Sensitive assay, based on hydroxy fatty acids from lipopolysaccharide lipid A, for Gram-negative bacteria in sediments

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.

The influence of increased precipitation and nitrogen deposition on the litter decomposition and soil microbial community structure in a semiarid grassland

Litter decomposition is a major method in which nutrients are recycled, especially carbon and nitrogen elements, in terrestrial ecosystems. However, how the responses of litter quality and soil microbial communities to global changes alter litter decomposition remains unclear. A 4-year field manipulative experiment based on the litterbag method was conducted in a typical temperate semiarid grassland in China to explore how increased precipitation and nitrogen deposition affect decomposition processes via litter quality and soil microbial communities. Our results showed that water and nitrogen addition treatments could accelerate litter carbon release and promote mass loss through different pathways. Water addition had a direct positive effect on litter decomposition. However, nitrogen addition could indirectly promote litter decomposition by improving litter quality and increasing the bacterial and fungal ratios. The water addition treatment increased litter mass loss by 7.37 %, and the N addition treatments increased litter mass loss by 5.83 %-16.93 %. Moreover, water and nitrogen additions had antagonistic effects on litter decomposition. These findings revealed that litter quality and the soil bacterial to fungal ratio were the factors controlling litter decomposition. The changes in precipitation and nitrogen deposition will impact ecosystem carbon and nitrogen cycling by altering litter decomposition processes in semiarid grassland ecosystems under the context of climate change.

Effects of mycorrhiza and hyphae on the response of soil microbial community to warming in eastern Tibetan Plateau

The effects of mycorrhiza and its external hyphae on the response of soil microbes to global warming remain unclear. This study investigates the role of mycorrhiza and its hyphae in regulating soil microbial community under warming by examining the microbial biomass and composition in the ingrowth cores of arbuscular mycorrhiza (AM) plant, Fargesia nitida, and ectomycorrhiza (ECM) plant, Picea asperata, with/without mycorrhiza/hyphae and experimental warming. The results showed that warming significantly increased the biomass of all soil microbes (by 19.89%-137.48%) and altered the microbial composition in both plant plots without mycorrhiza/hyphae. However, this effect was weakened in the presence of mycorrhiza or hyphae. In F. nitida plots, warming did not significantly affect biomass and composition of most soil microbial groups when mycorrhiza or hyphae were present. In P. asperata plots, warming significantly increased the total and ECM fungi (ECMF) biomass in the presence of hyphae (p < 0.05) and the total, Gn, and AM fungi (AMF) biomass in the presence of mycorrhiza (p < 0.05). Meanwhile, the response of enzyme activities to warming was also altered with mycorrhiza or hyphae. Additionally, soil microbial community composition was mainly influenced by soil available phosphorus (avaP), while enzyme activities depended on soil avaP, dissolved organic carbon (DOC), and nitrate concentrations. Our results indicate that mycorrhiza and its hyphae are essential in regulating the response of microbes to warming.

Assessment of actinobacteria use in the elimination of multidrug-resistant bacteria of Ibn Tofail hospital wastewater (Marrakesh, Morocco): a chemometric data analysis approach

The efficiency of the treatment of hospital wastewater by actinobacteria was investigated using two chemometric data analysis methods. Six strains of multi-resistant bacteria isolated from Marrakesh hospital wastewater and four strains of antagonistic actinobacteria isolated from Moroccan marine environment were characterized by fatty acids released as methyl esters by thermochemolysis-GC/MS. The hierarchical cluster analysis (HCA) and the principal component analysis (PCA) were used to correlate fatty acids (FA) distributions within strains. HCA allowed to discriminate between bacteria and actinobacteria. A lower Euclidean distance is noted for bacteria. With PCA, linear and branched-chained FAs correlated with bacteria whereas mono unsaturated FAs correlated more specifically with Gram (-) bacteria. Terminally branched-chained FAs correlated most likely with actinobacteria. A co-culture of actinobacteria and bacteria monitored during 15 days demonstrated the efficiency of the biological treatment for 2 of the 4 studied actinobacteria. The effect is more important on Gram-negative bacteria. Antagonistic actinobacteria seem to be poorly efficient against Gram-positive bacteria.

Identification and Quantitation of Hydroxy Fatty Acids in Fermented Sausage Samples

The quality of fermented sausage is strongly influenced by its fatty acid (FA). However, the role of a defined starter culture in modifying sausage FA composition, and especially in the production of hydroxy FAs (HFAs), has not been determined. In this study, the FA compositions of sausages fermented with Latilactobacillus sakei, with L. sakei plus Staphylococcus carnosus, and with an aseptic control were characterized by liquid chromatography-mass spectrometry (MS)/MS and gas chromatography-MS. The sausages fermented with L. sakei, and with L. sakei plus S. carnosus, showed a reduced accumulation of poly and/or diunsaturated FAs and distinct composition of HFAs compared to the aseptic control. 2-HFAs were enriched via high-speed counter-current chromatography and identified uniquely in the L. sakei plus S. carnosus fermented sausage. Through lipid analyses, this study illustrated how the choice of a defined starter culture affected the observed FA metabolism in fermented sausages, facilitating the development of starter cultures or additives that impart desirable characteristics to sausage.

Multivariate optimization of a method for the determination of fatty acids in dental biofilm by GC-MS

AIM

Phospholipid fatty acid methyl ester (FAME) analysis offers a simple option additionally to 16S rRNA sequencing to characterize microbial communities and to monitor changes. A method was established for the characterization of dental plaque via FAME profiles.

METHODOLOGY

Fatty acids were determined as FAMEs (direct, acidic transesterification) and analyzed by GC-MS using an optimized temperature gradient. The transesterification reaction was optimized using a fractional factorial central composite face-centered design.

RESULTS

Optimal conditions for the transesterification in methanol/toluene: hydrochloric acid concentration 2% (w/v), reaction time 40 min, temperature 110 °C. Method validation showed satisfactory accuracy, precision and linearity.

CONCLUSION

The method provides a useful tool to characterize plaque via FAME profiles and was successfully applied to samples from ten subjects demonstrating its applicability.

Pavilion lake microbialites: morphological, molecular and biochemical evidence for a cold-water transition to colonial aggregates

The presence of microbialite structures in a freshwater, dimictic mid-latitude lake and their establishment after the last ice age about 10,000 years ago is puzzling. Freshwater calcite microbialites at Pavilion Lake, British Columbia, Canada, consist of a complex community of microorganisms that collectively form large, ordered structured aggregates. This distinctive assemblage of freshwater calcite microbialites was studied through standard microbial methods, morphological observations, phospholipid fatty acid (PLFA) analysis, DNA sequencing and the identification of quorum sensing molecules. Our results suggest that the microbialites may represent a transitional form from the exclusively prokaryotic colonial precursors of stromatolites to the multicellular organismic aggregates that give rise to coral reefs.

Synthesis of Diyne Substituted 2-Hydroxy Acids, Esters, and Amides

A series of diyne substituted 2-hydroxy acids and derivatives have been prepared and characterized. Alkylation of butane-2,3-diacetal protected glycolic acid with haloalkyl substituted diyne compounds gave the corresponding diacetal protected diyne substituted 2-hydroxy acids. Diacetal deprotection through acid mediated hydrolysis, transesterification, or aminolysis afforded the 2-hydroxy-diyne acid, ester, or amide derivatives, respectively. A novel class of polydiacetylenes was produced through topochemical polymerization of a 2-hydroxy diyne acid and compared with the polymerization of non-hydroxylated diyne acids.

Assimilation of toluene carbon along a bacteria-protist food chain determined by 13C-enrichment of biomarker fatty acids

A food chain consisting of toluene, toluene-degrading Pseudomonas sp. PS+ and a bacterivorous flagellated amoebae Vahlkampfia sp. was established in a batch culture. This culture was amended with [U-13C]toluene and served as a model system to elucidate the flux of carbon in the food chain by quantifying bacterial biovolumes and 13C enrichment of phospholipid fatty acid (PLFA) biomarkers of the bacteria and the heterotrophic protists. Major PLFA detected in the batch co-culture included those derived from Pseudomonas sp. PS+ (16:1omega7c and 18:1omega7c) and Vahlkampfia sp. (20:4omega6c and 20:3omega6c). A numerical model including consumption of toluene by the bacteria and predation of the bacteria by the heterotrophic protists was adjusted to the measured toluene carbon, bacterial carbon and delta13C values of bacterial and protist biomass. Using this model, we estimated that 28+/-7% of the consumed toluene carbon was transformed into bacterial biomass, and 12+/-4% of the predated bacterial carbon was incorporated into heterotrophic protist biomass. Our study showed that the 13C enrichment of PLFA biomarkers coupled to biomass determination via biovolume calculations is a suitable method to trace carbon fluxes in protist-inclusive microbial food chains because it does not require the separation of protist cells from bacterial cells and soil particles.

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

Hydroxy fatty acids (OH-FAs) can be used in the characterization of microbial communities, especially Gram-negative bacteria. We prepared methyl esters of 2- and 3-OH-FAs from the lipid extraction residue of soil, sediment, and biofilm samples without further purification or derivatization of hydroxyl groups. OH-FA methyl esters were analyzed using a gas chromatograph equipped with a mass selective detector (GC-MS). The ions followed in MS were m/z 103 for 3-OH-FAs and m/z 90 and M-59 for 2-OH-FAs. The rapid determination of 3- and 2-OH-FAs concomitantly with phospholipid fatty acids provided more detailed information on the microbial communities present in soil, sediment, and drinking water biofilm.

Flash detection/identification of pathogens, bacterial spores and bioterrorism agent biomarkers from clinical and environmental matrices

We propose to develop an integrated rapid, semiportable, prototype point microbial detection/identification system for clinical specimens that is also capable of differentiating microbial bioterrorism attacks from threats or hoaxes by defining the pathogen. The system utilizes "flash" extraction/analytical system capable of detection/identification of microbes from environmental and clinical matrices. The system couples demonstrated technologies to provide quantitative analysis of lipid biomarkers of microbes including spores in a system with near-single cell (amol/microl) sensitivity. Tandem mass spectrometry increases specificity by providing the molecular structure of neutral lipids, phospholipids, and derivatized spore-specific bacterial biomarker, 2,6-dipicolinic acid (DPA) as well as the lipopolysaccharide-amide-linked hydroxy-fatty acids (LPS-ALHFA) of Gram-negative bacteria. The extraction should take about an hour for each sample but multiple samples can be processed simultaneously.

Determination of the gram-positive bacterial content of soils and sediments by analysis of teichoic acid components

Many gram-positive bacteria form substituted polymers of glycerol and ribitol phosphate esters known as teichoic acids. Utilizing the relative specificity of cold concentrated hydrofluoric acid in the hydrolysis of polyphosphate esters it proved possible to quantitatively assay the teichoic acid-derived glycerol and ribitol from gram-positive bacteria added to various soils and sediments. The lipids are first removed from the soils or sediments with a one phase chloroform-methanol extraction and the lipid extracted residue is hydrolyzed with cold concentrated hydrofluoric acid. To achieve maximum recovery of the teichoic acid ribitol, a second acid hydrolysis of the aqueous extract is required. The glycerol and ribitol are then acetylated after neutralization and analyzed by capillary gas-liquid chromatography. This technique together with measures of the total phospholipid, the phospholipid fatty acid, the muramic acid and the hydroxy fatty acids of the lipopolysaccharide lipid A of the gram-negative bacteria makes it possible to describe the community structure environmental samples. The proportion of gram-positive bacteria measured as the teichoic acid glycerol and ribitol is higher in soils than in sediments and increases with depth in both.

Identification of single cultured micro-organisms based on their whole-community fatty acid profiles, using an extended extraction procedure

Fatty acid profiles obtained from single cultured organisms have been used to estimate which taxonomic groups are actually represented. The lipid extraction was modified to liberate fatty acids with ester-linkages, as well as those with non-ester-linkages and classify them in different chemically relevant groups. The discriminatory power of fatty acids, in different chemically relevant fractions and subfractions varied considerably. Saturated fatty acids were least able to predict actual group membership (ca. 75%), while nonester-linked hydroxy fatty acids, which largely go undetected by the simple extraction procedure, gave the highest predictability values (ca. 94%). The discriminatory power of the method used was enhanced by increasing the number of well-defined fatty acid methyl esters. The estimation capacity of the results was improved, when the fatty acids, which were presumed to be common and widespread, were excluded from the whole-community fatty acid profiles prior to multivariate analysis.

Phospholipid fatty acid profiles in selected members of soil microbial communities

Fatty acids derived from phospholipids and lipopolysaccharides were investigated from 33 taxonomically different organisms (bacteria, fungi and plant cells) known a priori to inhabit soil (except E. coli). The extended extraction procedure used, liberated non-ester-linked fatty acids in addition to ester-linked fatty acids, hydroxy substituted fatty acids in three different fractions. The amount of non-ester-linked fatty acids was as high as 70% of the total phospholipid fatty acids in some fungi and varied considerably in different organisms. The cis vaccenic acid constituted about 50% of phospholipid fatty acids in selected bacteria belonging to the alpha subclass of Proteobacteria. These fatty acids were not found in other selected organisms. A large amounts of branched chain fatty acids were found in various organisms. If the branching are localised on positions other than iso and anteiso they were strong indicators for gram positive bacteria. The cyclopropyl fatty acids are mainly localized in gram negative bacteria. The beta hydroxy fatty acid of the outer membrane are widespread among bacterial taxa and fungi. These fatty acids are not recommended to use as "signature" fatty acids for gram negative bacteria.

Emission of Climate-Relevant Trace Gases and Succession of Microbial Communities during Open-Windrow Composting

Determination of different indicators of microbial biomass, community structure, and bioactivity by the fumigation extraction method, as well as determination of phospholipid fatty acids (PLFAs) and their subfractions and the measurement of trace gases, respectively, provides valuable information about microbial succession in composting processes. The emission rates of carbon dioxide (CO(inf2)), methane (CH(inf4)), and nitrous oxide (N(inf2)O) increased successively during compost maturation: initially in the presence of easily degradable nutrients, during high temperature, and after the temperature had cooled down, respectively. The emission rate patterns of these trace gases corresponded to the concentrations of PLFAs and their particular subfractions. (i) Similar to the CO(inf2) emission rates, microbial biomass estimations by fumigation extraction and by determination of the amount of total PLFAs showed a discontinuous decrease during the composting process, with a slight increase at the end of the observation period. (ii) An increase in ether lipids, indicating the enhanced presence of archaean methanogens, and an elevated CH(inf4) emission were observed at the same time. (iii) The period of enhanced N(inf2)O emission corresponded to the increase in beta and omega hydroxy fatty acids derived from the outer membrane. Additionally, the continuous increase in branched-chain fatty acids suggested an increase in gram-positive bacteria and actinomycetes, and the decrease in polyunsaturated fatty acids indicated a decrease in eukaryotic cells during the composting.

Lipopolysaccharide determination by reversed-phase high-performance liquid chromatography after fluorescence labeling

A sensitive method for the quantitative determination of lipid A, the covalently bound hydrophobic component of lipopolysaccharides (endotoxins), has been developed. The determination of lipid A was based on the quantitative measurement of beta-hydroxymyristic acid and beta-hydroxylauric acid by reversed-phase HPLC. beta-Hydroxy acids were liberated from ester and amide linkages in endotoxins by acid catalyzed methanolysis. The resulting methyl esters were derivatized with 9-anthracene-carboxyl chloride, 9-fluorene-carboxyl chloride and 4-(1-pyrenyl)butyric acid chloride and quantified with a fluorescence detector. The effectiveness of the three derivatizing agents was compared. As internal standards-beta-hydroxytridecanoic acid [beta-OH(13:0)] and beta-hydroxypentadecanoic acid [beta-OH(15:0)] ethyl esters were used. The limits of detection of beta-hydroxymyristic acid were 0.5 pg for the 9-anthroyl and 2 pg for the fluorenoyl and 4-(1-pyrenyl)butyroyl ester per sample (signal-to-noise ratio of 3). The detection limits of lipopolysaccharide from a smooth strain (Escherichia coli 0111:B4) was 20 pg, while that from two rough strains (E. coli Nissle 1917 and Salmonella typhimurium SL 1181) was 5 pg per sample after methanolysis and derivatization with 9-anthroyl chloride.

Isolation and characterization of an N-methylcarbamate insecticide-degrading methylotrophic bacterium

A gram-negative bacterium which hydrolyzed aryl N-methylcarbamate insecticides was isolated from an agricultural soil which quickly degraded these pesticides. This organism, designated strain ER2, grew on carbofuran as a sole source of carbon and nitrogen with a doubling time of 3 h in a mineral salts medium. The aromatic nucleus of the molecule was not metabolized, and carbofuran 7-phenol accumulated as the end product of metabolism. The insecticides carbaryl, bendiocarb, and propoxur were similarly hydrolyzed, with each yielding the corresponding phenol. Strain ER2 contained two plasmids (120 and 130 kb). A probe cloned from the pDL11 plasmid of Achromobacter sp. strain WM111, which encodes the carbofuran hydrolase (mcd) gene (P. H. Tomasek and J. S. Karns, J. Bacteriol. 171:4038-4044, 1989), hybridized to the 120-kb plasmid. Restriction fragment profiles of pDL11 and strain ER2 plasmid DNAs suggested that the 120-kb plasmid of strain ER2 is very similar to pDL11. On the basis of the results of biochemical tests, 16S rRNA sequence analysis, and membrane lipid analyses, strain ER2 was found to be a phylogenetically unique type II methylotroph. The constitutive carbofuran hydrolase activity in glucose-grown cells increased sevenfold when strain ER2 was grown in the presence of 100 mg of carbofuran per liter as the sole source of carbon and nitrogen or as the sole nitrogen source in the presence of glucose. Growth on carbofuran resulted in the induction of enzymes required for methylamine-dependent respiration and the serine pathway of formaldehyde assimilation. These results indicate that the carbofuran hydrolase mcd gene is conserved on a plasmid found in organisms from different geographic areas and that the specific activity of carbofuran degradation may increase in response to carbofuran treatment.

Phylogenetic analysis of a bacterial aerobic degrader of azo dyes

Eubacterial consensus oligonucleotide primers were used to amplify by polymerase chain reaction the nearly full-length 16S rRNA gene of isolate C7, a gram-negative rod capable of aerobic degradation of azo dyes. The DNA product was cloned and sequenced. Phylogenetic analysis based upon this DNA sequence places C7 within the alpha subdivision of proteobacteria, most closely related to Caulobacter subvibrioides. The phospholipid fatty acid pattern resembles that of caulobacters, with monounsaturated 16- and 18-carbon fatty acids predominating. C7 is unusual in having a monounsaturated branched fatty acid in the phospholipids and exclusively 2-hydroxy fatty acids in the lipid-extracted residue. This organism is of potential use in bioreactors operated for azo dye degradation.

Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals

The gram-negative metal-reducing microorganism, previously known as strain GS-15, was further characterized. This strict anaerobe oxidizes several short-chain fatty acids, alcohols, and monoaromatic compounds with Fe(III) as the sole electron acceptor. Furthermore, acetate is also oxidized with the reduction of Mn(IV), U(VI), and nitrate. In whole cell suspensions, the c-type cytochrome(s) of this organism was oxidized by physiological electron acceptors and also by gold, silver, mercury, and chromate. Menaquinone was recovered in concentrations comparable to those previously found in gram-negative sulfate reducers. Profiles of the phospholipid ester-linked fatty acids indicated that both the anaerobic desaturase and the branched pathways for fatty acid biosynthesis were operative. The organism contained three lipopolysaccharide hydroxy fatty acids which have not been previously reported in microorganisms, but have been observed in anaerobic freshwater sediments. The 16S rRNA sequence indicated that this organism belongs in the delta proteobacteria. Its closest known relative is Desulfuromonas acetoxidans. The name Geobacter metallireducens is proposed.

Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals

The gram-negative metal-reducing microorganism, previously known as strain GS-15, was further characterized. This strict anaerobe oxidizes several short-chain fatty acids, alcohols, and monoaromatic compounds with Fe(III) as the sole electron acceptor. Furthermore, acetate is also oxidized with the reduction of Mn(IV), U(VI), and nitrate. In whole cell suspensions, the c-type cytochrome(s) of this organism was oxidized by physiological electron acceptors and also by gold, silver, mercury, and chromate. Menaquinone was recovered in concentrations comparable to those previously found in gram-negative sulfate reducers. Profiles of the phospholipid ester-linked fatty acids indicated that both the anaerobic desaturase and the branched pathways for fatty acid biosynthesis were operative. The organism contained three lipopolysaccharide hydroxy fatty acids which have not been previously reported in microorganisms, but have been observed in anaerobic freshwater sediments. The 16S rRNA sequence indicated that this organism belongs in the delta proteobacteria. Its closest known relative is Desulfuromonas acetoxidans. The name Geobacter metallireducens is proposed.

Lipid A in Helicobacter pylori

Free lipid A of Helicobacter pylori was characterized with regard to chemical composition, reactivity with anti-lipid A antibodies, and activity in a Limulus lysate assay. The predominant fatty acids of H. pylori lipid A were 3-OH-18:0, 18:0, 3-OH-16:0, 16:0, and 14:0. Hexosamine was present in amounts similar to those in Campylobacter jejuni or Salmonella typhimurium lipid A. The lipopolysaccharide of H. pylori contained 2-keto-3-deoxyoctonic acid, a common constituent of enterobacterial and C. jejuni lipopolysaccharides. In the enzyme-linked immunosorbent assay, the doses of lipid A required to inhibit anti-lipid A by 50% (EI50 values) by absorption of the immune (rabbit) serum were 7.9, 1.2, and 1.4 micrograms of O-deacylated lipid A's from H. pylori, C. jejuni, and S. typhimurium per ml, respectively. The lower reactivity of H. pylori lipid A compared with those of the other two lipid A preparations (as shown by the higher EI50 value) was underscored by the use of a murine monoclonal anti-lipid A antibody in the inhibition assay. An EI50 value was not obtained at the concentrations tested for H. pylori lipid A; the corresponding figures for C. jejuni and S. typhimurium lipid A's were 13 and 14 micrograms/ml, respectively. No inhibition was obtained with H. pylori lipopolysaccharide, which showed a low-molecular-weight profile on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The activity of H. pylori lipid A in the Limulus assay was approximately 71 and 650 times lower than those of C. jejuni and S. typhimurium lipid A's, respectively. These findings suggest that lipid A is an integral part of the outer cell wall of H. pylori. The lower reactivity of H. pylori lipid A with anti-lipid A antibodies and in the Limulus assay compared with that of C. jejuni or S. typhimurium lipid A may be explained by a different composition of the fatty acids, especially the 3-hydroxy fatty acids, and a possible deviating phosphorylation pattern.

Acetonema longum gen. nov. sp. nov., an H2/CO2 acetogenic bacterium from the termite, Pterotermes occidentis

A previously undescribed, H2-oxidizing CO2-reducing acetogenic bacterium was isolated from gut contents of the wood-feeding termite, Pterotermes occidentis. Cells of representative strain APO-1 were strictly anaerobic. Gram-negative, endospore-forming motile rods which measured 0.30-0.40 x 6-60 microm. Cells were catalase positive, oxidase negative, and had 51.5 mol percent G + C in their DNA. Optimum conditions for growth on H2 + CO2 were at 30-33 degrees C and pH (initial) 7.8, and under these conditions cells formed acetate according to the equation: 4 H2 + 2 CO2----CH3COOH + 2 H2O. Other energy sources supporting good growth of strain APO-1 included glucose, ribose, and various organic acids. Acetate and butyrate were major fermentation products from most organic compounds tested, however propionate, succinate, and 1,2-propanediol were also formed from some substrates. Based on comparative analysis of 16S rRNA nucleotide sequences, strain APO-1 was related, to but distinct from, members of the genus Sporomusa. Moreover, physiological and morphological differences between strain APO-1 and the six known species of Sporomusa were significant. Consequently, it is proposed herewith that a new genus, Acetonema, be established with strain APO-1 as the type strain of the new species, Acetonema longum. A. longum may contribute to the nutrition of P. occidentis by forming acetate, propionate and butyrate, compounds which are important carbon and energy sources for termites.

Characterization of Bacteria That Suppress Rhizoctonia Damping-Off in Bark Compost Media by Analysis of Fatty Acid Biomarkers

Examination of cucumber roots ( Cucumis sativus L.) grown in bark compost media and of the surrounding edaphic substrate showed profiles of polar lipid fatty acids commonly found in bacteria. The composition of fatty acids in these profiles differed significantly between roots grown in a medium naturally suppressive to Rhizoctonia damping-off and roots from a conducive medium. Cucumber roots from the suppressive medium had higher proportions of cis -vaccenic acid (18:1 ω 7 c ) and the iso-branched monoenoic fatty acid i17:1 ω 8 but lower proportions of several iso- and anteiso-branched fatty acids compared with roots from the conducive medium. The concentrations of the bacterial fatty acids were significantly lower in the surrounding media. However, the suppressive and conducive growth substrates had differences in the composition of the bacterial fatty acids similar to those found between the cucumber roots proper. These results suggest major differences in bacterial community composition between suppressive and conducive systems. Fatty acid analyses were also utilized to examine the effects on bacterial community composition of root colonization by Flavobacterium balustinum 299, a biocontrol agent. The concentration of the most prominent fatty acid in this bacterium, i17:1 ω 8, was increased on roots produced from inoculated seeds in a medium rendered suppressive by the treatment. This change was concomitant with a significant increase in the concentration of 18:1 ω 7 c , not present in the lipids of the antagonist, indicating a shift in the microflora from a conducive to a suppressive bacterial community.

Determination of environmental levels of peptidoglycan and lipopolysaccharide using gas chromatography with negative-ion chemical-ionization mass spectrometry utilizing bacterial amino acids and hydroxy fatty acids as biomarkers

D-Alanine and diaminopimelic acid originating from bacterial peptidoglycans and hydroxy fatty acids from lipopolysaccharides (endotoxins) were analysed by gas chromatography using a chiral column (Chirasil-Val as stationary phase) and selected-ion monitoring detection with negative-ion chemical-ionization mass spectrometry. The amino acids were analysed as N-heptafluorobutyryl isobutyl esters after rapid hydrolysis of peptidoglycan followed by isolation of the amino acids with disposable ion-exchange columns. Racemization of amino acid enantiomers was controlled by using deuterium chloride in the hydrolysis. The hydroxy acids were analysed as O-pentafluorobenzoyl methyl esters. Most of the bacteria present in airborne dust from a poultry confinement building were found to be Gram-positive according to the analytical chemical method whereas the Limulus amoebocyte lysate test suggested the presence of appreciable amounts of lipopolysaccharides of Gram-negative bacteria. Further studies are required to compare the utility of these two methods for determining endotoxins in complex environments.

Equivalence of microbial biomass measures based on membrane lipid and cell wall components, adenosine triphosphate, and direct counts in subsurface aquifer sediments

An uncontaminated subsurface aquifer sediment contains a sparse microbial community consisting primarily of coccobacillary bacteria of relatively uniform size which can be counted directly with appropriate staining. The morphological simplicity and the relatively decreased cell numbers, when compared with surface soils and sediments, make the subsurface an ideal natural community with which to compare the utility of chemical measures of microbial biomass to direct microscopic counts. The membrane phospholipids (estimated as the polar lipid fatty acids, the lipid phosphate, and phosopholipid glycerol phosphate), lipopolysaccharide lipid A (estimated as the LPS hydroxy fatty acids), cell walls (estimated as the muramic acid), and adenosine triphosphate all give essentially identical estimates of cell numbers and dry weight as the direct counts, using conversion factors determined on subsurface microorganism monocultures. Assays of microbial cell components are thus validated by comparison with the classical direct count in at least one soil/sediment.

Determination of endotoxins by gas chromatography: evaluation of electron-capture and negative-ion chemical-ionization mass spectrometric detection of halogenated derivatives of beta-hydroxymyristic acid

The sensitivity and selectivity of gas chromatography for analysing several halogenated ester derivatives of beta-hydroxymyristic acid were studied using both selected-ion monitoring detection with negative-ion chemical-ionization mass spectrometry and electron-capture detection. Six different derivatization methods were compared with respect to yield, chemical stability and formation of by-products. Procedures for removal of excess reagents using disposable silica columns and thin-layer chromatography were elaborated. The 3-O-pentafluorobenzoyl-methyl ester was the preferred derivative since it provided high sensitivity and had the molecular ion as the base peak in the mass spectrum. The detection limit was 0.5 pg with electron-capture detection and 0.3 pg with the mass spectrometric system. Using beta-hydroxymyristic acid as a chemical marker it was possible to detect Escherichia coli endotoxin in aqueous solution at a level of 1 ng/ml.

Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences

The microorganisms inhabiting a 91 degrees C hot spring in Yellowstone National Park were characterized by sequencing 5S rRNAs isolated from the mixed, natural microflora without cultivation. By comparisons of these sequences with reference sequences, the phylogenetic relationships of the hot spring organisms to better characterized ones were established. Quantitation of the total 5S-sized rRNAs revealed a complex microbial community of three dominant members, a predominant archaebacterium affiliated with the sulfur-metabolizing (dependent) branch of the archaebacteria, and two eubacteria distantly related to Thermus spp. The archaebacterial and the eubacterial 5S rRNAs each constituted about half the examined population.