Gas chromatographic-mass spectrometric detection of 2- and 3-hydroxy fatty acids as methyl esters from soil, sediment and biofilm

Cross-family transfer of the Arabidopsis cell-surface immune receptor LORE to tomato confers sensing of 3-hydroxylated fatty acids and enhanced disease resistance

Plant pathogens pose a high risk of yield losses and threaten food security. Technological and scientific advances have improved our understanding of the molecular processes underlying host-pathogen interactions, which paves the way for new strategies in crop disease management beyond the limits of conventional breeding. Cross-family transfer of immune receptor genes is one such strategy that takes advantage of common plant immune signalling pathways to improve disease resistance in crops. Sensing of microbe- or host damage-associated molecular patterns (MAMPs/DAMPs) by plasma membrane-resident pattern recognition receptors (PRR) activates pattern-triggered immunity (PTI) and restricts the spread of a broad spectrum of pathogens in the host plant. In the model plant Arabidopsis thaliana, the S-domain receptor-like kinase LIPOOLIGOSACCHARIDE-SPECIFIC REDUCED ELICITATION (AtLORE, SD1-29) functions as a PRR, which senses medium-chain-length 3-hydroxylated fatty acids (mc-3-OH-FAs), such as 3-OH-C10:0, and 3-hydroxyalkanoates (HAAs) of microbial origin to activate PTI. In this study, we show that ectopic expression of the Brassicaceae-specific PRR AtLORE in the solanaceous crop species Solanum lycopersicum leads to the gain of 3-OH-C10:0 immune sensing without altering plant development. AtLORE-transgenic tomato shows enhanced resistance against Pseudomonas syringae pv. tomato DC3000 and Alternaria solani NL03003. Applying 3-OH-C10:0 to the soil before infection induces resistance against the oomycete pathogen Phytophthora infestans Pi100 and further enhances resistance to A. solani NL03003. Our study proposes a potential application of AtLORE-transgenic crop plants and mc-3-OH-FAs as resistance-inducing biostimulants in disease management.

Hydroxy fatty acids in the surface Earth system

Lipids are ubiquitous and highly abundant in a wide range of organisms and have been found in various types of environmental media. These molecules play a crucial role as organic tracers by providing a chemical perspective on viewing the material world, as well as offering a wealth of information on metabolic activities. Among the diverse lipid compounds, hydroxy fatty acids (HFAs) with one to multiple hydroxyl groups attached to the carbon chain stand out as important biomarkers for different sources of organic matter. HFAs are widespread in nature and are involved in biotransformation and oxidation processes in living organisms. The unique chemical and physical properties attributed to the hydroxyl group make HFAs ideal biomarkers in biomedicine and environmental toxicology, as well as organic geochemistry. The molecular distribution patterns of HFAs can be unique and diagnostic for a given class of organisms, including animals, plants, and microorganisms. Thus, HFAs can act as a valuable proxy for understanding the ecological relationships between different organisms and their environment. Furthermore, HFAs have numerous industrial applications due to their higher reactivity, viscosity, and solvent miscibility. This review paper integrates the latest research on the sources and chemical analyses of HFAs, as well as their applications in industrial/medicinal production and as biomarkers in environmental studies. This review article also provides insights into the biogeochemical cycles of HFAs in the surface Earth system, highlighting the importance of these compounds in understanding the complex interactions between living organisms and the environment.

Membrane lipid adaptation of soil Bacteroidetes isolates to temperature and pH

3-hydroxy fatty acids (3-OH FAs) are characteristic components of the Gram-negative bacterial membrane, recently proposed as promising temperature and pH (paleo) proxies in soil. Nevertheless, to date, the relationships between the 3-OH FA distribution and temperature/pH are only based on empirical studies, with no ground truthing work at the microbial level. This work investigated the influence of growth temperature and pH on the lipid composition of three strains of soil Gram-negative bacteria belonging to the Bacteroidetes phylum. Even though non-hydroxy FAs were more abundant than 3-OH FAs in the investigated strains, our results suggest that 3-OH FAs are involved in the membrane adaptation of these bacteria to temperature. The strains shared a common adaptation mechanism to temperature, with a significant increase in the ratio of anteiso vs. iso or normal 3-OH FAs at lower temperature. In contrast with temperature, no common adaptation mechanism to pH was observed, as the variations in the FA lipid profiles differed from one strain to another. We suggest that models reconstructing environmental changes in soils should include the whole suite of 3-OH FAs present in the membrane of Gram-negative bacteria, as all of them could be influenced by temperature or pH at the microbial level.

A new method for detecting mixed bacteria based on multi-wavelength transmission spectroscopy technology

Previously, we successfully realized the identification of a single species of bacteria based on the multi-wavelength transmission spectrum of bacteria. The current research is focused on realizing the spectral analysis of mixed bacteria. Principal component analysis-Monte Carlo (PCA-MC) model was developed for the implementation of spectral separation of mixed bacteria by obtaining the ratio of components. And, the separated spectrum was regarded as the model input of the neural network concentration inversion model to obtain the concentration of each bacteria in the mix. Mean relative errors in component analysis of mixing S.aureus with K.pneumoniae, mixing S.aureus with S.typhimurium twice, mixing K.pneumoniae with S.typhimurium are 3%, 2%, 3.9% and 6.1%, respectively. The coefficient of determination (R²) of validation set and test set are 0.9947 and 0.9954 in concentration inversion model. The results show that this method can quickly and accurately determine the component ratio and concentration information in the mixed bacteria. A new method was proposed to separate the spectrum of mixed bacteria effectively and measure its concentration quickly, which makes a big step forward in the detection and online monitoring of waterborne microbial contamination based on multi-wavelength transmission spectroscopy.

Artificial neural networks combined multi-wavelength transmission spectrum feature extraction for sensitive identification of waterborne bacteria

Present research is focused on the rapid and accurate identification of bacterial species based on artificial neural networks combined with spectral data processing technology. The spectra of different bacterial species in the logarithmic growth phase were obtained. Model input features were extracted from the raw spectra using signal processing techniques, including normalization, principal component analysis (PCA) and area-based feature value extraction. The identification models based on artificial neural network of back propagation neural networks (BPNN), generalized regression neural networks (GRNN) and probabilistic neural networks (PNN) were developed using the extracted features in order to ascertain whether the different species of bacteria could be differentiated. The performance of developed models and its corresponding signal processing techniques is tested by the recognition accuracy of validation set and test set, and model error. The maximum recognition accuracy of normalized spectrum combined with BPNN was 95.5% (error: 10%, test accuracy: 100%). The total recognition accuracy of PCA-reduced features (200-400 nm) combined with GRNN resulted in 96.3%~96.8% (error: 3.3%~6.7%, test accuracy: 97.5%~100%). While the overall recognition accuracy of area-based features combined with GRNN reached 97.3% with test accuracy of 100% (model error: 5.0%). Choosing of model and signal processing techniques has a positive influence on improving classification accuracy, so as to make it possible to realize the rapid detection and online monitoring of waterborne microbial contamination.

Detailed analysis of the fatty acid composition of six plant-pathogenic bacteria

Bacteria show distinct and characteristic fatty acid (FA) patterns which can be modified by environmental conditions. In this study, we cultivated six plant-pathogenic bacteria of agricultural concern and performed a detailed analysis of the fatty acid composition. The study covered four strains of the gram-negative Xanthomonas campestris pathovar (pv) campestris (Xcc), Xanthomonas perforans (Xp), Acidovorax citrulli (Ac) and Pseudomonas syringae pv. tomato (Pst), and two strains of the gram-positive Clavibacter michiganensis subsp. michiganensis (Cmm) and Streptomyces scabies (Ssc). After cultivation, freeze-dried bacteria samples were transesterified and analysed by gas chromatography with mass spectrometry in full scan and selected ion monitoring (SIM) modes. Altogether, 44 different FAs were detected in the six strains with individual contributions of 0.01-43.8% to the total FAs. The variety in the six strains ranged between 12 and 31 individual FAs. The FA composition of Xcc, Xp, Cmm and Ssc were dominated by iso- and anteiso-fatty acids (especially i15:0, a15:0, i16:0), which is typical for most bacteria. In contrast to this, Ac and Pst showed only saturated and monounsaturated FAs. Four of the six bacteria showed similar FA patterns as reported before in the literature. Differences were observed in the case of Cmm where many more FAs were detected in the present study. In addition, to the best of our knowledge, the FA pattern of Xp was presented for the first time.

Fatty Acid and Hopanoid Adaption to Cold in the Methanotroph Methylovulum psychrotolerans

Three strains of aerobic psychrotolerant methanotrophic bacteria Methylovulum psychrotolerans, isolated from geographically remote low-temperature environments in Northern Russia, were grown at three different growth temperatures, 20, 10 and 4°C and were found to be capable of oxidizing methane at all temperatures. The three M. psychrotolerans strains adapted their membranes to decreasing growth temperature by increasing the percent of unsaturated fatty acid (FAs), both for the bulk and intact polar lipid (IPL)-bound FAs. Furthermore, the ratio of βOH-C_16:0 to n-C_16:0 increased as growth temperature decreased. The IPL head group composition did not change as an adaption to temperature. The most notable hopanoid temperature adaptation of M. psychrotolerans was an increase in unsaturated hopanols with decreasing temperature. As the growth temperature decreased from 20 to 4°C, the percent of unsaturated M. psychrotolerans bulk-FAs increased from 79 to 89 % while the total percent of unsaturated hopanoids increased from 27 to 49 %. While increased FA unsaturation in response to decreased temperature is a commonly observed response in order to maintain the liquid-crystalline character of bacterial membranes, hopanoid unsaturation upon cold exposition has not previously been described. In order to investigate the mechanisms of both FA and hopanoid cold-adaption in M. psychrotolerans we identified genes in the genome of M. psychrotolerans that potentially code for FA and hopanoid desaturases. The unsaturation of hopanoids represents a novel membrane adaption to maintain homeostasis upon cold adaptation.

Silver nanoparticles-coated monolithic column for in-tube solid-phase microextraction of monounsaturated fatty acid methyl esters

Based on our developed sodium hyaluronate-functionalized urea-formaldehyde (HA-UF) monolith, a silver nanoparticles-coated monolithic column has been fabricated via the interaction between silver nanoparticles (Ag NPs) and HA. The successful coating of Ag NPs on the parent monolith was proven by SEM, EDAX, UV-vis spectrum and XPS. Nitrogen adsorption desorption isotherms and Barret-Joyner-Halenda (BJH) pore size distributions of the parent and resultant monolith were also performed. Due to the Ag⁺-like affinity interaction caused by the contact of unsaturated compounds and Ag NPs, the Ag NPs-coated monolith showed satisfactory extraction efficiency towards these compounds, and was applied for in-tube solid-phase microextraction (SPME) of monounsaturated fatty acid methyl esters (MUFAMEs). Several factors for in-tube SPME, such as ACN percentage in the sampling solution, elution volume, sampling and elution flow rate, were investigated with respect to the extraction efficiency of model MUFAMEs. Under the optimized SPME conditions, a simple in tube SPME-Ag⁺-HPLC method for detection of model MUFAMEs has been proposed, the limits of detection (LODs) were less than 5.2 μg/kg, and the recoveries of spiked French fry samples were ranged from 86.6% to 96.1% with relative standard deviations (RSDs) less than 5.2%. This study provided an Ag NPs-coated monolith with good reproducibility and repeatable extraction performance, and developed an efficient method for in-tube SPME of MUFAMEs in practical food samples.

Biofilm vs. Planktonic Lifestyle: Consequences for Pesticide 2,4-D Metabolism by Cupriavidus necator JMP134

The development of bacterial biofilms in natural environments may alter important functions, such as pollutant bioremediation by modifying both the degraders' physiology and/or interactions within the matrix. The present study focuses on the influence of biofilm formation on the metabolism of a pesticide, 2,4-dichlorophenoxyacetic acid (2,4-D), by Cupriavidus necator JMP134. Pure cultures were established in a liquid medium with 2,4-D as a sole carbon source with or without sand grains for 10 days. Bacterial numbers and 2,4-D concentrations in solution were followed by spectrophotometry, the respiration rate by gas chromatography and the surface colonization by electron microscopy. In addition, isotopic techniques coupled with Fatty Acid Methyl Ester (FAME) profiling were used to determine possible metabolic changes. After only 3 days, approximately 80% of the cells were attached to the sand grains and microscopy images showed that the porous medium was totally clogged by the development of a biofilm. After 10 days, there was 25% less 2,4-D in the solution in samples with sand than in control samples. This difference was due to (1) a higher (+8%) mineralization of 2,4-D by sessile bacteria and (2) a retention (15%) of 2,4-D in the biofilm matrix. Besides, the amount of carbohydrates, presumably constituting the biofilm polysaccharides, increased by 63%. Compound-specific isotope analysis revealed that the FAME isotopic signature was less affected by the biofilm lifestyle than was the FAME composition. These results suggest that sessile bacteria differ more in their anabolism than in their catabolism compared to their planktonic counterparts. This study stresses the importance of considering interactions between microorganisms and their habitat when studying pollutant dynamics in porous media.

AFM structural characterization of drinking water biofilm under physiological conditions

Insights into the complex morphology of multi-species drinking water biofilm using atomic force microscopy (AFM).

Depth, soil type, water table, and site effects on microbial community composition in sediments of pesticide-contaminated aquifer

Microbial community compositions in pesticide-contaminated aquifers have not been studied, although such information is important for remediation and maintaining freshwater sources clean under changing climate. Therefore, phospholipid (PLFAs), glycolipid (GLFAs), and neutral lipid (NLFAs) fatty acids were determined from sand and clay sediments at depths of 0.3-24.8 m, all contaminated with triazines and dichlobenil/2,6-dichlorobenzamide. The portion of fungi and Gram-negative bacteria at 0.3 m was greater than at 0.8 m, where the percentage of Gram-positive bacteria, actinobacteria, and sulfate-reducing bacteria (SRB) increased. In deeper sediments, microbial biomass, activity, and diversity decreased. Clay sediments seemed to serve as a reservoir for slow pesticide elution to groundwater, and their biomarker portion for all bacteria except actinobacteria was greater than in sand sediments. The slow pesticide dissipation seemed to occur in the main groundwater flow zone, resulting in nitrogen release simultaneously with organic matter elution from gardening and bank filtration. As a result, microbial biomass, activity, and diversity were increased. This shift in conditions towards that in surface soil may be appropriate for enhanced natural attenuation of pesticides in groundwater sources.

The rhizobacterium Arthrobacter agilis produces dimethylhexadecylamine, a compound that inhibits growth of phytopathogenic fungi in vitro

Plant diseases caused by fungal pathogens such as Botrytis cinerea and the oomycete Phytophthora cinnamomi affect agricultural production worldwide. Control of these pests can be done by the use of fungicides such as captan, which may have deleterious effects on human health. This study demonstrates that the rhizobacterium Arthrobacter agilis UMCV2 produces volatile organic compounds that inhibit the growth of B. cinerea in vitro. A single compound from the volatile blends, namely dimethylhexadecylamine (DMHDA), could inhibit the growth of both B. cinerea and P. cinnamomi when supplied to the growth medium in low concentrations. DMHDA also inhibited the growth of beneficial fungi Trichoderma virens and Trichoderma atroviride but at much higher concentrations. DMHDA-related aminolipids containing 4, 8, 10, 12, and 14 carbons in the alkyl chain were tested for their inhibitory effect on the growth of the pathogens. The results show that the most active compound from those tested was dimethyldodecylamine. This effect correlates with a decrease in the number of membrane lipids present in the mycelium of the pathogen including eicosanoic acid, (Z)-9-hexadecenoic acid, methyl ester, and (Z)-9-octadecenoic acid, methyl ester. Strawberry leaflets treated with DMHDA were not injured by the compound. These data indicate that DMHDA and related compounds, which can be produced by microorganisms may effectively inhibit the proliferation of certain plant pathogens.

Some monohydroxy tetradecanoic acid isomers as novel urease and elastase inhibitors and as new antioxidants

A series of some 3-,6-,7-,9-,12- monohydroxy tetradecanoic acids were evaluated for their antiurease, antielastase and antioxidant activities for the first time in this study. All the test compounds exhibited antioxidant, antielastase and antiurease activities. The relationship between the position of the hydroxy group and the enzyme inhibition effect is studied in this work. The mentioned biological activities are depending on the position of hydroxy group of tetradecanoic acid isomers. The results obtained in this work are indicating that 3-,6-,7-,9-,12-monohydroxy tetradecanoic acid isomers can be used in agriculture, pharmacy and cosmetic industries due to their excellent antielastase, antiurease and antioxidant activities.

Source correlation of biomarkers in a mangrove ecosystem on Santa Catarina Island in southern Brazil

The relative distribution of several compounds identified in four samples of recently deposited sediments of the Itacorubi Mangrove located on the Santa Catarina Island, southern Brazil, was compared with similar data on compounds extracted from fresh leaves of three mangrove species (Avicennia schaueriana, the dominant species in the area, Rhizophora mangle and Laguncularia racemosa) and the Gramineae Spartinna alterniflora. Terpenols, previously identified in mangrove species in northern Brazil, were also found. A. schaueriana mainly contains β-amyrin (90.6 μg g-1 of extractable organic matter); low amounts of friedelin, betulin and germanicol were detected only in the leaf extract of this species. R. mangle also contained a significant amount of β-amyrin and it was the only species where taraxerol was detected. In contrast to the leaves, sediment extracts were dominated by germanicol, α-amyrin and campesterol. Despite its chemical lability, betulin was also detected. Two homologous series of α and ω-hydroxy fatty acids were detected in the acid-alkaline fraction. In spite of being reported in the literature as components of terrigenous plants, saturated ω-hydroxy acids were not identified. Our results indicate that although triterpenols may be used as biomarkers for mangrove-derived organic matter, their relative distribution can change according to the region.

Organic matter in sediments of an acidic mining lake as assessed by lipid analysis. Part I: fatty acids

Fatty acid (FA) patterns of sediments collected from the bottom of an acidic mine pit lake (AML) at different depths (surface sediment: 0 to 1cm; deep sediment: 4 to 5 cm) were studied to characterize microbial communities and the sources of sedimentary organic matter (SOM). Studies were performed on the molecular level utilizing source-specific, diagnostic FA biomarkers. The biomarker-based approach has been used widely in marine sediment studies, but has not been applied for sediments from AMLs so far. Combined FA concentrations in the surface sediment were higher compared to those in the deep sediment (497 vs. 127 μg g(-1)d.w., respectively). This was related to deposition of autochthonous biomass and higher terrestrial plants onto the surface sediment, as well as--to lesser extent--with higher bacterial activity on the sediment-water interface. The FA distribution in both sediments was characterized by a strong even-over-odd preference and was bimodal in nature: there was a cluster at nC(14)-nC(18) characteristic of chiefly autochthonous (algal and bacterial) SOM production, and another cluster at nC(22-28) related to input from higher plants. The FA distribution in the surface sediment pointed to higher terrestrial input compared to autochthonous contribution to SOM (67%:33%) as an estimate. Fingerprinting of viable bacteria was accomplished through signature FA markers including branched C(15) and C(17) surrogates, cyclopropanoic acids, 3-hydroxy (OH) acids and monounsaturated surrogates with unusual double bond localization. The abundance of Gram-negative bacteria was higher in the surface sediment as evidenced by total diagnostic 3-OH-fatty acids (37 μg g(-1) versus 25 μg g(-1)). Potential source taxa in both sediment layers included acidophilic iron- and sulfur-oxidizing bacteria including Acidithiobacillus ferrooxidans. High abundances of terminally branched C(15) and C(17) surrogates in both sediments pointed to sulfate- and iron-reducing bacteria. Signature FAs characteristic of methanotrophs were virtually lacking in both sediments.

The effects of hydroxy fatty acids on the hyphal branching of germinated spores of AM fungi

Two hydroxy fatty acids, tentatively identified previously in carrot root exudates, were tested for their effects on hyphal growth of the arbuscular mycorrhizal (AM) fungus, Gigaspora gigantea (Nicol. and Gerd.) Gerdemann and Trappe. Best results were achieved with a long-term bioassay (7-8d) with nanomolar concentrations throughout the Petri dish in contrast to the rapid microinjection bioassay (16-24h) in which nanogram quantities were injected near growing hyphal tips. When 5nM 2-hydroxy fatty acids of various chain length were tested, the length of the hydroxyl fatty acid was significant since only 2-hydroxytetradecanoic acid (2OH-TDA) and to a slightly lesser degree, 2-hydroxydodecanoic acid (2OH-DDA) induced a hyphal growth response while 2-hydroxydecanoic acid (2OH-DA) and 2-hydroxyhexadecanoic (2OH-HDA) acid did not. The position of the hydroxyl group was critical since 5nM 3-hydroxytetradecanoic acid (3OH-TDA) had no effect on hyphal growth. The length of the non-hydroxy containing straight chain fatty acid, per se, did not appear significant since none of these fatty acids had an effect on hyphal growth. The morphological growth response promoted by 2OH-TDA consisted of multiple lateral branches, spaced fairly regularly apart, along the primary germ tubes as well as some lateral branch formation off the major secondary hyphae. This growth response was identical to that observed when germinated spores were allowed to grow towards cultured carrot roots in vitro. This response to 2OH-TDA also was observed with an unidentified Gigaspora species but no morphological response was observed with Glomus intraradices Schenck and Smith. The results indicate that 2-hydroxy fatty acids are another putative category of root exudate signals perceived by Gigaspora species, stimulating an increase in elongated lateral branches.

Gas chromatography/electron-capture negative ion mass spectrometry for the quantitative determination of 2- and 3-hydroxy fatty acids in bovine milk fat

2- and 3-hydroxy fatty acids (2- and 3-OH-FAs) are bioactive substances reported in sphingolipids and bacteria. Little is known of their occurrence in food. For this reason, a method suitable for the determination of OH-FAs at trace levels in bovine milk fat was developed. OH-FAs (and conventional fatty acids in samples) were converted into methyl esters and the hydroxyl group was derivatized with pentafluorobenzoyl (PFBO) chloride to give PFBO- O-FA methyl esters. These derivatives with strong electron affinity were determined by gas chromatography interfaced to mass spectrometry using electron-capture negative ion in the selected ion monitoring mode (GC/ECNI-MS-SIM). This method proved to be highly sensitive and selective for PFBO-O-FA methyl esters. For the analysis of samples, two internal standards were used. For this purpose, 9,10-dideutero-2-OH-18:0 methyl ester (ISTD-1) from 2-OH-18:1(9 c) methyl ester as well as the ethyl ester of 3-PFBO-O-12:0 (ISTD-2) was synthesized. ISTD-1 served as a recovery standard whereas ISTD-2 was used for GC/MS measurements. The whole-sample cleanup consisted of accelerated solvent extraction of dry bovine milk, addition of ISTD 1, saponification, conversion of fatty acids into methyl esters by use of boron trifluoride, separation of the methyl esters of OH-FAs from nonsubstituted FAs on activated silica, conversion of OH-FAs methyl esters into PFBO-O-FA methyl esters, addition of ISTD-2, and measurement by GC/ECNI-MS-SIM. By this method, ten OH-FAs were quantified in bovine milk fat with high precision in the range from 0.02 +/- 0.00 to 4.49 +/- 0.29 mg/100 g of milk fat.

Suppression of ionization and optimization of assay for 3-hydroxy fatty acids in house dust using ion-trap mass spectrometry

BACKGROUND

3-Hydroxy fatty acids (3-OHFAs), components of lipid A of gram-negative bacteria are useful chemical markers of endotoxin.

METHODS

We analyzed 3-OHFAs in house dust as trimethylsilyl (TMS) methyl ester derivatives in the electron impact ionization mode using gas chromatography ion-trap mass spectrometry. Linear calibrations with r > 0.995 were observed for all the 3-OHFA methyl ester external standards.

RESULTS

Recovery efficiency experiments with house dust demonstrated that accurate quantification requires calibration curves to be subjected to phase separation and solid phase extraction (SPE) because of differing clean-up losses according to chain length of 3-OHFAs. Recovery experiments also demonstrated interference with detection of C16:0 by the ion trap, which may be due to suppression of ionization by a constituent in house dust. Interference was overcome by injecting 1:4 dilutions of derivatized samples. The range of recoveries was 89.3%-111.5% for 3-OHFAs added to house dust. The reproducibility of injections was high (CV for C14:0 = 2.36%). The limit of detection (LOD) was 0.15 ng/mg for each 3-OHFA.

CONCLUSIONS

The modifications we made included: use of 3-hydroxy C11:0 and C13:0 methyl esters as internal standards, subjecting calibration standards to phase separation and SPE; addition of water to phase separation; addition of 1-pentadecanol as a carrier; injecting 1:4 diluted TMS derivatives of 3-OHFAs; and monitoring both m/z 131 and 133 ions to improve stability of area measurements for product ions. This method of optimization establishes an appropriate technique for quantification of 3-OHFAs in house dust.

A survey of the methods for the characterization of microbial consortia and communities

A survey of the available literature on methods most frequently used for the identification and characterization of microbial strains, communities, or consortia is presented. The advantages and disadvantages of the various methodologies were examined from several perspectives including technical, economic (time and cost), and regulatory. The methods fall into 3 broad categories: molecular biological, biochemical, and microbiological. Molecular biological methods comprise a broad range of techniques that are based on the analysis and differentiation of microbial DNA. This class of methods possesses several distinct advantages. Unlike most other commonly used methods, which require the production of secondary materials via the manipulation of microbial growth, molecular biological methods recover and test their source materials (DNA) directly from the microbial cells themselves, without the requirement for culturing. This eliminates both the time required for growth and the biases associated with cultured growth, which is unavoidably and artificially selective. The recovered nucleic acid can be cloned and sequenced directly or subpopulations can be specifically amplified using polymerase chain reaction (PCR), and subsequently cloned and sequenced. PCR technology, used extensively in forensic science, provides researchers with the unique ability to detect nucleic acids (DNA and RNA) in minute amounts, by amplifying a single target molecule by more than a million-fold. Molecular methods are highly sensitive and allow for a high degree of specificity, which, coupled with the ability to separate similar but distinct DNA molecules, means that a great deal of information can be gleaned from even very complex microbial communities. Biochemical methods are composed of a more varied set of methodologies. These techniques share a reliance on gas chromatography and mass spectrometry to separate and precisely identify a range of biomolecules, or else investigate biochemical properties of key cellular biomolecules. Like the molecular biological methods, some biochemical methods such as lipid analyses are also independent of cultured growth. However, many of these techniques are only capable of producing a profile that is characteristic of the microbial community as a whole, providing no information about individual members of the community. A subset of these methodologies are used to derive taxonomic information from a community sample; these rely on the identification of key subspecies of biomolecules that differ slightly but characteristically between species, genera, and higher biological groupings. However, when the consortium is already growing in chemically defined media (as is often the case with commercial products), the rapidity and relatively low costs of these procedures can mitigate concerns related to culturing biases. Microbiological methods are the most varied and the least useful for characterizing microbial consortia. These methods rely on traditional tools (cell counting, selective growth, and microscopic examination) to provide more general characteristics of the community as a whole, or else to narrow down and identify only a small subset of the members of that community. As with many of the biochemical methods, some of the microbiological methods can fairly rapidly and inexpensively create a community profile, which can be used to compare 2 or more entire consortia. However, for taxonomic identification of individual members, microbiological methods are useful only to screen for the presence of a few key predetermined species, whose preferred growth conditions and morphological characteristics are well defined and reproducible.Key words: microbial communities, microbial consortia, characterization methods, taxonomic identification.

Microbiology, chemistry and biofilm development in a pilot drinking water distribution system with copper and plastic pipes

We studied the changes in water quality and formation of biofilms occurring in a pilot-scale water distribution system with two generally used pipe materials: copper and plastic (polyethylene, PE). The formation of biofilms with time was analysed as the number of total bacteria, heterotrophic plate counts and the concentration of ATP in biofilms. At the end of the experiment (after 308 days), microbial community structure, viable biomass and gram-negative bacterial biomass were analysed via lipid biomarkers (phospholipid fatty acids and lipopolysaccharide 3-hydroxy fatty acids), and the numbers of virus-like particles and total bacteria were enumerated by SYBR Green I staining. The formation of biofilm was slower in copper pipes than in the PE pipes, but after 200 days there was no difference in microbial numbers between the pipe materials. Copper ion led to lower microbial numbers in water during the first 200 days, but thereafter there were no differences between the two pipe materials. The number of virus-like particles was lower in biofilms and in outlet water from the copper pipes than PE pipes. Pipe material influenced also the microbial and gram-negative bacterial community structure in biofilms and water.

Microbial community structure and biomass in developing drinking water biofilms

Traditional techniques to study microbes, such as culturable counts, microbial biomass, or microbial activity, do not give information on the microbial ecology of drinking water systems. The aim of this study was to analyze whether the microbial community structure and biomass differed in biofilms collected from two Finnish drinking water distribution systems (A and B) receiving conventionally treated (coagulation, filtration, disinfection) surface water. Phospholipid fatty acid methyl esters (PLFAs) and lipopolysaccharide 3-hydroxy fatty acid methyl esters (LPS 3-OH-FAs) were analyzed from biofilms as a function of water residence time and development time. The microbial communities were rather stabile through the distribution systems, as water residence time had minor effects on PLFA profiles. In distribution system A, the microbial community structure in biofilms, which had developed in 6 weeks, was more complex than those grown for 23 or 40 weeks. The microbial communities between the studied distribution systems differed, possibly reflecting the differences in raw water, water purification processes, and distribution systems. The viable microbial biomass, estimated on the basis of PLFAs, increased with increasing water residence time in both distribution systems. The quantitative amount of LPS 3-OH-FAs increased with increasing development time of biofilms of distribution system B. In distribution system A, LPS 3-OH-FAs were below the detection limit.Key words: biofilm, distribution system, 3-hydroxy fatty acid, microbial community, PLFA.

Derivatization in mass spectrometry-3. Alkylation (arylation)

The review is devoted to alkylation (arylation) as a widely employed derivatization procedure for the protection of OH (carboxylic acids, phosphoric acids, sulfonic acids, alcohols, polyols, phenols, enols), SH (thiols) and NH (amines, amides) groups in order to increase volatility, to improve the chromatographic properties and, if possible, mass spectral properties of derivatives. Chemical aspects of derivatization and various alkylation (arylation) reagents and reaction procedures are described. Specific mass spectral (electron ionization, chemical ionization) features of derivatives helpful in identification, structure elucidation, profiling and quantitative determination of the above-mentioned polar compounds by coupled gas chromatography or high-performance liquid chromatography are discussed. Some common analytical applications of the procedures in organic chemistry, clinical chemistry, environmental chemistry etc. are briefly summarized.

Fatty acids of lipid fractions in extracellular polymeric substances of activated sludge flocs

Phospholipid (PL), glycolipid (GL), and neutral lipid (NL) FA, and the lipopolysaccharide 2- and 3-hydroxy (LPS 2-OH and 3-OH) FA of activated sludges and extracted extracellular polymeric substances (EPS) were determined on samples collected from two wastewater treatment plants. EPS extracted from sludges by means of sonication and cation exchange contained proteins (43.4%), humic-like substances (11.5%), nucleic acids (10.9%), carbohydrates (9.9%), and lipid-bound FA (1.8%). The lipids associated with EPS were composed of GL, PL, NL, and LPS acids in proportions of 61, 21, 16, and 2%, respectively. The profiles of lipid-bound FA in activated sludges and EPS were similar (around 85 separate FA were identified). The FA signatures observed can be attributed to the likely presence of yeasts, fungi, sulfate-reducing bacteria, gram-positive and gram-negative bacteria, and, in lesser quantities, mycobacteria. Comparison of data from the dates of sampling (January and September) showed that there were more unsaturated PLFA in the EPS extracted from the activated sludges sampled in January. This observation could be partly related to microorganism adaptation to temperature variations. The comparison between two wastewater treatment plants showed that the FA profiles were similar, although differences in microbial community structure were also seen. Most of the FA in sludges had an even number of carbons.