Fatty acid metabolism in bacteria

Dietary pentadecanoic acid supplementation at weaning in essential fatty acid-deficient rats shed light on the new family of odd-chain n-8 PUFAs

Pentadecanoic acid (C15:0) is a saturated odd-chain fatty acid (OCFA), mainly found in dairy products. Its physiological and nutritional effects are still unknown, yet some recent evidences suggest it might be beneficial to human health. Moreover, pentadecanoic acid has recently been suspected of having essential roles in humans, although the mechanisms are not described. We therefore questioned the potential essentiality of this fatty acid (FA). We investigated in vivo the effect of a C15:0 supplementation on essential fatty acid (EFA) deficient Wistar rats. Female rats were fed an EFA-deficient diet 2 weeks before mating, during pregnancy and lactation. Weaned pups were fed the EFA-deficient diet or were switched to a diet supplemented with C15:0 or linoleic acid (LA) for 11 weeks. A control group was fed with EFA during the whole study. Since linoleic acid deficiency is known to induce growth delay, weights were measured throughout the experiment and FA content in collected tissues were analyzed to evaluate biochemical markers of the deficiency. As expected, EFA-deficient rats showed growth retardation, compared to control rats. Supplementation of C15:0 at weaning increased early growth rate compared to deficient animals, as also did the supplementation of C18:2 n-6. Furthermore, the supplementation of C15:0 in the diet of EFA-deficient animals induced the previously undescribed synthesis of odd-chain PUFAs of the n-8 family (C19:3, C21:3 and C21:4 n-8). These results suggest dietary C15:0 might counteract EFA induced growth retardation, possibly through the synthesis of odd-chain n-8 PUFAs, yet mechanisms are to be deciphered for further validation.

Metabolic adaptations of Escherichia coli to extended zinc exposure: insights into tricarboxylic acid cycle and trehalose synthesis

Balanced bacterial metabolism is essential for cell homeostasis and growth and can be impacted by various stress factors. In particular, bacteria exposed to metals, including the nanoparticle form, can significantly alter their metabolic processes. It is known that the extensive and intensive use of food and feed supplements, including zinc, in human and animal nutrition alters the intestinal microbiota and this may negatively impact the health of the host. This study examines the effects of zinc (zinc oxide and zinc oxide nanoparticles) on key metabolic pathways of Escherichia coli. Transcriptomic and proteomic analyses along with quantification of intermediates of tricarboxylic acid (TCA) were employed to monitor and study the bacterial responses. Multi-omics analysis revealed that extended zinc exposure induced mainly oxidative stress and elevated expression/production of enzymes of carbohydrate metabolism, especially enzymes for synthesis of trehalose. After the zinc withdrawal, E. coli metabolism returned to a baseline state. These findings shed light on the alteration of TCA and on importance of trehalose synthesis in metal-induced stress and its broader implications for bacterial metabolism and defense and consequently for the balance and health of the human and animal microbiome.

Varying the position of phospholipid acyl chain unsaturation modulates hopanoid and sterol ordering

The cell membrane must balance mechanical stability with fluidity to function as both a barrier and an organizational platform. Key to this balance is the ordering of hydrocarbon chains and the packing of lipids. Many eukaryotes synthesize sterols, which are uniquely capable of modulating the lipid order to decouple membrane stability from fluidity. Ancient sterol analogs known as hopanoids are found in many bacteria and proposed as ancestral ordering lipids. The juxtaposition of sterols and hopanoids in extant organisms prompts us to ask why both pathways persist, especially in light of their convergent ability to order lipids. In this work, simulations, monolayer experiments, and cellular assays show that hopanoids and sterols order unsaturated phospholipids differently based on the position of double bonds in the phospholipid acyl chain. We find that cholesterol and diplopterol's methyl group distributions lead to distinct effects on unsaturated lipids. In Mesoplasma florum, diplopterol's constrained ordering capacity reduces membrane resistance to osmotic stress, unlike cholesterol. These findings suggest that cholesterol's broader lipid-ordering ability may have facilitated the exploration of a more diverse lipidomic landscape in eukaryotic membranes.

Comparative genomics, pangenomics, and phenomic studies of Pectobacterium betavasculorum strains isolated from sugar beet, potato, sunflower, and artichoke: insights into pathogenicity, virulence determinants, and adaptation to the host plant

Introduction

Bacteria of genus Pectobacterium, encompassing economically significant pathogens affecting various plants, includes the species P. betavasculorum, initially associated with beetroot infection. However, its host range is much broader. It causes diseases of sunflower, potato, tomato, carrots, sweet potato, radish, squash, cucumber, and chrysanthemum. To explain this phenomenon, a comprehensive pathogenomic and phenomic characterisation of P. betavasculorum species was performed.

Methods

Genomes of P. betavasculorum strains isolated from potato, sunflower, and artichoke were sequenced and compared with those from sugar beet isolates. Metabolic profiling and pathogenomic analyses were conducted to assess virulence determinants and adaptation potential. Pathogenicity assays were performed on potato tubers and chicory leaves to confirm in silico predictions of disease symptoms. Phenotypic assays were also conducted to assess the strains ability to synthesise homoserine lactones and siderophores.

Results

The genome size ranged from 4.675 to 4.931 kbp, and GC % was between 51.0% and 51.2%. The pangenome of P. betavasculorum is open and comprises, on average, 4,220 gene families. Of these, 83% of genes are the core genome, and 2% of the entire pangenome are unique genes. Strains isolated from sugar beet have a smaller pangenome size and a higher number of unique genes than those from other plants. Interestingly, genomes of strains from artichoke and sunflower share 391 common CDS that are not present in the genomes of other strains from sugar beet or potato. Those strains have only one unique gene. All strains could use numerous sugars as building materials and energy sources and possessed a high repertoire of virulence determinants in the genomes. P. betavasculorum strains were able to cause disease symptoms on potato tubers and chicory leaves. They were also able to synthesise homoserine lactones and siderophores.

Discussion

The findings underscore the adaptability of P. betavasculorum to diverse hosts and environments. Strains adapted to plants with high sugar content in tissues have a different composition of fatty acids in membranes and a different mechanism of replenishing nitrogen in case of deficiency of this compound than strains derived from other plant species. Extensive phenomics and genomic analyses performed in this study have shown that P. betavasculorum species is an agronomically relevant pathogen.

19F solid-state NMR approaches to probe antimicrobial peptide interactions with membranes in whole cells

To address the global problem of bacterial antibiotic resistance, antimicrobial peptides (AMPs) are considered promising therapeutic candidates due to their broad-spectrum and membrane-lytic activity. As preferential interactions with bacteria are crucial, it is equally important to investigate and understand their impact on eukaryotic cells. In this study, we employed 19F solid-state nuclear magnetic resonance (ssNMR) as a novel approach to examine the interaction of AMPs with whole red blood cells (RBCs). We used RBC ghosts (devoid of hemoglobin) and developed a protocol to label their lipid membranes with palmitic acid (PA) monofluorinated at carbon positions 4, 8, or 14 on the acyl chain, allowing us to probe different locations in model and intact RBC ghost membranes. Our work revealed that changes in the 19F chemical shift anisotropy, monitored through a CF bond order parameter (SCF), can provide insights into lipid bilayer dynamics. This information was also obtained using magic-angle spinning 19F ssNMR spectra with and without 1H decoupling, by studying alterations in the second spectral moment (M2) as well as the 19F isotropic chemical shift, linewidth, T1, and T2 relaxation times. The appearance of an additional isotropic peak with a smaller chemical shift anisotropy, a narrower linewidth, and a shorter T1, induced by the AMP caerin 1.1, supports the presence of high-curvature regions in RBCs indicative of pore formation, analogous to its antimicrobial mechanism. In summary, the straightforward incorporation of monofluorinated FAs and rapid signal acquisition offer promising avenues for the study of whole cells using 19F ssNMR.

Varying the position of phospholipid acyl chain unsaturation modulates hopanoid and sterol ordering

The cell membrane must balance mechanical stability with fluidity to function as both a barrier and an organizational platform. Key to this balance is the thermodynamic ordering of lipids. Most Eukaryotes employ sterols, which are uniquely capable of modulating lipid order to decouple membrane stability from fluidity. Ancient sterol analogues known as hopanoids are found in many bacteria and are proposed as ancestral ordering lipids. The juxtaposition of sterols and hopanoids in extant organisms prompts us to ask why both pathways persist, especially in light of their convergent ability to order lipids. We reveal that both hopanoids and sterols order unsaturated phospholipids differently based on the position of double bonds in the phospholipid's acyl chain. We find that cholesterol and diplopterol's methyl group distributions lead to distinct effects on unsaturated lipids. In Mesoplasma florum, diplopterol's constrained ordering capacity reduces membrane resistance to osmotic stress, unlike cholesterol. These findings suggest cholesterol's broader lipid ordering ability may have facilitated the exploration of a more diverse lipidomic landscape in eukaryotic membranes.

Pseudomonas violetae sp. nov. and Pseudomonas emilianonis sp. nov., two new species with the ability to degrade TNT isolated from soil samples at Deception Island, maritime Antarctica

Two motile, rod-shaped, Gram-stain-negative bacterial strains, TNT11T and TNT19T, were isolated from soil samples collected at Deception Island, Antarctica. According to the 16S rRNA gene sequence similarity, both strains belong to the genus Pseudomonas. Further genomic analyses based on ANI and dDDH suggested that these strains were new species. Growth of strain TNT11T is observed at 0-30 ℃ (optimum, 20 ℃), pH 4.0-9.0 (optimum, pH 6.0) and in the presence of 0-5.0% NaCl (optimum, 1% NaCl), while for TNT19T is observed at 0-30 ℃ (optimum between 15 and 20 ℃), pH 5.0-9.0 (optimum, pH 6.0) and in the presence of 0-5.0% NaCl (optimum between 0 and 1% NaCl). The fatty acid profile consists of the major compounds; C16:0 and C16:1 ω6 for TNT11T, and C16:0 and C12:0 for TNT19T. Based on the draft genome sequences, the DNA G + C content for TNT11T is 60.43 mol% and 58.60 mol% for TNT19T. Based on this polyphasic study, TNT11T and TNT19T represent two novel species of the genus Pseudomonas, for which the proposed names are Pseudomonas violetae sp. nov. and Pseudomonas emilianonis sp. nov., respectively. The type strains are Pseudomonas violetae TNT11T (= RGM 3443T = LMG 32959T) and Pseudomonas emilianonis TNT19T (= RGM 3442T = LMG 32960T). Strains TNT11T and TNT19T were deposited to CChRGM and BCCM/LMG with entry numbers RGM 3443/LMG 32959 and RGM 3442/LMG 32960, respectively.

Can individual fatty acids be used as functional biomarkers of dairy fat consumption in relation to cardiometabolic health? A narrative review

In epidemiological studies, dairy food consumption has been associated with minimal effect or decreased risk of some cardiometabolic diseases (CMD). However, current methods of dietary assessment do not provide objective and accurate measures of food intakes. Thus, the identification of valid and reliable biomarkers of dairy product intake is an important challenge to best determine the relationship between dairy consumption and health status. This review investigated potential biomarkers of dairy fat consumption, such as odd-chain, trans- and branched-chain fatty acids (FA), which may improve the assessment of full-fat dairy product consumption. Overall, the current use of serum/plasma FA as biomarkers of dairy fat consumption is mostly based on observational evidence, with a lack of well-controlled, dose-response intervention studies to accurately assess the strength of the relationship. Circulating odd-chain SFA and trans-palmitoleic acid are increasingly studied in relation to CMD risk and seem to be consistently associated with a reduced risk of type 2 diabetes in prospective cohort studies. However, associations with CVD are less clear. Overall, adding less studied FA such as vaccenic and phytanic acids to the current available evidence may provide a more complete assessment of dairy fat intake and minimise potential confounding from endogenous synthesis. Finally, the current evidence base on the direct effect of dairy fatty acids on established biomarkers of CMD risk (e.g. fasting lipid profiles and markers of glycaemic control) mostly derives from cross-sectional, animal and in vitro studies and should be strengthened by well-controlled human intervention studies.

Effect of Seasonality on Microbiological Variability of Raw Cow Milk from Apulian Dairy Farms in Italy

Raw cow milk is one of the most complex and unpredictable food matrices shaped by the interaction between biotic and abiotic factors. Changes in dairy farming conditions impact the quality and safety of milk, which largely depend on seasonality. Changes in microbiome composition and relative metabolic pathways are derived from microbial interactions, as well as from seasonality, mammary, and extramammary conditions (e.g., farm management and outdoor environment). Breeding data from >600 Apulian farms were examined, and the associated physicochemical parameters were processed by a reductionist approach to obtain a raw cow milk sample subset. We investigated the microbiological variability in cultivable and 16S rRNA sequencing microbiota as affected by seasonal fluctuations at two time points (winter and summer seasons). We identified families (Xanthomonadaceae, Enterobacteriaceae, and Pseudomonadaceae) whose increased abundance during winter may cause a shift toward a pathobiont microbial niche that leads to lower milk quality. Apulian summer season conditions were advantageous to the presence of specific taxa, i.e., Streptococcaceae (i.e., Lactococcus) and Limosilactobacillus fermentum, which in turn may favor better milk preservation.

IMPORTANCE The strength of this study lies in the microbiological characterization of a wide range of farm management data to achieve a more comprehensive framework of Apulian milk. Specific regional pedoclimatic and management conditions impact the taxa present and their abundances within this ecological food niche. The obtained results lay the groundwork for comparison with other worldwide extensive farming areas.

Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control

Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.

Effects of Regioisomerism on the Antiproliferative Activity of Hydroxystearic Acids on Human Cancer Cell Lines

A series of regioisomers of the hydroxystearic acid (HSA) was prepared, and the effect of the position of the hydroxyl group along the chain on a panel of human cancer cell lines was investigated. Among the various regioisomers, those carrying the hydroxyl at positions 5, 7, and 9 had growth inhibitor activity against various human tumor cell lines, including CaCo-2, HT29, HeLa, MCF7, PC3, and NLF cells. 10-HSA and 11-HSA showed a very weak effect. 8-HSA did not show inhibitory activity in all cell lines. The biological role of 7-HSA and 9-HSA is widely recognized, while little is known about the effects of 5-HSA. Therefore, the biological effects of 5-HSA in HeLa, HT29, MCF7, and NLF cell lines were investigated using the Livecyte's ptychography technology, which allows correlating changes in proliferation, motility, and morphology as a function of treatment at the same time. 5-HSA not only reduces cell proliferation but also induces changes in cell displacement, directionality, and speed. It is important to characterize the biological effects of 5-HSA, this molecule being an important component of fatty acyl esters of hydroxy fatty acids (FAHFA), a class of endogenous mammalian lipids with noticeable anti-diabetic and anti-inflammatory effects.

The Effects of Freeze-Thaw and UVC Radiation on Microbial Survivability in a Selected Mars-like Environment

The purpose of this study was to determine survivability of Escherichia coli, Deinococcus radiodurans and Paraburkholderia fungorum under Mars-simulated conditions for freeze-thawing (−80 °C to +30 °C) and UV exposure alone and in combination. E. coli ATCC 25922, D. radiodurans and P. fungorum remained viable following 20 successive freeze-thaw cycles, exhibiting viabilities of 2.3%, 96% and 72.6%, respectively. E. coli ATCC 9079 was non-recoverable by cycle 9. When exposed to UV irradiation, cells withstood doses of 870 J/m² (E. coli ATCC 25922), 200 J/m² (E. coli ATCC 9079), 50,760 J/m² (D. radiodurans) and 44,415 J/m² (P. fungorum). Data suggests P. fungorum is highly UV-resistant. Combined freeze-thawing with UV irradiation showed freezing increased UV resistance in E. coli ATCC 25922, E. coli DSM 9079 and D. radiodurans by 6-fold, 30-fold and 1.2-fold, respectively. Conversely, freezing caused P. fungorum to exhibit a 1.75-fold increase in UV susceptibility. Strain-dependent experimentation demonstrated that freezing increases UV resistance and prolongs survival. These findings suggest that exposure to short wavelength UV rays (254 nm) and temperature cycles resembling the daily fluctuating conditions on Mars do not significantly affect survival of D. radiodurans, P. fungorum and E. coli ATCC 25922 following 20 days of exposure.

Rhodococcus as Biofactories for Microbial Oil Production

Bacteria belonging to the Rhodococcus genus are frequent components of microbial communities in diverse natural environments. Some rhodococcal species exhibit the outstanding ability to produce significant amounts of triacylglycerols (TAG) (>20% of cellular dry weight) in the presence of an excess of the carbon source and limitation of the nitrogen source. For this reason, they can be considered as oleaginous microorganisms. As occurs as well in eukaryotic single-cell oil (SCO) producers, these bacteria possess specific physiological properties and molecular mechanisms that differentiate them from other microorganisms unable to synthesize TAG. In this review, we summarized several of the well-characterized molecular mechanisms that enable oleaginous rhodococci to produce significant amounts of SCO. Furthermore, we highlighted the ability of these microorganisms to degrade a wide range of carbon sources coupled to lipogenesis. The qualitative and quantitative oil production by rhodococci from diverse industrial wastes has also been included. Finally, we summarized the genetic and metabolic approaches applied to oleaginous rhodococci to improve SCO production. This review provides a comprehensive and integrating vision on the potential of oleaginous rhodococci to be considered as microbial biofactories for microbial oil production.

Engineering precursor pools for increasing production of odd-chain fatty acids in Yarrowia lipolytica

Microbial production of lipids is one of the promising alternatives to fossil resources with increasing environmental and energy concern. Odd-chain fatty acids (OCFA), a type of unusual lipids, are recently gaining a lot of interest as target compounds in microbial production due to their diverse applications in the medical, pharmaceutical, and chemical industries. In this study, we aimed to enhance the pool of precursors with three-carbon chain (propionyl-CoA) and five-carbon chain (β-ketovaleryl-CoA) for the production of OCFAs in Yarrowia lipolytica. We evaluated different propionate-activating enzymes and the overexpression of propionyl-CoA transferase gene from Ralstonia eutropha increased the accumulation of OCFAs by 3.8 times over control strain, indicating propionate activation is the limiting step of OCFAs synthesis. It was shown that acetate supplement was necessary to restore growth and to produce a higher OCFA contents in total lipids, suggesting the balance of the precursors between acetyl-CoA and propionyl-CoA is crucial for OCFA accumulation. To improve β-ketovaleryl-CoA pools for further increase of OCFA production, we co-expressed the bktB encoding β-ketothiolase in the producing strain, and the OCFA production was increased by 33% compared to control. Combining strain engineering and the optimization of the C/N ratio promoted the OCFA production up to 1.87 ​g/L representing 62% of total lipids, the highest recombinant OCFAs titer reported in yeast, up to date. This study provides a strong basis for the microbial production of OCFAs and its derivatives having high potentials in a wide range of applications.

Dioxin impacts on lipid metabolism of soil microbes: towards effective detection and bioassessment strategies

Dioxins are the most toxic known environmental pollutants and are mainly formed by human activities. Due to their structural stability, dioxins persist for extended periods and can be transported over long distances from their emission sources. Thus, dioxins can be accumulated to considerable levels in both human and animal food chains. Along with sediments, soils are considered the most important reservoirs of dioxins. Soil microorganisms are therefore highly exposed to dioxins, leading to a range of biological responses that can impact the diversity, genetics and functional of such microbial communities. Dioxins are very hydrophobic with a high affinity to lipidic macromolecules in exposed organisms, including microbes. This review summarizes the genetic, molecular and biochemical impacts of dioxins on the lipid metabolism of soil microbial communities and especially examines modifications in the composition and architecture of cell membranes. This will provide a useful scientific benchmark for future attempts at soil ecological risk assessment, as well as in identifying potential dioxin-specific-responsive lipid biomarkers. Finally, potential uses of lipid-sequestering microorganisms as a part of biotechnological approaches to the bio-management of environmental contamination with dioxins are discussed.

Short communication: Odd-chain and branched-chain fatty acid concentrations in bovine colostrum and transition milk and their stability under heating and freezing treatments

Although odd-chain fatty acids (OCFA) and branched-chain fatty acids (BCFA) are found in bovine milk and have some positive influences on human and animal health, their concentrations in bovine colostrum and transition milk have not been reported. In this study, we reported the OCFA and BCFA concentrations in colostrum and transition milk and their stability after heating or freezing treatments (or both), which are processes commonly applied in dairy calf management. Milk samples were collected from 12 Holstein dairy cows (6 primiparous and 6 multiparous) at the first milking (colostrum), fifth milking (transition milk), and ninth milking (mature milk) after calving, respectively, and were used for fatty acid analysis using gas chromatography. The sum concentration of OCFA and BCFA (termed OBCFA) was 134 mg/100 g of milk in the colostrum, which was 24% and 35% lower than that in the transition milk and mature milk, respectively. Among these fatty acids detected, C15:0 and C17:0 were the top 2 abundant fatty acids in all milk types, accounting for 20 to 25% and 21 to 24% of the total concentration of OBCFA, respectively. Additionally, anteiso-C17:0 was the most abundant BCFA, followed by iso-C17:0, anteiso-C15:0, iso-C16:0, iso-C15:0, iso-C18:0, and iso-C14:0 in 3 types of milk. Significant interactions between milk type and cow parity were observed for all OCFA and BCFA concentrations. The milk samples were also treated with heating (at 65°C for 60 min), freezing (at -20°C for 30 d), and heating and freezing (at 65°C for 60 min and then at -20°C for 30 d), and milk OCFA and BCFA concentrations were similar between these treatments. In conclusion, the OBCFA concentration was lower in colostrum, compared with transition and mature milks, and it remained stable after heating and freezing treatments.

Niche Partitioning between Coastal and Offshore Shelf Waters Results in Differential Expression of Alkane and Polycyclic Aromatic Hydrocarbon Catabolic Pathways

In the wake of the Deepwater Horizon oil spill, the taxonomic response of marine microbial communities to oil and dispersants has been extensively studied. However, relatively few studies on the functional response of these microbial communities have been reported, especially in a longitudinal fashion. Moreover, despite the fact that marine oil spills typically impact thousands of square kilometers of both coastal and offshore marine environments, little information is available on how the microbial response to oil and dispersants might differ between these biomes. The results of this study help fill this critical knowledge gap and provide valuable insight into how oil spill response efforts, such as chemically dispersing oil, may have differing effects in neighboring coastal and offshore marine environments.

Marine oil spills can impact both coastal and offshore marine environments, but little information is available on how the microbial response to oil and dispersants might differ between these biomes. Here, we describe the compositional and functional response of microbial communities to different concentrations of oil and chemically dispersed oil in coastal and offshore surface waters from the Texas-Louisiana continental shelf. Using a combination of analytical chemistry and 16S rRNA amplicon and metatranscriptomic sequencing, we provide a broad, comparative overview of the ecological response of hydrocarbon-degrading bacteria and their expression of hydrocarbon-degrading genes in marine surface waters over time between two oceanic biomes. We found evidence for the existence of different ecotypes of several commonly described hydrocarbon-degrading bacterial taxa which behaved differentially in coastal and offshore shelf waters despite being exposed to similar concentrations of oil, dispersants, and nutrients. This resulted in the differential expression of catabolic pathways for n-alkanes and polycyclic aromatic hydrocarbons (PAHs)—the two major categories of compounds found in crude oil—with preferential expression of n-alkane degradation genes in coastal waters while offshore microbial communities trended more toward the expression of PAH degradation genes. This was unexpected as it contrasts with the generally held view that n-alkanes, being more labile, are attacked before the more refractory PAHs. Collectively, our results provide new insights into the existence and potential consequences of niche partitioning of hydrocarbon-degrading taxa between neighboring marine environments.

IMPORTANCE In the wake of the Deepwater Horizon oil spill, the taxonomic response of marine microbial communities to oil and dispersants has been extensively studied. However, relatively few studies on the functional response of these microbial communities have been reported, especially in a longitudinal fashion. Moreover, despite the fact that marine oil spills typically impact thousands of square kilometers of both coastal and offshore marine environments, little information is available on how the microbial response to oil and dispersants might differ between these biomes. The results of this study help fill this critical knowledge gap and provide valuable insight into how oil spill response efforts, such as chemically dispersing oil, may have differing effects in neighboring coastal and offshore marine environments.

Unsaturation Elements and Other Modifications of Phospholipids in Bacteria: New Insight from Ultraviolet Photodissociation Mass Spectrometry

Glycerophospholipids (GPLs), one of the main components of bacterial cell membranes, exhibit high levels of structural complexity that are directly correlated with biophysical membrane properties such as permeability and fluidity. This structural complexity arises from the substantial variability in the individual GPL structural components such as the acyl chain length and headgroup type and is further amplified by the presence of modifications such as double bonds and cyclopropane rings. Here we use liquid chromatography coupled to high-resolution and high-mass-accuracy ultraviolet photodissociation mass spectrometry for the most in-depth study of bacterial GPL modifications to date. In doing so, we unravel a diverse array of unexplored GPL modifications, ranging from acyl chain hydroxyl groups to novel headgroup structures. Along with characterizing these modifications, we elucidate general trends in bacterial GPL unsaturation elements and thus aim to decipher some of the biochemical pathways of unsaturation incorporation in bacterial GPLs. Finally, we discover aminoacyl-PGs not only in Gram-positive bacteria but also in Gram-negative C. jejuni, advancing our knowledge of the methods of surface charge modulation that Gram-negative organisms may adopt for antibiotic resistance.

Pseudomonas putida KT2440 is naturally endowed to withstand industrial-scale stress conditions

Pseudomonas putida is recognized as a very promising strain for industrial application due to its high redox capacity and frequently observed tolerance towards organic solvents. In this research, we studied the metabolic and transcriptional response of P. putida KT2440 exposed to large-scale heterogeneous mixing conditions in the form of repeated glucose shortage. Cellular responses were mimicked in an experimental setup comprising a stirred tank reactor and a connected plug flow reactor. We deciphered that a stringent response-like transcriptional regulation programme is frequently induced, which seems to be linked to the intracellular pool of 3-hydroxyalkanoates (3-HA) that are known to serve as precursors for polyhydroxyalkanoates (PHA). To be precise, P. putida is endowed with a survival strategy likely to access cellular PHA, amino acids and glycogen in few seconds under glucose starvation to obtain ATP from respiration, thereby replenishing the reduced ATP levels and the adenylate energy charge. Notably, cells only need 0.4% of glucose uptake to build those 3-HA-based energy buffers. Concomitantly, genes that are related to amino acid catabolism and β-oxidation are upregulated during the transient absence of glucose. Furthermore, we provide a detailed list of transcriptional short- and long-term responses that increase the cellular maintenance by about 17% under the industrial-like conditions tested.

Changes in Cell Membrane Fatty Acid Composition of Streptococcus thermophilus in Response to Gradually Increasing Heat Temperature

In this study, a method of heat adaptation was implemented in an attempt to increase the upper thermal threshold of two Streptococcus thermophilus found in South Korea and identified the alterations in membrane fatty acid composition to adaptive response to heat. In order to develop heat tolerant lactic acid bacteria, heat treatment was continuously applied to bacteria by increasing temperature from 60°C until the point that no surviving cell was detected. Our results indicated significant increase in heat tolerance of heat-adapted strains compared to the wild type (WT) strains. In particular, the survival ratio of basically low heat-tolerant strain increased even more. In addition, the strains with improved heat tolerance acquired cross protection, which improved their survival ratio in acid, bile salts and osmotic conditions. A relation between heat tolerance and membrane fatty acid composition was identified. As a result of heat adaptation, the ratio of unsaturated to saturated fatty acids (UFA/SFA) and C18:1 relative concentration were decreased. C6:0 in only heatadapted strains and C22:0 in only the naturally high heat tolerant strain were detected. These results support the hypothesis, that the consequent increase of SFA ratio is a cellular response to environmental stresses such as high temperatures, and it is able to protect the cells from acid, bile salts and osmotic conditions via cross protection. This study demonstrated that the increase in heat tolerance can be utilized as a mean to improve bacterial tolerance against various environmental stresses.

Temperature Driven Membrane Lipid Adaptation in Glacial Psychrophilic Bacteria

Bacteria inhabiting non-polar glaciers are exposed to large variations in temperature, which significantly affects the fluidity of bacterial cell membranes. In order to maintain normal functions of the cell membranes, psychrophilic bacteria adapt by changing the composition of cell membrane fatty acids. However, information on the exact pattern of cell membrane adaptability in non-polar low-temperature habitats is scarce. In the present study, 42 bacterial strains were isolated from the Ghulmet, Ghulkin, and Hopar glaciers of the Hunza Valley in the Karakoram Mountain Range, Pakistan and their cell membrane fatty acid distributions studied, using gas chromatography/mass spectrometry (GC-MS) for the analysis of fatty acid methyl esters (FAMEs) liberated by acid-catalyzed methanolysis. Furthermore, Gram-negative and Gram-positive groups were grown under different temperature settings (5, 15, 25, and 35°C) in order to determine the effect of temperature on cell membrane (CM) fatty acid distribution. The analyses identified the major groups of cell membrane fatty acids (FA) as straight-chain monounsaturated fatty acids (n-MUFAs) and branched fatty acids (br-FAs), accounting for more than 70% of the fatty acids analyzed. The distribution of br-FAs and n-FAs in bacterial cell membranes was significantly affected by temperature, with the level of br-FAs decreasing relative to n-FAs with increasing temperature. Notably, the production of polyunsaturated fatty acids (PUFAs) was only seen at lower temperatures. This study contributes to understanding, for the first time, the role of br-FAs in the maintenance of cell membrane fluidity of bacteria inhabiting non-polar habitats.

Fatty Acid Methyl Ester (FAME) Profiling Identifies Carbapenemase-Producing Klebsiella pneumoniae Belonging to Clonal Complex 258

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is one of the most extensively antibiotic-resistant pathogens encountered in the clinical setting today. A few studies to-date suggest that CRKP and carbapenem-susceptible K. pneumoniae (CSKP) differ from one another not only with respect to their underlying genetics, but also their transcriptomic and metabolomic fingerprints. Within this context, we characterize the fatty acid methyl ester (FAME) profiles of these pathogens in vitro. Specifically, we evaluated the FAME profiles of six Klebsiella pneumoniae carbapenemase (KPC)-producing isolates belonging to the CC258 lineage (KPC+/258+), six KPC-producing isolates belonging to non-CC258 lineages (KPC+/258−), and six non-KPC-producing isolates belonging to non-CC258 lineages (KPC−/258−). We utilized a single-step sample preparation method to simultaneously lyse bacterial cells and transesterify the lipid fraction, and identified 14 unique FAMEs using gas chromatography-mass spectrometry. The machine learning algorithm Random Forest identified four FAMEs that were highly discriminatory between CC258 and non-CC258 isolates (9(Z)-octadecenoate, 2-phenylacetate, pentadecanoate, and hexadecanoate), of which three were also significantly different in relative abundance between these two groups. These findings suggest that distinct differences exist between CC258 and non-CC258 K. pneumoniae isolates with respect to the metabolism of both fatty acids and amino acids, a hypothesis that is supported by previously-acquired transcriptomic data.

Short communication: Changes under low ambient temperatures in the milk lipodome and metabolome of mid-lactation cows after dehorning as a calf

Horns are living tissue and cows can use their horns for thermoregulatory purposes. We investigated the effect of the presence of horns on the metabolome of milk serum and lipidome of milk fat, to assess the physiological effect of dehorning. Milk sampling took place at low ambient temperatures of -6 to 2°C. Horned and dehorned cows were kept in a mixed herd of Holstein Friesian and Brown Swiss cows. The hypothesis was that horned cows needed to increase their metabolism to compensate for additional heat loss through the presence of their horns. No differences were observed in milk yield, milk solids, and somatic cell counts between horned and dehorned cows. For the milk metabolome, horned cows showed an upregulation of several glucogenic AA that could be transformed into glucose for energy supply and a downregulation of sugar intermediates and γ-glutamylcysteine compared with dehorned cows. The fatty acid (FA) composition in horned cows showed a shift toward decreased odd medium-chain FA (C7:0, C9:0, and C11:0) and increased cis-vaccenic acid (C18:1n-7 cis-11) and stearidonic acid (C18:4n-3). The changes in milk composition related to additional heat loss in horned cows indicate a competition in C3 metabolism for glucose synthesis and de novo FA synthesis under cold stress.

Capturing protein communities by structural proteomics in a thermophilic eukaryote

The arrangement of proteins into complexes is a key organizational principle for many cellular functions. Although the topology of many complexes has been systematically analyzed in isolation, their molecular sociology in situ remains elusive. Here, we show that crude cellular extracts of a eukaryotic thermophile, Chaetomium thermophilum, retain basic principles of cellular organization. Using a structural proteomics approach, we simultaneously characterized the abundance, interactions, and structure of a third of the C. thermophilum proteome within these extracts. We identified 27 distinct protein communities that include 108 interconnected complexes, which dynamically associate with each other and functionally benefit from being in close proximity in the cell. Furthermore, we investigated the structure of fatty acid synthase within these extracts by cryoEM and this revealed multiple, flexible states of the enzyme in adaptation to its association with other complexes, thus exemplifying the need for in situ studies. As the components of the captured protein communities are known—at both the protein and complex levels—this study constitutes another step forward toward a molecular understanding of subcellular organization.

Unexpected Formation of Low Amounts of (R)-Configurated anteiso-Fatty Acids in Rumen Fluid Experiments

Anteiso-fatty acids (aFA) with odd carbon number are a class of branched-chain fatty acids (BCFA) mainly produced by bacteria. Bacterial sources are also made responsible for their occurrence in the low percent-range in lipids of ruminants (meat and milk) and fish. aFAs are chiral molecules and typically occur predominantly in form of (S)-enantiomers, and their primary precursor has been noted to be isoleucine. Yet, low proportions of (R)-aFAs were also detected in fish and cheese samples. Here we investigated the potential formation of (R)-aFAs by means of incubation experiments with rumen fluid from fistulated cows. Supplementation of rumen fluid with both L- and DL-isoleucine, resulted in a significant (α <0.05) increase of the aFA concentrations but in both cases enantiopure (S)-aFAs were observed. By contrast, incubations without addition of any isoleucine lead to a significant (α <0.05) formation of small proportions of (R)-aFAs similarly to those previously observed in fish and cheese. These results were consistently reproduced in three different years with rumen fluid from different cows fed different diets. All findings point to the existence of a further biosynthesis pathway of aFAs with different stereospecificity than the classic one using isoleucine as primer.

Predictions of methane emission levels and categories based on milk fatty acid profiles from dairy cows

Milk fatty acid (MFA) have already been used to model methane (CH4) emissions from dairy cows. However, the data sets used to develop these models covered limited variation in dietary conditions, reducing the robustness of the predictions. In this study, a data set containing 140 observations from nine experiments (41 Holstein cows) was used to develop models predicting CH4 expressed as g/day, g/kg dry matter intake (DMI) and g/kg milk. The data set was divided into a training (n=112) and a test data set (n=28) for model development and validation, respectively. A generalized linear mixed model was fitted to the data using the marginal R 2 (m) and the Akaike information criterion to evaluate the models. The coefficient of determination of validation (R 2 (v)) for different models developed ranged between 0.18 and 0.41. Form the intake-related parameters, only inclusion of total DMI improved the prediction (R 2 (v)=0.58). In addition, in an attempt to further explore the relationships between MFA and CH4 emissions, the data set was split into three categories according to CH4 emissions: LOW (lowest 25% CH4 emissions); HIGH (highest 25% CH4 emissions); and MEDIUM (50% remaining observations). An ANOVA revealed that concentrations of several MFA differed for observations in HIGH compared with observations in LOW. Furthermore, the Gini coefficient was used to describe the MFA distribution for groups of MFA in each CH4 emission category. The relative distribution of the MFA, particularly of the odd- and branched-chain fatty acids and mono-unsaturated fatty acids of observations in category HIGH differed from those in the other categories. Finally, in an attempt to validate the potential of MFA to identify cases of high or low emissions, the observations were re-classified into HIGH, MEDIUM and LOW according to the proportion of each individual MFA. The proportion of observations correctly classified were recorded. This was done for each individual MFA and for the calculated Gini coefficients, finding that a maximum of 67% of observations were correctly classified as HIGH CH4 (trans-12 C18:1) and a maximum of 58% of observations correctly classified as LOW CH4 (cis-9 C17:1). Gini coefficients did not improve this classification. These results suggest that MFA are not yet reliable predictors of specific amounts of CH4 emitted by a cow, while holding a modest potential to differentiate cases of high or low emissions.

Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate

Lactococcus lactis is essential for most cheese making, and this mesophilic bacterium has its growth optimum around 30 °C. We have, through adaptive evolution, isolated a mutant TM29 that grows well up to 39 °C, and continuous growth at 40 °C is possible if pre-incubated at a slightly lower temperature. At the maximal permissive temperature for the wild-type, 38 °C, TM29 grows 33% faster and has a 12% higher specific lactate production rate than its parent MG1363, which results in fast lactate accumulation. Genome sequencing was used to reveal the mutations accumulated, most of which were shown to affect thermal tolerance. Of the mutations with more pronounced effects, two affected expression of single proteins (chaperone; riboflavin transporter), two had pleiotropic effects (RNA polymerase) which changed the gene expression profile, and one resulted in a change in the coding sequence of CDP-diglyceride synthase. A large deletion containing 10 genes was also found to affect thermal tolerance significantly. With this study we demonstrate a simple approach to obtain non-GMO derivatives of the important L. lactis that possess properties desirable by the industry, e.g. thermal robustness and increased rate of acidification. The mutations we have identified provide a genetic basis for further investigation of thermal tolerance.

Fatty acids in bacterium Dietzia sp. grown on simple and complex hydrocarbons determined as FAME by GC-MS

The influence of growth substrates on the fatty acids produced by Dietzia sp. A14101 has been studied to investigate how qualitative and semi-quantitative information on fatty acids correlates with the ability of this strain to access and utilize a wide range of water-immiscible HC-substrates by modifying the FA content and thus also the properties of the cellular membrane. After incubation on different substrates and media, the profiles of fatty acids (FA) were analyzed by gas chromatography and mass spectrometry (GC-MS). The equivalent chain length (ECL) index calibration system was employed to identify FA. The effect of each substrate on the cell surface charge and on the hydrophobicity of the cellular membrane was also investigated. The results indicate that the variation of the content of saturated fatty acids (SAT-FA) versus mono-unsaturated fatty acids (MUFA) was found to be the most pronounced while branched FA exhibited much less variation in spite of different substrate regimes. The regulation of the ratio of SAT-FA and MUFA seems to be coupled with the regulation of the charge and hydrophobicity of the outer cellular surface. The exposure to a water immiscible substrate led to the development of the negative cellular surface charge, production of carotenoid-type pigments and increased hydrophobicity of the cellular surface. The specific aspects of the adaptation mechanism could have implications for bioremediation and/or (M)EOR applications.

Conformational diversity of bacterial FabH: implications for molecular recognition specificity

The molecular basis of variable substrate and inhibitor specificity of the highly conserved bacterial fatty acid synthase enzyme, FabH, across different bacterial species remains poorly understood. In the current work, we explored the conformational diversity of FabH enzymes to understand the determinants of diverse interaction specificity across Gram-positive and Gram-negative bacteria. Atomistic molecular dynamics simulations reveal that FabH from E. coli and E. faecalis exhibit distinct native state conformational ensembles and dynamic behaviors. Despite strikingly similar substrate binding pockets, hot spot assessment using computational solvent mapping identified quite different favorable binding interactions between the two homologs. Our data suggest that FabH utilizes protein dynamics and seemingly minor sequence and structural differences to modulate its molecular recognition and substrate specificity across bacterial species. These insights will potentially facilitate the rational design and development of antibacterial inhibitors against FabH enzymes.

Characterizing estuarine plume discharge into the coastal ocean using fatty acid biomarkers and pigment analysis

The transformation of estuaries by human activities continues to alter the biogeochemical balance of the coastal ocean. The disruption of this balance can negatively impact the provision of goods and services, including fisheries, commerce and transportation, recreation and esthetic enjoyment. Here we examine a link, between the Elkhorn Slough and the coastal ocean in Monterey Bay, California (USA) using a novel application of fatty acid and pigment analysis. Fatty acid analysis of filtered water samples showed biologically distinct water types between the Elkhorn Slough plume and the receiving waters of the coastal ocean. A remarkable feature of the biological content of the plume entering the coastal ocean was the abundance of bacteria-specific fatty acids, which correlated well with concentrations of colored dissolved organic matter (CDOM). Pigment analysis showed that plume waters contained higher concentrations of diatoms and cryptophytes, while the coastal ocean waters showed higher relative concentrations of dinoflagellates. Bacteria and cryptophytes can provide a source of labile, energy-rich organic matter that may be locally important as a source of food for pelagic and benthic communities. Surface and depth surveys of the plume show that the biogeochemical constituents of the slough waters are injected into the coastal waters and become entrained in the northward flowing, nearshore current of Monterey Bay. Transport of these materials to the northern portion of the bay can fuel a bloom incubator, which exists in this region. This study shows that fatty acid markers can reveal the biogeochemical interactions between estuaries and the coastal ocean and highlights how man-made changes have the potential to influence coastal ecological change.

Diversity of secondary metabolites from marine Bacillus species: chemistry and biological activity

Marine Bacillus species produce versatile secondary metabolites including lipopeptides, polypeptides, macrolactones, fatty acids, polyketides, and isocoumarins. These structurally diverse compounds exhibit a wide range of biological activities, such as antimicrobial, anticancer, and antialgal activities. Some marine Bacillus strains can detoxify heavy metals through reduction processes and have the ability to produce carotenoids. The present article reviews the chemistry and biological activities of secondary metabolites from marine isolates. Side by side, the potential for application of these novel natural products from marine Bacillus strains as drugs, pesticides, carotenoids, and tools for the bioremediation of heavy metal toxicity are also discussed.

Aerobic biodegradation kinetics and mineralization of six petrodiesel/soybean-biodiesel blends

The aerobic biodegradation kinetics and mineralization of six petrodiesel/soybean-biodiesel blends (B0, B20, B40, B60, B80, and B100), where B100 is 100% biodiesel, were investigated by acclimated cultures. The fatty acid methyl esters (FAMEs) of biodiesel were found to undergo rapid abiotic transformation in all experiments. The C10-C21 n-alkanes of petrodiesel were metabolized at significantly higher microbial utilization rates in the presence of biodiesel. The rates of mineralization of the blends were also enhanced in the presence of biodiesel; yet a similar enhancement in the extent of mineralization was not observed. Abiotic fuel-blends/aqueous-phase equilibration experiments revealed that the FAMEs of biodiesel were capable of cosolubilizing the n-alkanes of petrodiesel, a mechanism that fully explains the faster utilization and mineralization kinetics of petrodiesel in the presence of biodiesel without necessarily enhancing the extent of biomineralization. The biodegradation of six targeted aromatic compounds present in petrodiesel was also influenced by the amount of biodiesel in a blend. While toluene, o-xylene, and tetralin were not degraded in the B0 and B20 treatments, all of the targeted aromatic compounds were degraded to below detection limits in the B40 and B80 treatments. Biomass acclimated to B60, however, was unable to degrade most of the aromatic compounds. These results indicate that the amount of biodiesel in a blend significantly affects the absolute and relative abundance of the dissolved and bioavailable constituents of biodiesel and petrodiesel in a way that can considerably alter the biodegrading capacity of microbial cultures.

Adaptation dynamics of Clostridium butyricum in high 1,3-propanediol content media

Aim of the present study was to evaluate the effect of exogenous additions of 1,3-propanediol (1,3-PDO) on microbial growth and metabolites production of Clostridium butyricum VPI 1718 strain, during crude glycerol fermentation. Preliminary batch cultures in anaerobic Duran bottles revealed that early addition of 1,3-PDO caused growth cessation in rather low quantities (15 g/L), while 1,3-PDO additions during the middle exponential growth phase up to 70 g/L resulted in an almost linear decrease of the specific growth rate (μ), accompanied by reduced glycerol assimilation, with substrate consumption being used mainly for energy of maintenance requirements. During batch trials in a 3-L bioreactor, the strain proved able to withstand more than 70 g/L of both biologically produced and externally added 1,3-PDO, whereas glycerol assimilation and metabolite production were carried on at a lower rate. Adaptation of the strain in high 1,3-PDO concentration environments was validated during its continuous cultivation with pulses of 1,3-PDO in concentrations of 31 and 46 g/L, where no washout phenomena were noticed. As far as C. butyricum cellular lipids were concerned, during batch bioreactor cultivations, 1,3-PDO addition was found to favor the biosynthesis of unsaturated fatty acids. Also, fatty acid composition was studied during continuous cultures, in which additions of 1,3-PDO were performed at steady states. Lipids were globally more saturated compared to batch cultures, while by monitoring of the transitory phases, it was noticed that the gradual diol washout had an evident impact in the alteration of the fatty acid composition, by rendering them more unsaturated.

Characterization of Pseudomonas aeruginosa fatty acid profiles in biofilms and batch planktonic cultures

The fatty acid composition of Pseudomonas aeruginosa PAO1 was compared between biofilm and batch planktonic cultures. Strain PAO1 biofilms were able to maintain a consistent fatty acid profile for up to 6 days, whereas strain PAO1 batch planktonic cultures showed a gradual loss of cis-monounsaturated fatty acids over 4 days. Biofilms exhibited a greater proportion of hydroxy fatty acids but a lower proportion of both cyclopropane fatty acids and saturated fatty acids (SAFAs). SAFAs with ≥16 carbons, in particular, decreased in biofilms when compared with that in batch planktonic cultures. A reduced proportion of SAFAs and a decline in overall fatty acid chain length indicate more fluidic biophysical properties for cell membranes of P. aeruginosa in biofilms. Separating the biofilms into 2 partitions and comparing their fatty acid compositions revealed additional trends that were not observed in the whole biofilm: the shear-nonremovable layer consistently showed greater proportions of hydroxy fatty acid than the bulk liquid + shear-removable portion of the biofilm. The shear-nonremovable portion demonstrated a relatively immediate decline in the proportion of monounsaturated fatty acids between days 2 and 4; which was offset by an increase in the proportion of cyclopropane fatty acids, specifically 19:0cyc(11,12). Simultaneously, the shear-removable portion of the biofilm showed an increase in the proportion of trans-monounsaturated fatty acids and cyclopropane fatty acids.

Differences in fatty acid composition between vegetative cells and N(2)-fixing vesicles of Frankia sp. strain CpI1

When growing on N(2), actinomycetes from the genus Frankia form multicellular structures that contain nitrogenase. The structures are referred to as vesicles and are indistinguishable from vesicles formed when Frankia sp. are in root-nodule symbioses. Vesicles isolated from N(2)-grown cells of Frankia sp. strain CpI1 had a significantly higher amount and different composition of fatty acids than did vegetative cells recovered from NH(4) (+)-containing medium. Lipids from vesicles, whole cells grown on N(2), and whole cells grown on NH(4) (+) were fractionated by silicic acid chromatography into neutral lipids, glycolipids, and polar lipids. The fatty acids were transesterified by methanolysis and analyzed by gas chromatography and mass spectrometry. Vesicles had considerably higher amounts of fatty acids in the neutral and glycolipid fractions but lower amounts of polar lipid fatty acids than did vegetative cells. Polar lipids from vesicles had a higher proportion of mono-unsaturated and cyclopropane fatty acids and a lower proportion of isobranched fatty acids than did polar lipids from NH(4) (+)-grown or N(2)-grown cells. The neutral lipid and glycolipid fractions contained several long-chain compounds with molecular ions at m/z 408 and 410. The proportions of these compounds were significantly higher in the lipids from vesicles than from vegetative cells. These results suggest that lipids in vesicles might be involved in the protection of nitrogenase from O(2) and suggest a parallel with the glycolipids involved in protecting nitrogenase from O(2) in the cyanobacterial heterocysts.

Distribution of polyunsaturated Fatty acids in bacteria present in intestines of deep-sea fish and shallow-sea poikilothermic animals

The lipid and fatty acid compositions in nine obligate and facultative barophilic bacteria isolated from the intestinal contents of seven deep-sea fish were determined. Phospholipid compositions were simple, with phosphatidylethanolamine and phosphatidylglycerol predominating in all strains. Docosahexaenoic acid (DHA; 22:6n-3), which has not been reported in procaryotes except for deep-sea bacteria, was found to be present in eight strains at a level of 8.1 to 21.5% of total fatty acids. In the other strain, eicosapentaenoic acid (EPA; 20:5n-3) was present at a level of 31.5% of total fatty acids. Other fatty acids observed in all strains were typical of marine gram-negative bacteria. Subcultures from pouches prepared from intestinal contents of five deep-sea fish by the most-probable-number (MPN) method were analyzed for fatty acids, and all subcultures contained DHA and/or EPA. Accordingly, viable cell counts of bacteria containing DHA and EPA were estimated at a maximum of 1.3 x 10(sup8) and 2.4 x 10(sup8) cells per ml, respectively, and accounted for 14 and 30%, respectively, of the total cell counts in the intestinal contents of the deep-sea fish. In the case of 10 shallow-sea poikilothermic animals having bacterial populations of 1.1 x 10(sup6) to 1.9 x 10(sup9) CFU per ml in intestinal contents, no DHA was found in the 112 isolates examined, while production of EPA was found in 40 isolates from cold- and temperate-sea samples. These results suggest that DHA and EPA are involved in some adaptations of bacteria to low temperature and high pressure.

Isolation and characterization of a mutant of the marine bacterium Alcanivorax borkumensis SK2 defective in lipid biosynthesis

In many microorganisms, the key enzyme responsible for catalyzing the last step in triacylglycerol (TAG) and wax ester (WE) biosynthesis is an unspecific acyltransferase which is also referred to as wax ester synthase/acyl coenzyme A (acyl-CoA):diacylglycerol acyltransferase (WS/DGAT; AtfA). The importance and function of two AtfA homologues (AtfA1 and AtfA2) in the biosynthesis of TAGs and WEs in the hydrocarbon-degrading marine bacterium Alcanivorax borkumensis SK2 have been described recently. However, after the disruption of both the AtfA1 and AtfA2 genes, reduced but substantial accumulation of TAGs was still observed, indicating the existence of an alternative TAG biosynthesis pathway. In this study, transposon-induced mutagenesis was applied to an atfA1 atfA2 double mutant to screen for A. borkumensis mutants totally defective in biosynthesis of neutral lipids in order to identify additional enzymes involved in the biosynthesis of these lipids. At the same time, we have searched for a totally TAG-negative mutant in order to study the function of TAGs in A. borkumensis. Thirteen fluorescence-negative mutants were identified on Nile red ONR7a agar plates and analyzed for their abilities to synthesize lipids. Among these, mutant 2 M(131) was no longer able to synthesize and accumulate TAGs if pyruvate was used as the sole carbon source. The transposon insertion was localized in a gene encoding a putative cytochrome c family protein (ABO_1185). Growth and TAG accumulation experiments showed that the disruption of this gene resulted in the absence of TAGs in 2 M(131) but that growth was not affected. In cells of A. borkumensis SK2 grown on pyruvate as the sole carbon source, TAGs represented about 11% of the dry weight of the cells, while in the mutant 2 M(131), TAGs were not detected by thin-layer and gas chromatography analyses. Starvation and lipid mobilization experiments revealed that the lipids play an important role in the survival of the cells. The function of neutral lipids in A. borkumensis SK2 is discussed.

Ecology of speciation in the genus Bacillus

Microbial ecologists and systematists are challenged to discover the early ecological changes that drive the splitting of one bacterial population into two ecologically distinct populations. We have aimed to identify newly divergent lineages ("ecotypes") bearing the dynamic properties attributed to species, with the rationale that discovering their ecological differences would reveal the ecological dimensions of speciation. To this end, we have sampled bacteria from the Bacillus subtilis-Bacillus licheniformis clade from sites differing in solar exposure and soil texture within a Death Valley canyon. Within this clade, we hypothesized ecotype demarcations based on DNA sequence diversity, through analysis of the clade's evolutionary history by Ecotype Simulation (ES) and AdaptML. Ecotypes so demarcated were found to be significantly different in their associations with solar exposure and soil texture, suggesting that these and covarying environmental parameters are among the dimensions of ecological divergence for newly divergent Bacillus ecotypes. Fatty acid composition appeared to contribute to ecotype differences in temperature adaptation, since those ecotypes with more warm-adapting fatty acids were isolated more frequently from sites with greater solar exposure. The recognized species and subspecies of the B. subtilis-B. licheniformis clade were found to be nearly identical to the ecotypes demarcated by ES, with a few exceptions where a recognized taxon is split at most into three putative ecotypes. Nevertheless, the taxa recognized do not appear to encompass the full ecological diversity of the B. subtilis-B. licheniformis clade: ES and AdaptML identified several newly discovered clades as ecotypes that are distinct from any recognized taxon.

Use of fatty acid methyl ester profiles for discrimination of Bacillus cereus T-strain spores grown on different media

The goal of this study was to determine if cellular fatty acid methyl ester (FAME) profiling could be used to distinguish among spore samples from a single species (Bacillus cereus T strain) that were prepared on 10 different medium formulations. To analyze profile differences and identify FAME biomarkers diagnostic for the chemical constituents in each sporulation medium, a variety of statistical techniques were used, including nonmetric multidimensional scaling (nMDS), analysis of similarities (ANOSIM), and discriminant function analysis (DFA). The results showed that one FAME biomarker, oleic acid (18:1 omega9c), was exclusively associated with spores grown on Columbia agar supplemented with sheep blood and was indicative of blood supplements that were present in the sporulation medium. For spores grown in other formulations, multivariate comparisons across several FAME biomarkers were required to discern profile differences. Clustering patterns in nMDS plots and R values from ANOSIM revealed that dissimilarities among FAME profiles were most pronounced when spores grown with disparate sources of complex additives or protein supplements were compared (R > 0.8), although other factors also contributed to FAME differences. DFA indicated that differentiation could be maximized with a targeted subset of FAME variables, and the relative contributions of branched FAME biomarkers to group dissimilarities changed when different media were compared. When taken together, these analyses indicate that B. cereus spore samples grown in different media can be resolved with FAME profiling and that this may be a useful technique for providing intelligence about the production methods of Bacillus organisms in a forensic investigation.