Fatty Acid Methyl Ester Profiles Research Articles

The Effects of Indicator Organism Type on Phenotypic Characterization of Host-Specificity and the Implications for Microbial Source Tracking

The Effects of Indicator Organism Type on Phenotypic Characterization of Host-Specificity and the Implications for Microbial Source TrackingThe objective of this study was to investigate the effects of indicator organism type on the host specificity of fatty acid methyl ester (FAME) profiles. For that purpose, the FAME profiles of enterococcus, Escherichia coli, fecal coliform (FC), and total coliform (TC) isolates cultured from fecal samples of 5 hosts (cow, swine, poultry, deer, and water fowl) and sewage were developed. These four...Author(s)Deniz YurtseverBerat Z. HaznedarogluTimur DunaevMetin DuranSourceProceedings of the Water Environment FederationSubjectSession 88: Bacteria: More Than a MovementDocument typeConference PaperPublisherWater Environment FederationPrint publication date Oct, 2007ISSN1938-6478SICI1938-6478(20071001)2007:11L.7063;1-DOI10.2175/193864707787223556Volume / Issue2007 / 11Content sourceWEFTECFirst / last page(s)7063 - 7071Copyright2007Word count422Subject keywordsFAME PROFILINGINDICATOR ORGANISMSMICROBIAL SOURCE TRACKINGTMDL

Use of Fatty Acid Methyl Ester Profiles to Compare Copper-Tolerant and Copper-Sensitive Strains of Pantoea ananatis

ABSTRACT A survey was conducted to evaluate differences in fatty acid methyl ester (FAME) profiles among strains of Pantoea ananatis, causal agent of center rot of onion (Allium cepa), isolated from 15 different onion cultivars in three different sites in Georgia. Differences in FAME composition were determined by plotting principal components (PCs) in two-dimensional plots. Euclidean distance squared (ED(2)) values indicated a high degree of similarity among strains. Plotting of PCs calculated from P. ananatis strains capable of growing on media amended with copper sulfate pentahydrate (200 mug/ml) indicated that copper-tolerant strains grouped into tight clusters separate from clusters formed by wild-type strains. However, unlike copper-sensitive strains, the copper-tolerant strains tended to cluster by location. A total of 80, 60, and 73% of the strains from Tift1, Tift2, and Tattnall, respectively, exhibited either confluent growth or partial growth on copper-amended medium. However, all strains were sensitive to a mixture of copper sulfate pentahydrate (200 mug/ml) and maneb (40 mug/ml). When copper-tolerant clones were analyzed and compared with their wild-type parents, in all cases the plotting of PCs developed from copper-tolerant clones formed tight clusters separate from clusters formed by the parents. Eigenvalues generated from these tests indicated that two components provided a good summary of the data, accounting for 98, 98, and 96% of the standardized variance for strains Pna 1-15B, Pna 1-12B, and Pna 2-5A, respectively. Furthermore, feature 4 (cis-9-hexadecenoic acid/2-hydroxy-13-methyltetradecanoic acid) and feature 7 (cis-9/trans-12/cis-7-octadecenoic acid) were the highest or second highest absolute values for PC1 in all three strains of the parents versus copper-tolerant clones, and hexadecanoic acid was the highest absolute value for PC2 in all three strains. Along with those fatty acids, dodecanoic acid and feature 3 (3-hydroxytetradecanoic acid/14-methylpentadecenoic acid) also had an impact on the differences observed between copper-sensitive parents and copper-resistant mutants. Finding these changes in bacterial fatty acid composition could lead to the development of a laboratory assay to identify copper-tolerant strains using gas chromatography as well as providing clues to further elucidate the mode of action of copper tolerance.

Determination of the carbon isotopic composition of whole/intact biological specimens using at-line direct thermal desorption to effect thermally assisted hydrolysis/methylation

In this paper, we discuss the use of a direct thermal desorption (DTD) interface as an alternative to Curie-point flash pyrolysis system as an inlet technique in gas chromatography–combustion isotope-ratio mass spectrometry (GC/C-IRMS) analysis of whole/intact phytoplankton and zooplankton specimens. The DTD in combination with a combipal auto-injector is programmed to perform the injection, evaporation of solvents, transport of capped programmed-temperature vaporizer (PTV) liners to the PTV injector and chemical derivatisation (thermally assisted hydrolysis/methylation; THM) such that a profile of a cellular fatty acids is obtained. Flow-cytometric sorted microalgae and handpicked zooplankton are used as samples with trimethylsulfonium hydroxide (TMSH) as methylating reagent. A major advantage of this novel approach over the Curie-point technique is the automation of the total procedure, which allows unattended analysis of large sample series. The profiles and δ 13C carbon isotopic signatures of the fatty acid methyl esters (FAMEs) produced are very similar to those obtained using the Curie-point flash pyrolysis method. It is shown that algal samples must be kept no longer than 48 h in the DTD sample tray prior to the THM-analysis in order to maintain the integrity of their FAME profile.

Fatty acid profiling of raw human plasma and whole blood using direct thermal desorption combined with gas chromatography–mass spectrometry

Gas chromatography (GC) has in recent times become an important tool for the fatty acid profiling of human blood and plasma. An at-line procedure used in the fatty acid profiling of whole/intact aquatic micro-organisms without any sample preparation was adapted for this work. A direct thermal desorption (DTD) interface was used to profile the fatty acid composition of human plasma and whole human blood of eight volunteers in a procedure omitting the usual lipid extraction steps that precede sample methylation in the traditional (off-line) protocols. Trimethylsulfonium hydroxide (TMSH) was used as reagent for thermally assisted methylation. In a fully automated manner, the liner of the GC injector is used as a sample-and-reaction container with the aid of the DTD interface. The fatty acid methyl ester (FAME) profiles obtained using this novel approach, were very identical to those obtained when the traditional off-line protocol was applied. FAME yields obtained in the at-line DTD method were found to be very similar for saturated fatty acids, but significantly higher for polyunsaturated fatty acids compared to off-line yields. As a result of the contribution of circulating cell membranes in blood, substantial differences were observed when the amount of FAMEs obtained in whole human blood and human plasma samples were compared after their analysis. Thanks to the fully automated operation of this novel procedure, large series of analyses can easily be performed.

Influence of ripening container on the lactic acid bacteria population in Tulum cheese

The objective of the present study was to investigate the influence of container material (plastic or goat-skin bag) on the growth of lactic acid bacteria in Tulum cheese during 9 months of ripening. The lactic acid bacteria in Tulum cheeses were periodically counted on MRS and M17 agars throughout ripening. Results showed that the highest counts of lactic acid bacteria on MRS or M17 were observed at the beginning of ripening and their counts decreased during later stages of ripening. The cheese samples ripened in plastic bags exhibited higher numbers of LAB on MRS and M-17 agars than those ripened in goat-skin bags. A total of 112 strains of lactic acid bacteria were isolated from Tulum cheeses ripened in plastic or goat-skin bags during ripening. The lactic acid bacteria present in the cheese were classified by Microbial Identification System (MIS) based on a comparison of the fatty acid methyl ester profiles. Different species including Enteroccocus, Lactobacillus, Streptococcus, Lactococcus and Pediococcus genera were found in unripened cheese. As ripening proceeded, the species Streptococcus and Lactococcus disappeared and the percentages of the species Enterococcus was unchanged in both containers. There were slight differences between the cheeses ripened in plastic or goat-skin bags in terms of the profiles of lactic acid bacteria isolated. Some species including L. brevis, L. mesenteroides subsp. dextranicum, P. damnosus and E. mundtii were isolated only in the cheeses ripened in plastic bags; however, L. coryniformis and L. malafermentans were isolated only in the cheeses ripened in goat-skin bags at 6 or 9 months of ripening. Also the numbers of E. faecalis isolates were higher in the cheeses ripened in plastic containers than cheeses ripened goat-skin bags at the 6 or 9 months of ripening. The results showed that Lactobacillus and Enterococcus were the predominant species in matured Tulum cheeses in both ripening containers. It seemed possible to produce Tulum cheese with similar characteristics from both the containers used.

Effect of temperature on the microbial ecology of a hydrocarbon-contaminated Antarctic soil: Implications for high temperature remediation

A series of nutrient-amended microcosms was used to investigate changing microbial communities during biodegradation in hydrocarbon-contaminated Antarctic soils at 4, 10 and 42 °C. Although sample heterogeneity resulted in no statistically significant reduction in total petroleum hydrocarbons, biodegradation ratios indicate significant mineralisation. The number of culturable bacterial grown at 4 and 10 °C increased from 3 × 105 g− 1 dry soil then peaked after 5 days incubation at 5 × 107 g− 1 dry soil, before decreasing to and remaining stable at ca. 2 × 107 g− 1 dry soil. While the bacterial population grown at 42 °C was initially a minor constituent of the total culturable bacterial population, after 40 days there was similar numbers of bacteria estimated at all temperatures investigated. Denaturing gradient gel electrophoresis indicated significant differences in the microbial community between the 4 and 10 °C and the 42 °C microcosms. Numerically dominant culturable hydrocarbon degrading bacteria were isolated at each temperature; 16S rRNA gene sequences identified the 4 and 10 °C isolates as Pseudomonas spp., and the 42 °C isolates as Paenibacillus spp. Fatty acid methyl ester profiles of the cultures were consistent with these identifications. The results from this study indicate that bioremediation treatments will substantially alter the soil microbial ecosystem. All isolates from this study were capable of growth at 28 °C. The presence of autochthonous hydrocarbon degrading microbes capable of growth at higher temperatures introduces the possibility of in situ remediation treatment options involving heating (ca. 10–28 °C) to accelerate the rate of hydrocarbon degradation.

Effects of glyphosate on soil microbial communities and its mineralization in a Mississippi soil

Transgenic glyphosate-resistant (GR) soybean [Glycine max (L.) Merr.] has enabled highly effective and economical weed control. The concomitant increased application of glyphosate could lead to shifts in the soil microbial community. The objective of these experiments was to evaluate the effects of glyphosate on soil microbial community structure, function and activity. Field assessments on soil microbial communities were conducted on a silt loam soil near Stoneville, MS, USA. Surface soil was collected at time of planting, before initial glyphosate application and 14 days after two post-emergence glyphosate applications. Microbial community fatty acid methyl esters (FAMEs) were analyzed from these soil samples and soybean rhizospheres. Principal component analysis of the total FAME profile revealed no differentiation between field treatments, although the relative abundance of several individual fatty acids differed significantly. There was no significant herbicide effect in bulk soil or rhizosphere soils. Collectively, these findings indicate that glyphosate caused no meaningful whole microbial community shifts in this time period, even when applied at greater than label rates. Laboratory experiments, including up to threefold label rates of glyphosate, resulted in up to a 19% reduction in soil hydrolytic activity and small, brief (<7 days) changes in the soil microbial community. After incubation for 42 days, 32-37% of the applied glyphosate was mineralized when applied at threefold field rates, with about 9% forming bound residues. These results indicate that glyphosate has only small and transient effects on the soil microbial community, even when applied at greater than field rates.

First Report of Yersinia ruckeri Biotype 2 in the USA

A polyphasic characterization of atypical isolates of Yersinia ruckeri (causative agent of enteric redmouth disease in trout) obtained from hatchery-reared brown trout Salmo trutta in South Carolina was performed. The Y. ruckeri isolates were biochemically and genetically distinct from reference cultures, including the type strain, but were unequivocally ascribed to the species Y. ruckeri, based on API 20E, VITEK, fatty acid methyl ester profiles, and 16S rRNA gene sequencing analysis. These isolates were nonmotile and unable to hydrolyze Tween 20/80 and were therefore classified as Y. ruckeri biotype 2. Genetic fingerprint typing of the isolates via enterobacterial repetitive intergenic consensus (amplified by polymerase chain reaction) and fragment length polymorphism showed biotype 2 as a homogeneous group distinguishable from other Y. ruckeri isolates. This is the first report of Y. ruckeri biotype 2 in the USA.

Phenotypic characterization of Escherichia coli through whole-cell fatty acid profiling to investigate host specificity

The objective of the study was to investigate whole-cell fatty acid methyl ester (FAME) profiles of 605 Escherichia coli isolates to determine their host specificity. The isolates were cultured from six possible sources of fecal pollution; 180 isolates from sewage, 85 from dairy cow, 98 from chicken, 76 from swine, 94 from deer, and 72 from waterfowl, mostly geese and ducks. The FAME profiles were presented as the relative masses of 12 FAMEs identified in the isolates and it was found that none of the six hosts carried a “signature” FAME, a FAME that is uniquely associated with a particular host category. However, two-sample t-test analyses indicated that the mean relative masses of seven FAMEs out of the 12 identified showed statistically significant differences (95% confidence interval) between isolates of human and non-human origins. In addition, a linear discriminant function based on mean relative mass variations in individual FAMEs classified the known-source isolates into their respective host categories with a 47.6% average rate of correct classification (ARCC) in a six-way discriminant analysis. The ARCC increased to 61.3% when the individual hosts were pooled into larger categories of human, livestock, and wildlife. The accuracy was 75.5% when isolates of human origin were discriminated against those of non-human origins. Random cluster formation analysis indicated that the library size was sufficient to prevent random grouping among the isolates.

Taxonomic diversity of predominant culturable bacteria associated with microaggregates from two different agroecosystems and their ability to aggregate soil in vitro

Soil macroaggregates (>250 μm) are easily disrupted when wetted quickly, whereas microaggregates (50–250 μm) are highly stable. There is little knowledge of functional groups of bacteria from microaggregates that can stabilize soil and their diversity. We isolated the predominant bacteria from microaggregates collected from two agroecosystems: a site cropped to barley (40 years with tillage) and to alfalfa (9 years with no tillage) and assayed for their potential to aggregate soil in an in vitro assay. Soil suspensions from physically disrupted microaggregates were spiral-plated and bacterial colonies were isolated from the most dilute portion of the spiral then purified. To characterize the culturable bacteria thus isolated, fatty acid methyl ester (FAME) profiles, substrate utilization patterns (Biolog), and DNA sequence analysis using 16s rRNA amplification region were performed for bacterial identification. Principal component analysis of FAME profiles and Biolog patterns was conducted to describe patterns of community composition of bacterial species within each agroecosystem. Gram-negative bacteria in microaggregates from barley soil consisted entirely of Pseudomonas spp. whereas Stenotrophomonas, Sphingobacterium, Chryseobacterium, and Acinetobacter spp. were found in addition to the Pseudomonas in microaggregates of alfalfa soil. Artificial aggregates were generated by amending a sandy soil with pure cultures of various species identified from microaggregates of both soils and tested for their water stability and their strength. The results indicated that Stenotrophomonas and Sphingobacterium species exhibited the greatest ability to stabilize soil and to increase aggregate strength among several species tested. This study demonstrated that microaggregates harbor functional groups of bacterial species capable of aggregating soil particles in vitro, and there were a greater range of such species in microaggregates of non-disturbed soil (alfalfa) than in disturbed, yearly tilled soil (barley).

The use of fatty acid methyl esters as biomarkers to determine aerobic, facultatively aerobic and anaerobic communities in wastewater treatment systems

The use of fatty acid methyl esters (FAME) as biomarkers to identify groups of microorganisms was studied. A database was constructed using previously published results that identify FAME biomarkers for aerobic, anaerobic and facultatively aerobic bacteria. FAME profiles obtained from pure cultures were utilized to confirm the predicted presence of biomarkers. Principal component analysis demonstrated that the FAME profiles can be used to determine the incidence of these bacterial groups. The presence of aerobic, anaerobic and facultatively aerobic bacteria in the communities, in four bioreactors being used to treat different wastewaters, was investigated by applying FAME biomarkers.

Characterization of isolates of binucleate Rhizoctonia spp. associated with strawberry black root rot complex using fatty acid methyl ester (FAME) profiles

Black root rot is an important disease of strawberry caused by a complex of fungi that includes species of Rhizoctonia. In this study, a modified MIDI method (Microbial Identification System) was investigated for its utility to differentiate isolates of the three different anastomosis groups (AGs) of binucleate Rhizoctonia spp., associated with strawberry black root rot complex representing AG-A, AG-G, and AG-I. A total of 11 fatty acids were detected, and the FAME profiles for isolates of the three different AGs of Rhizoctonia spp. varied quantitatively and qualitatively. Moreover, the modified MIDI method will be a useful discriminatory tool for fungal identification and classification of the AGs of binucleate Rhizoctonia spp. associated with strawberry black root rot complex.

Detection and characterization of bacteria from the potato rhizosphere degradingN-acyl-homoserine lactone

Quorum sensing plays a role in the regulation of soft rot diseases caused by the plant pathogenic bacterium Pectobacterium carotovorum subsp. carotovorum. The signal molecules involved in quorum sensing in P. carotovorum subsp. carotovorum belong to the group of N-acyl homoserine lactones (AHLs). In our study, we screened bacteria isolated from the potato rhizosphere for the ability to degrade AHLs produced by P. carotovorum subsp. carotovorum. Six isolates able to degrade AHLs were selected for further studies. According to 16S rDNA sequence analysis and fatty acid methyl ester profiling, the isolates belonged to the genera Ochrobactrum, Rhodococcus, Pseudomonas, Bacillus, and Delftia. For the genera Ochrobactrum and Delftia, for the first time AHL-degrading isolates were found. Data presented in this study revealed for the first time that Ochrobactrum sp. strain A44 showed the capacity to inactivate various synthetic AHL molecules; the substituted AHLs were inactivated with a lower efficiency than the unsubstituted AHLs. Compared with the other isolates, A44 was very effective in the degradation of AHLs produced by P. carotovorum subsp. carotovorum. It was verified by polymerase chain reaction, DNA-DNA hybridization, and a lactone ring reconstruction assay that Ochrobactrum sp. strain A44 did not possess AHL lactonase activity. AHL degradation in Ochrobactrum sp. strain A44 occurred intracellularly; it was not found in the culture supernatant. AHL-degrading activity of A44 was thermo sensitive. Experiments in planta revealed that Ochrobactrum sp. strain A44 significantly inhibited the maceration of potato tuber tissue. Since A44 did not produce antibiotics, the attenuation of the decay might be due to the quenching of quorum- sensing-regulated production of pectinolytic enzymes. The strain can potentially serve to control P. carotovorum subsp. carotovorum in potato.

Comparison of two fatty acid analysis protocols to characterize and differentiate Fusarium oxysporum f. sp. lycopersici and F. oxysporum f. sp. radicis-lycopersici

The utility of fatty acid methyl ester (FAME) profiles for characterization and differentiation of isolates of Fusarium oxysporum f. sp. lycopersici and F. oxysporum f. sp. radicis-lycopersici was investigated. Two fatty acid analysis protocols of the normal (MIDI) and a modified MIDI method were used for their utility. Only the modified MIDI method allowed a clear differentiation between F. oxysporum f. sp. lycopersici and F. oxysporum f. sp. radicislycopersici. FAME profiles using the modified MIDI method gave the most consistent and reproducible analyzed fatty acid data. Evaluation of the FAME profiles based on cluster analysis and principal-component analysis revealed that FAME profiles from tested isolates were correlated with the same vegetative compatibility groups (VCGs) compared to the same races in F. oxysporum f. sp. lycopersici. Results indicated that FAME profiles could be an additional tool useful for characterizing isolates and forma species of F. oxysporum obtained from tomato.

Cultivation-dependent characterization of rhizobacterial communities from field grown Chinese cabbage Brassica campestris ssp pekinensis and screening of traits for potential plant growth promotion

The composition of the bacterial community associated with plant roots is influenced by a variety of plant, environmental factors and also management practices. Our study aimed at detecting the root associated bacterial communities of Chinese cabbage under different fertilization regimes using cultivation dependent methods. The cultivable population was studied using plate count assay, fatty acid methyl ester (FAME) analysis and carbon substrate utilization␣(SU)using BIOLOG™ plates. Taxonomical identification of the isolates by FAME resulted in about 83% identification and they represented 9 and 14 different known bacterial genera from the rhizosphere and root interior respectively from Proteobacteria (α, β, and γ), firmicutes (actinobacteria and the Bacillus groups) and Bacteroidetes. Pseudomonas and Bacillus were associated with the plants grown under all the fertilized conditions and actinobacteria could be observed only in rhizosphere of plants grown on unfertilized plots. FAME and BIOLOG profiles of the rhizosphere and endophytic isolates could separate them with reference to fertilization. Principal component analysis (PCA) on the BIOLOG SU revealed that the isolates were metabolically dissimilar. The diversity, as revealed by the diversity indices was greater among the isolates obtained from unfertilized samples than that of fertilized ones. The isolates analyzed for different traits related to plant growth promotion revealed differences between rhizosphere and endophytic isolates and also with reference to the treatments. The highest percentage of phosphate solubilizing bacteria (PSB) and 1-aminocyclopropane-1-carboxylic acid (ACC) utilizers was recorded in chemical fertilizer treated samples, followed by the organic fertilizer treated. The results from this study indicate that fertilizers have an effect on the root associated bacterial communities of Chinese cabbage and also on their physiological characteristics related to plant growth promotion.

Using FAME profiles for the characterization of animal wastes and vermicomposts

This study investigated the possibility of fingerprinting different organic wastes (cow, pig and horse manure) and the vermicomposts produced by different earthworm species ( Eisenia andrei, Eudrilus eugeniae and Lumbricus rubellus) analyzing the profiles of fatty acid methyl esters (FAMEs). We found clear differences between their microbial communities, demonstrating the power and sensitivity of the total FAME analysis. In addition, qualitative and quantitative analyses of specific biomarkers permitted to determine differences between samples and to evaluate the effect of earthworms in the decomposition of organic matter. Fatty acid profiles were largely determined by the different vermicomposting earthworm species. Fatty acid 18:2ω6 increased significantly in horse manure vermicomposted by L. rubellus and in cow manure vermicomposted by the three earthworm species, whereas it decreased significantly in pig manure vermicomposted by L. rubellus and E. eugeniae. Fatty acid 20:4ω6 increased significantly in all vermicomposts obtained with the three earthworm species.

First Report of Bacterial Leaf Spot on Leafy Brassica Greens Caused by Pseudomonas syringae pv. maculicola in South Carolina.

As of 2001, South Carolina ranked second in the United States in acreage of turnip greens (Brassica rapa) and collard (B. oleracea) and third in acreage of mustard (B. juncea). In June 2001, a leaf disease was found on turnip greens (cv. Alamo), mustard (cvs. Southern Giant Curled and Florida Broadleaf), and rape salad greens (B. napus var. napus cv. Essex) on a commercial farm in Lexington County, South Carolina. Symptoms appeared after a heavy rainstorm that included blowing sand. The disease was found in May and June 2002 on three additional farms in the same county on turnip greens cv. Topper and Royal Crown and collard cv. Top Bunch. Symptoms included small tan spots, water soaking, yellowing, and brown necrosis of leaves after spots coalesced on the lower halves of plants. Yellowing was more prevalent on older than on younger leaves. Leaf samples were collected in 2001 and 2002 from the affected hosts on the four farms. Bacterial streaming was evident from these samples and 27 strains were isolated on nutrient agar or King's medium B (KMB). All strains were gram negative and fluoresced bluegreen or yellow under UV light after 48-h growth at 28°C on Pseudomonas agar F (PAF). On the basis of LOPAT tests, the strains were identified as P. syringae (2). All 27 strains were tested for pathogenicity to rape salad greens cv. Essex and then to turnip greens cv. Topper. Plants were grown in peat-vermiculite potting mix in 10-cm-diameter pots in a greenhouse. P. syringae pv. maculicola F41, isolated from turnip in Oklahoma, and P. syringae pv. tomato F33, isolated from tomato in Oklahoma, were included as positive and negative controls along with a noninoculated control. Bacteria were grown on KMB for 48 h at 24°C, and bacterial suspensions were prepared and adjusted to 0.1 optical density at 600 nm. Three-week-old plants were held at 95 to 100% relative humidity (RH) for 48 h before they were sprayed just to runoff with inoculum and then held at 95 to 100% RH for 48 h after inoculation (4). After an additional 5 to 8 days in a greenhouse, nine strains and F41 caused symptoms on both Topper and Essex similar to symptoms observed in the field. No symptoms were observed on noninoculated plants or plants inoculated with F33. On the basis of repetitive sequence-based polymerase chain reactions with the BOXA1R primer, the DNA fingerprint of each of the nine pathogenic strains from South Carolina was nearly identical to that of F41. Bacteria isolated from inoculated, symptomatic turnip leaves had identical LOPAT and BOXA1R profiles to the corresponding original strains. Pathogenic strains had bluegreen fluorescence on PAF, whereas nonpathogenic strains fluoresced yellow. Five pathogenic strains, as well as F41, were further identified to species and pathovar with fatty acid methyl ester profiles as P. syringae pv. maculicola. To our knowledge, this is the first report of P. syringae pv. maculicola from South Carolina. Over the past 10 years, P. syringae pv. maculicola has been found in Oklahoma (4), California (1), and Ohio (3). Bacterial leaf spot has occurred yearly in South Carolina since the initial outbreaks. Currently, it is the disease that causes the greatest yield losses of leafy brassica greens in the state.

Characterization of Armillaria spp. from peach orchards in the southeastern United States using fatty acid methyl ester profiling

Limited information is available regarding the composition of cellular fatty acids in Armillaria and the extent to which fatty acid profiles can be used to characterize species in this genus. Fatty acid methyl ester (FAME) profiles generated from cultures of A. tabescens, A. mellea, and A. gallica consisted of 16–18 fatty acids ranging from 12–24 carbons in length, although some of these were present only in trace amounts. Across the three species, 9- cis,12- cis-octadecadienoic acid (9,12-C18:2), hexadecanoic acid (16:0), heneicosanoic acid (21:0), 9- cis-octadecenoic acid (9-C18:1), and 2-hydroxy-docosanoic acid (OH-22:0) were the most abundant fatty acids. FAME profiles from different thallus morphologies (mycelium, sclerotial crust, or rhizomorphs) displayed by cultures of A. gallica showed that thallus type had no significant effect on cellular fatty acid composition ( P > 0.05), suggesting that FAME profiling is sufficiently robust for species differentiation despite potential differences in thallus morphology within and among species. The three Armillaria species included in this study could be distinguished from other lignicolous basidiomycete species commonly occurring on peach ( Schizophyllum commune, Ganoderma lucidum, Stereum hirsutum, and Trametes versicolor) on the basis of FAME profiles using stepwise discriminant analysis (average squared canonical correlation = 0.953), whereby 9-C18:1, 9,12-C18:2, and 10- cis-hexadecenoic acid (10-C16:1) were the three strongest contributors. In a separate stepwise discriminant analysis, A. tabescens, A. mellea, and A. gallica were separated from one another based on their fatty acid profiles (average squared canonical correlation = 0.924), with 11- cis-octadecenoic acid (11-C18:1), 9-C18:1, and 2-hydroxy-hexadecanoic acid (OH-16:0) being most important for species separation. When fatty acids were extracted directly from mycelium dissected from naturally infected host tissue, the FAME-based discriminant functions developed in the preceding experiments classified all samples ( n = 16) as A. tabescens; when applied to cultures derived from the same naturally infected samples, all unknowns were similarly classified as A. tabescens. Thus, FAME species classification of Armillaria unknowns directly from infected tissues may be feasible. Species designation of unknown Armillaria cultures by FAME analysis was identical to that indicated by IGS-RFLP classification with AluI.

Characterization of Escherichia Coli Isolates from Different Fecal Sources by Means of Classification Tree Analysis of Fatty Acid Methyl Ester (Fame) Profiles

Microbial source tracking (MST) methods need to be rapid, inexpensive and accurate. Unfortunately, many MST methods provide a wealth of information that is difficult to interpret by the regulators who use this information to make decisions. This paper describes the use of classification tree analysis to interpret the results of a MST method based on fatty acid methyl ester (FAME) profiles of Escherichia coli isolates, and to present results in a format readily interpretable by water quality managers. Raw sewage E. coli isolates and animal E. coli isolates from cow, dog, gull, and horse were isolated and their FAME profiles collected. Correct classification rates determined with leaveone-out cross-validation resulted in an overall low correct classification rate of 61%. A higher overall correct classification rate of 85% was obtained when the animal isolates were pooled together and compared to the raw sewage isolates. Bootstrap aggregation or adaptive resampling and combining of the FAME profile data increased correct classification rates substantially. Other MST methods may be better suited to differentiate between different fecal sources but classification tree analysis has enabled us to distinguish raw sewage from animal E. coli isolates, which previously had not been possible with other multivariate methods such as principal component analysis and cluster analysis.

Cropping system effects on soil biological characteristics in the Great Plains

AbstractSoil biological quality can affect key soil functions that support food production and environmental quality. The objective of this study was to determine the effects of management and time on soil biological quality in contrasting dryland cropping systems at eight locations in the North American Great Plains. Alternative (ALT) cropping systems were characterized by greater cropping intensity (less fallow), more diverse crop sequences, and/or reduced tillage than conventional (CON) cropping systems. Soil biological properties were assessed at depths of 0–7.5, 7.5–15, and 15–30 cm from 1999 to 2002 up to three times per year. Compared to CON, ALT cropping systems had greater microbial biomass and potentially mineralizable N. ALT cropping systems also had greater water stable aggregates in the surface 7.5 cm, but only at four locations. Total glomalin (TG), an organic fraction produced by fungi associated with aggregate stability, differed only at one location (Mandan), where the ALT cropping system had 27% more TG than the CON cropping system. Fatty acid methyl ester (FAME) profiles were highly location dependent, but total extracted FAME tended to be higher in ALT cropping systems. Soil biological properties fluctuated over time at all locations, possibly in response to weather, apparent changes in soil condition at sampling, and the presence or absence of fallow and/or legumes in rotation. Consequently, preplant and post-harvest sampling, when weather and soil conditions are most stable, is recommended for comparison of soil biological properties among management practices. Overall, ALT cropping systems enhanced soil function through: (1) improved retention and cycling of nutrients and (2) maintenance of biodiversity and habitat, implying improved agro-ecosystem performance over time.