dramatically and Acutely Changed under Ischemic Stroke in the Mouse Model

Although plasma biomarkers would facilitate rapid and accurate diagnosis of ischemic stroke for immediate treatment, no such biomarkers have been developed to date. In the present study, we tested our hypothesis that plasma unesterified fatty acids (FFA) are altered at early stages of acute ischemic stroke. Plasma was collected from mice 2 h after the permanent middle cerebral artery occlusion (pMCAo) onset, as well as from sham operated and control animals. After 2 h, pMCAo significantly changed the plasma FFA profile with the most dramatic 2- to 3-fold relative increase in very long n-3 and n-6 FFA including 20:4n-6, 22:4n-6, 22:5n-6, and 22:6n-3. Changes in the plasma FFA profile are consistent with FFA liberation from brain phospholipid hydrolyzed under ischemic insult. These results identify, for the first time, the plasma FFA profile as a potential biomarker for an early ischemic stroke within the therapeutic window for thrombolytic treatment. Further studies are required to confirm its specificity and sensitivity in clinical settings.

Temperature and pressure adaptation of a sulfate reducer from the deep subsurface

Microbial life in deep marine subsurface faces increasing temperatures and hydrostatic pressure with depth. In this study, we have examined growth characteristics and temperature-related adaptation of the Desulfovibrio indonesiensis strain P23 to the in situ pressure of 30 MPa. The strain originates from the deep subsurface of the eastern flank of the Juan de Fuca Ridge (IODP Site U1301). The organism was isolated at 20°C and atmospheric pressure from ~61°C-warm sediments approximately 5 m above the sediment-basement interface. In comparison to standard laboratory conditions (20°C and 0.1 MPa), faster growth was recorded when incubated at in situ pressure and high temperature (45°C), while cell filamentation was induced by further compression. The maximum growth temperature shifted from 48°C at atmospheric pressure to 50°C under high-pressure conditions. Complementary cellular lipid analyses revealed a two-step response of membrane viscosity to increasing temperature with an exchange of unsaturated by saturated fatty acids and subsequent change from branched to unbranched alkyl moieties. While temperature had a stronger effect on the degree of fatty acid saturation and restructuring of main phospholipids, pressure mainly affected branching and length of side chains. The simultaneous decrease of temperature and pressure to ambient laboratory conditions allowed the cultivation of our moderately thermophilic strain. This may in turn be one key to a successful isolation of microorganisms from the deep subsurface adapted to high temperature and pressure.