Bacterial Fatty Acid Methyl Ester Research Articles

No‐till marginally mitigates the impact of harvesting corn stover on soil microbial parameters

AbstractHarvesting corn stover can negatively impact soil chemical and physical properties, but less is known regarding its effects on soil microbiology. We evaluated the impact of corn (Zea mays L.) stover removal level (SRL) on soil microbial biomass (MB) and extracellular enzyme activities (EEAs) in irrigated, continuous corn located in eastern Nebraska. Soil fatty acid‐methyl esters (FAMEs) and EEA of eight soil enzymes were measured over 2 years, 0‐ to 20‐cm soil depth, under conventional disk tillage (CT) and no‐till (NT) under three SRLs. Soil chemical properties were measured as explanatory variables for changes in soil microbial communities and their enzymatic potential. Potential EEA of all enzymes decreased with stover removal and tillage. Soil bacterial biomass (BB) and fungal biomass (FB) decreased with SRL, while mycorrhizal biomass was unresponsive. Impacts of tillage on MB groups varied by year; however, FB was consistently higher under CT. At all growth stages, NT with all stover retained, a “soil conservation target” had distinct soil enzyme and bacterial FAME profiles compared to CT across all SRLs and to NT under high and sometimes moderate SRLs. Principal component analysis of soil properties was dominated by SRL with EEAs, BB, soil organic matter (SOM), water‐extractable carbon, and H3A‐extractable potassium being positively correlated to stover retention. Reduced input of microbial substrates also led to a loss of fine particulate organic matter, an indicator correlated to stable macroaggregation. Because NT partially ameliorated the negative impact of stover removal on BB, SOM fractions, and soil enzymes critical to nutrient cycling, pairing NT with stover removal may be more sustainable in the long term.

A green garlic (Allium sativum L.) based intercropping system reduces the strain of continuous monocropping in cucumber (Cucumis sativus L.) by adjusting the micro-ecological environment of soil.

The continuous cropping obstacle of cucumber (Cucumis sativus L.) under facility cultivation is more prevalent in China. This is associated with an imbalance in soil microbial and ecological environment in long-term monocultures. It was postulated that intercropping with green garlic would relieve the continuous cropping obstacle of cucumber by altering the soil micro-ecology status. A pot-based experiment was conducted to investigate the green garlic-cucumber intercropping and cucumber monocropping systems. The results showed that the cucumber shoot biomass was improved by intercropping with green garlic. However, the population of soil bacteria and actinomycetes increased, while the fungal population decreased. The fatty acid methyl ester (FAME) profiles indicated that soil contained more fungal FAME biomarkers (18:1ω9c, 18:2ω6, 9) and higher fungal:bacterial ratio in the monoculture system, whereas clustering of more bacterial FAME biomarkers (cy17:0, cy19:0, 16:1ω7c10, Me16:0, 10Me17:0, 10Me18:0) was observed under intercropping conditions. Moreover, significantly (P < 0.05) higher soil invertase and alkaline phosphatase activities, organic matter, and available N, P and K contents were observed under intercropping systems. These were high in both bulk and rhizosphere soils in the intercropping system when compared to monocropping system. These findings suggest that intercropping with green garlic can alleviate continuous cropping obstacle of cucumber by improving the diverse composition of soil microbial community, enzyme activities, and nutrient availability.

Qualitative and Quantitative Estimation of Bacterial Lipid Production.

An ever increasing energy demand and fast depletion of fossil fuels have led to increased consideration of bacterial lipids as a renewable biofuel source. Many methods are available for both physical and chemical extraction of bacterial lipids. The method of choice will depend on the nature of sample to be analyzed, combinations of solvent systems preferred, content and quality of the lipid to be analyzed, types of equipment available, and time of the extraction procedures employed. Here we describe the most reliable, routine method of extracting bacterial lipids and evaluating the growth kinetic parameters like biomass and lipid productivity and lipid content. We also describe the method of comparing bacterial fatty acid methyl ester peaks with standard peaks for analysis.

Effect of gasification biochar application on soil quality: Trace metal behavior, microbial community, and soil dissolved organic matter.

Compared to pyrolysis biochar (PBC), gasification biochar (GBC) differs in both composition and surface functionalities due to the use of an oxidizing purging gas. This work compares the effect of using PBC and GBC as soil amendments on the soil properties, trace metal bioavailability, soil microbial activity, and soil dissolved organic matter (DOM). Biochar-driven reduction of bioavailable metals does not necessarily result in a positive impact on the soil microbial growth. The DOM in the soil was strongly related to the soil microbial activity, as revealed by the strong correlation between the soil dehydrogenase activity (DHA) and soil dissolved organic carbon (r = 0.957, p < 0.01). Three identified fluorescent components (C1, C2, C3) in the soil DOM were closely associated with the soil microbial activity, for instance, with a clear positive correlation between the soil DHA and C1 (r = 0.718, p < 0.05) and a significant negative correlation between the total bacterial fatty acid methyl ester content and C3 (r = -0.768, p < 0.05). The bioavailability of Cd and Zn is not only related to the pH and surface functionalities of the biochar, but also to its aromatic carbon and inorganic mineral composition. This study further demonstrates that a fluorescence excitation-emission matrix coupled with parallel factor analysis is a useful tool to monitor changes in the soil quality after application of biochar, which is greatly relevant to the soil biota.

Variation of anionic moieties of dicationic ionic liquid GC stationary phases: Effect on stability and selectivity

Dicationic ionic liquids (DILs) are more and more accepted as a new class of high temperature and polar stationary phases for gas chromatography (GC). This study deals with the effect of seven different fluorosulfonyl derivatized anions associated with two dications: 1,3-di(3-methylimidazolium)-2-methylpropane [2mC3(mim)2], and 1,3-di(3-methylimidazolium)-isobutene [i-eneC4(mim)2]. Thermophysical properties of the 14 synthesized DILs were evaluated in terms of melting point, viscosity, and thermal stability. The optimal physicochemical properties of 13 DILs allowed preparing 13 GC capillary columns. Accordingly, the polarity and selectivity of the DILs were evaluated by determining the Rohrschneider-McReynolds constants and the equivalent chain lengths of C18 fatty acid methyl esters (FAMEs). The symmetrical fluoroalkylsulfonyl and the trifluorosulfonate anions seem to produce the most polar DILs. Compared to classical polyethyleneglycol phases, the DILs showed substantially decreased retention of apolar compounds and a much stronger retention of the polar ones. Unique selectivities were observed with unsaturated FAMEs, polyaromatic hydrocarbons, and bacterial specific FAMEs. The two applications presented included a biodiesel and bacterial FAME analyses.

Analysis of bacterial FAMEs using gas chromatography – vacuum ultraviolet spectroscopy for the identification and discrimination of bacteria

The identification of microorganisms is very important in different fields and alternative methods are necessary for a rapid and simple identification. The use of fatty acids for bacterial identification is gaining attention as phenotypic characteristics are reflective of the genotype and are more easily analyzed. In this work, gas chromatography-vacuum ultraviolet spectroscopy (GC-VUV) was used to determine bacteria fatty acid methyl esters (FAMEs), to identify and discriminate different environmental bacteria based on their fatty acid profile. Microorganisms were grown in agar and their fatty acids extracted, saponified, and esterified before analysis. Unique FAME profiles were obtained for each microorganism mainly composed of branched, cyclopropane, hydroxy, saturated, and unsaturated fatty acid methyl esters. S. maltophilia showed a higher diversity of fatty acids while Bacillus species showed higher complexity in terms of branched-chain FAMEs, with several iso and anteiso forms. 12 different bacteria genera and 15 species were successfully differentiated based on their fatty acid profiles after performing PCA and cluster analysis. Some difficult to differentiate species, such as Bacillus sp., which are genetically very similar, were differentiated with the developed method.

Cover cropping frequency is the main driver of soil microbial changes during six years of organic vegetable production

Soil microbes play a key role in soil health, and understanding the functional role of this living component of soil organic matter is critical to developing sustainable systems in major vegetable production regions like Salinas, California. Soil microbial community size and composition was evaluated after six years of commercial-scale production in five organic vegetable systems in a long-term systems experiment. All systems produced lettuce, and spinach or broccoli annually, and differed in yard-waste compost inputs (none or 15.2 Mg ha−1 year−1), winter cover crop frequency (annually or every 4th year), and cover crop type (legume-rye, mustard, or rye). The same levels of irrigation, and supplemental fertilizer were applied to all systems. Cumulative organic matter inputs from compost and cover crop shoots over the six years ranged from 7.4 to 136.8 Mg ha−1 and caused differences in microbial biomass C (MBC) and N (MBN), and soil organic C (SOC). MBC increased by 40 mg C kg−1 soil with compost and infrequent cover cropping, and to levels that were relatively high (200–250 mg C kg−1 soil) for a loamy sand soil in systems with annual cover cropping. Changes in SOC between systems were caused primarily by compost while changes in MBC and MBN were more related to cover cropping frequency. Fatty acid methyl ester (FAME) analysis revealed differences in microbial community structure that were consistent with differences between systems in MBC and MBN. Across systems, the ratio of fungal: bacterial FAME indicators decreased over time while indicators of invertebrates, and gram positive bacteria increased. High-throughput sequencing revealed relatively few differences in bacterial phyla between systems, but the increase in cropping intensity across all systems changed the relative abundance of some bacterial phyla (Bacteroidetes, Deinococcus-Thermus) and genera (Flavobacterium, Nocardioidetes). Cover crop type and frequency also influenced the abundance of two bacterial genera (Pseudomonas, Agromyces). These results provide evidence that carbon (C) inputs from frequent cover cropping are the primary driver of changes in the soil food web and soil health in high-input, tillage-intensive organic vegetable production systems.

Profiling of soil fatty acids using comprehensive two-dimensional gas chromatography with mass spectrometry detection

Profiling of phospholipid fatty acids (PLFA) represents a challenging goal for distinguishing the diversity of microbial communities and biomass in the complex and heterogeneous soil ecosystem. Comprehensive two-dimensional gas chromatography (GC×GC) coupled with simultaneous flame ionisation and mass spectrometry detection was applied as a culture-independent method for PLFA profiling of microbial classification in forest soil. A number of column sets were evaluated for the GC×GC separation of fatty acid methyl esters (FAME). Due to better isomeric separation and compound patterns on the 2D contour plot, an apolar–polar column combination was selected for soil microbial PLFA characterisation. A comprehensive view of PLFA composition with carbon chain length varying from 12 to 20 was observed in forest soil samples, with the commonly reported bacterial FAME of iso-/anteiso-, methyl-branched-, cyclopropyl-, and hydroxyl-substituted FA identified by their mass spectral and retention time according to authentic standards. Notably, some uncommon oxygenated FAME were found in high abundance and were further characterised by GC×GC coupled with high resolution mass spectrometry. This tentatively revealed geometric pairs of methyl 9,10-epoxyoctadecanoate isomers.

Diversity of culturable marine bacteria on the coastline of the central area of San Jorge Gulf, Argentina

This study aims to isolate and identify culturable marine bacteria from 4 locations in the San Jorge Gulf. A total of 1,532 strains were isolated using oligotrophic, heterotrophic and hydrocarbon- degrading bacteria media, and identified with reference to bacterial fatty acid methyl ester (FAME) profiles. Gram-negative bacteria were the most abundant, Pseudoalteromonas comprised 17% of the isolated bacteria, followed by Pseudomonas, with 11.14%. The Gram-positive bacteria genera identified were Staphylococcus, Bacillus and Micrococcus. In addition, those bacteria able to degrade hydrocarbons were: Arthrobacter, Dietzia, Acinetobacter, Microbacterium, Micrococcus, Bacillus, Pseudomonas and Pseudoalteromonas.

FAME Profiling and Activity of Microbial Communities During Jatropha curcas L. Residue Decomposition in Semiarid Soils

There is widespread interest in the renewable biofuel potential of Jatropha curcas L., a shrub that exists under indigenous conditions in India. Following oil extraction from seeds, the remaining shell and cake residue can be used as a soil amendment. Microbial decomposition of organic residues can improve the quality of soils, but little is known about Jatropha as a soil amendment. Therefore, the objective of this study was to determine the influence of Jatropha residue on soil microbial community structure during decomposition. Soil microcosms amended with Jatropha leaves, cake, or fruit shell or an unamended control were incubated in the laboratory and destructively sampled at 3, 10, 20, 40, and 60 days. At each sampling, soil microbial communities were analyzed using fatty acid methyl ester (FAME) profiles, and enzyme assays performed for β-glucosidase, cellulase, and urease. Microbial biomass (FAMEtot) and bacterial and fungal FAME concentrations were significantly higher in cake-amended soil compared with other treatments. Averaged across all treatments, FAMEtot and fungal and bacterial FAMEs were highest on Day 3 and subsequently decreased significantly. Higher fungal-to-bacterial FAME ratios were found in residue-amended soils over control, with the highest ratio occurring in fruit shell-amended soil (except Day 3). A significantly lower ratio of the stress indicator (saturated to monounsaturated FAMEs) was found in cake-amended soil compared with other amendments. Fungal, bacterial, and actinomycetes biomarkers were significantly correlated with β-glucosidase and cellulase activities. The study shows that decomposition of Jatropha affected the soil microbial community, differently depending on residue type, but overall had positive effects in promoting the microbial diversity and activity, thus making Jatropha residue a favorable amendment for soils.

Classification of bacteria by simultaneous methylation–solid phase microextraction and gas chromatography/mass spectrometry analysis of fatty acid methyl esters

Direct methylation and solid-phase microextraction (SPME) were used as a sample preparation technique for classification of bacteria based on fatty acid methyl ester (FAME) profiles. Methanolic tetramethylammonium hydroxide was applied as a dual-function reagent to saponify and derivatize whole-cell bacterial fatty acids into FAMEs in one step, and SPME was used to extract the bacterial FAMEs from the headspace. Compared with traditional alkaline saponification and sample preparation using liquid-liquid extraction, the method presented in this work avoids using comparatively large amounts of inorganic and organic solvents and greatly decreases the sample preparation time as well. Characteristic gas chromatography/mass spectrometry (GC/MS) of FAME profiles was achieved for six bacterial species. The difference between Gram-positive and Gram-negative bacteria was clearly visualized with the application of principal component analysis of the GC/MS data of bacterial FAMEs. A cross-validation study using ten bootstrap Latin partitions and the fuzzy rule building expert system demonstrated 87 +/- 3% correct classification efficiency.

Relationship Between Microbial Community and Soil Properties During Natural Succession of Abandoned Agricultural Land

The changes of microbial biomass carbon (MBC) and nitrogen (MBN) and microbial community in the topsoil of the abandoned agricultural land on the semi-arid Loess Plateau in China during the natural succession were evaluated to understand the relationship between microbial community and soil properties. MBC and MBN were measured using fumigation extraction, and microbial community was analyzed by the method of fatty acid methyl ester (FAME). The contents of organic C, total N, MBC, MBN, total FAME, fungal FAME, bacterial FAME and Gram-negative bacterial FAME at the natural succession sites were higher than those of the agricultural land, but lower than those of the natural vegetation sites. The MBC, MBN and total FAME were closely correlated with organic C and total N. Furthermore, organic C and total N were found to be positively correlated with fungal FAME, bacterial FAME, fungal/bacterial and Gram-negative bacterial FAME. Natural succession would be useful for improving soil microbial properties and might be an important alternative for sustaining soil quality on the semi-arid Loess Plateau in China.

Analysis of bacterial fatty acids by flow modulated comprehensive two-dimensional gas chromatography with parallel flame ionization detector/mass spectrometry

Comprehensive two-dimensional gas chromatography (GC × GC) offers an interesting tool for profiling bacterial fatty acids. Flow modulated GC × GC using a commercially available system was evaluated, different parameters such as column flows and modulation time were optimized. The method was tested on bacterial fatty acid methyl esters (BAMEs) from Stenotrophomonas maltophilia LMG 958 T by using parallel flame ionization detector (FID)/mass spectrometry (MS). The results are compared to data obtained using a thermal modulated GC × GC system. The data show that flow modulated GC × GC-FID/MS method can be applied in a routine environment and offers interesting perspectives for chemotaxonomy of bacteria.

Microanatomy and bacterial flora of the perineal glands of the North American porcupine

The perineal glands of the porcupine, Erethizon dorsatum (L., 1758), are sexually dimorphic, paired pockets sprouting osmetrichial hairs. They lie between the anus and urethra, lateral to the midline, amid a sebaceous glandular expanse. In their active state, the glandular pockets secrete an amber substance with a terpenoid odor. When inactive, the glands produce no stain or odor. In males, activation of the glands is associated with fully descended testes. The glandular pockets yield a microbiota (“microflora”) in both their active and inactive states. We hypothesize that the active-state microflora transforms a sebaceous secretion into a pheromonally active product that is disseminated by anal dragging. The glandular microflora was characterized by gas chromatography of bacterial fatty acid methyl esters (GC-FAME) and polymerase chain reaction – denaturing gradient gel electrophoresis (PCR-DGGE) of 16S ribosomal RNA gene fragments of bacteria. PCR-DGGE results showed the resulting bacteria profiles were the same in both sexes, but differed between the active and inactive states. Active-state microfloras were dominated by members of the Actinobacteria and showed greater coefficients of similarity than inactive-state microfloras. The microflora of individual animals changed with time and with secretory state. We argue for a reproductive role for the activated perineal glands.

Evaluating the effect of fertilizer application on soil microbial community structure in rice based cropping system using fatty acid methyl esters (FAME) analysis

The present study was undertaken to observe the effects of chemical fertilizers and compost amendments on microbial community structure in rice based cropping system under long term fertilizer application experiment. Changes in microbial community structure assessed by the relative abundance of fatty acid methyl ester (FAME) profiles revealed that compost amendments led to promoting the abundance of Gram-positive bacterial FAMEs. Multivariate analysis of FAME profiles separated the treatments primarily on the basis of the amount of added compost. A link between different fertilizer application treatment and soil microbial components was tentatively established, but it needs to be verified in further studies.

Towards large-scale FAME-based bacterial species identification using machine learning techniques

In the last decade, bacterial taxonomy witnessed a huge expansion. The swift pace of bacterial species (re-)definitions has a serious impact on the accuracy and completeness of first-line identification methods. Consequently, back-end identification libraries need to be synchronized with the List of Prokaryotic names with Standing in Nomenclature. In this study, we focus on bacterial fatty acid methyl ester (FAME) profiling as a broadly used first-line identification method. From the BAME@LMG database, we have selected FAME profiles of individual strains belonging to the genera Bacillus, Paenibacillus and Pseudomonas. Only those profiles resulting from standard growth conditions have been retained. The corresponding data set covers 74, 44 and 95 validly published bacterial species, respectively, represented by 961, 378 and 1673 standard FAME profiles. Through the application of machine learning techniques in a supervised strategy, different computational models have been built for genus and species identification. Three techniques have been considered: artificial neural networks, random forests and support vector machines. Nearly perfect identification has been achieved at genus level. Notwithstanding the known limited discriminative power of FAME analysis for species identification, the computational models have resulted in good species identification results for the three genera. For Bacillus, Paenibacillus and Pseudomonas, random forests have resulted in sensitivity values, respectively, 0.847, 0.901 and 0.708. The random forests models outperform those of the other machine learning techniques. Moreover, our machine learning approach also outperformed the Sherlock MIS (MIDI Inc., Newark, DE, USA). These results show that machine learning proves very useful for FAME-based bacterial species identification. Besides good bacterial identification at species level, speed and ease of taxonomic synchronization are major advantages of this computational species identification strategy.

Relationships between microbial communities and environmental parameters at sites impacted by mining of volcanogenic massive sulfide deposits, Prince William Sound, Alaska

Abstract The relations among geochemical parameters and sediment microbial communities were examined at three shoreline sites in the Prince William Sound, Alaska, which display varying degrees of impact by acid-rock drainage (ARD) associated with historic mining of volcanogenic massive sulfide deposits. Microbial communities were examined using total fatty acid methyl esters (FAMEs), a class of compounds derived from lipids produced by eukaryotes and prokaryotes (bacteria and Archaea); standard extraction techniques detect FAMEs from both living (viable) and dead (non-viable) biomass, but do not detect Archaeal FAMEs. Biomass and diversity (as estimated by FAMEs) varied strongly as a function of position in the tidal zone, not by study site; subtidal muds, Fe oxyhydroxide undergoing biogenic reductive dissolution, and peat-rich intertidal sediment had the highest values. These estimates were lowest in acid-generating, intertidal zone sediment; if valid, the estimates suggest that only one or two bacterial species predominate in these communities, and/or that Archeal species are important members of the microbial community in this sediment. All samples were dominated by bacterial FAMEs (median value >90%). Samples with the highest absolute abundance of eukaryotic FAMEs were biogenic Fe oxyhydroxides from shallow freshwater pools (fungi) and subtidal muds (diatoms). Eukaryotic FAMEs were practically absent from low-pH, sulfide-rich intertidal zone sediments. The relative abundance of general microbial functional groups such as aerobes/anaerobes and gram(+)/gram(−) was not estimated due to severe inconsistency among the results obtained using several metrics reported in the literature. Principal component analyses (PCAs) were performed to investigate the relationship among samples as separate functions of water, sediment, and FAMEs data. PCAs based on water chemistry and FAMEs data resulted in similar relations among samples, whereas the PCA based on sediment chemistry produced a very different sample arrangement. Specifically, the sediment parameter PCA grouped samples with high bulk trace metal concentration regardless of whether the metals were incorporated into secondary precipitates or primary sulfides. The water chemistry PCA and FAMEs PCA appear to be less prone to this type of artifact. Signature lipids in sulfide-rich sediments could indicate the presence of acid-tolerant and/or acidophilic members of the genus Thiobacillus or they could indicate the presence of SO4-reducing bacteria. The microbial community documented in subtidal and offshore sediments is rich in SRB and/or facultative anaerobes of the Cytophaga–Flavobacterium group; both could reasonably be expected in PWS coastal environments. The results of this study provide evidence for substantial feedback between local (meter to centimeter-scale) geochemical variations, and sediment microbial community composition, and show that microbial community signatures in the intertidal zone are significantly altered at sites where ARD drainage is present relative to sites where it is not, even if the sediment geochemistry indicates net accumulation of ARD-generated trace metals in the intertidal zone.

Increased N availability in grassland soils modifies their microbial communities and decreases the abundance of arbuscular mycorrhizal fungi

Two complementary studies were performed to examine (1) the effect of 18 years of nitrogen (N) fertilization, and (2) the effects of N fertilization during one growing season on soil microbial community composition and soil resource availability in a grassland ecosystem. N was added at three different rates: 0, 5.44, and 27.2 g N m −2 y −1. In both studies, Schizachyrium scoparium was the dominant plant species before N treatments were applied. Soil microbial communities from each experiment were characterized using fatty acid methyl ester (FAME) analysis. Discriminant analysis of the FAMEs separated the three N fertilizer treatments in both experiments, indicating shifts in the composition of the microbial communities. In general, plots that received N fertilizer at low or high application rates for 18 years showed increased proportions of bacterial FAMEs and decreased fungal FAMEs. In particular, control plots contained a significantly higher proportion of fungal FAMEs C18:1( cis9) and C18:2( cis9,12) and of the arbuscular mycorrhizal fungal (AMF) FAME, C16:1( cis11), than both of the N addition treatment plots. A significant negative effect of N fertilization on the AMF FAME, C16:1( cis11), was measured in the short-term experiment. Our results indicate that high rates of anthropogenic N deposition can lead to significant changes in the composition of soil microbial communities over short periods and can even disrupt the relationship between AMF and plants.

Identification of foodborne bacteria by infrared spectroscopy using cellular fatty acid methyl esters

Identification of bacterial species by profiling fatty acid methyl esters (FAMEs) has commonly been carried out by using a 20-min capillary gas chromatographic procedure followed by library matching of FAME profiles using commercial MIDI databases and proprietary pattern recognition software. Fast GC (5 min) FAME procedures and mass spectrometric methodologies that require no lipid separation have also been reported. In this study, bacterial identification based on the rapid (2 min) infrared measurement of FAME mixtures was demonstrated. The microorganisms investigated included Gram positive bacteria Staphylococcus aureus, Listeria monocytogenes, Bacillus anthracis, and Bacillus cereus, and Gram negative bacteria from the family Enterobacteriacae: Yersinia enterocolitica, Salmonella typhimurium, Shigella sonnei, and Escherichia coli (four strains of E. coli), and non-Enterobacteriacae: Vibrio cholerae, Vibrio vulnificus, and Vibrio parahemolyticus. Foodborne bacterial mixtures of FAMEs were measured by using an attenuated total reflection (ATR)–Fourier transform infrared (FTIR) spectroscopic procedure and discriminated by multivariate analysis. Results showed that the Enterobacteriacae could be discriminated from the vibrios. The identification was at the level of species (for the Bacillus and Vibrio genera) or strains (for the E. coli species). A series of bacterial FAME test samples were prepared and analyzed for accuracy of identification, and all were correctly identified. Our results suggest that this infrared strategy could be used to identify foodborne pathogens.

Seasonal, soil type, and alternative management influences on microbial communities of vegetable cropping systems

Microbial community responses to alternative management may be indicative of soil quality change. In this study, soils were collected from research plots over 2 years and from commercial grower fields over 1 year. Treatments at the sites included 1–9 years of either winter cover cropping or winter fallow practices. Soils were assayed for microbial fatty acid methyl esters (FAMEs), direct count microscopy and Biolog substrate utilization potentials to assess management and environmental influences on soil communities. The strongest influence was season. Soils in early spring (prior to termination of the cover crop) utilized fewer carboxylic acids and generally were enriched in eukaryotic FAMEs, whereas proportionally more bacterial FAMEs were detected in soils at canopy closure and harvest of the summer vegetable crop. Within a season, community FAME and Biolog patterns were related to field properties. FAME profiles from grower fields in early spring and harvest were correlated significantly with soil texture, cation exchange capacity, and carbon content. Changes in community structure and Biolog potential occurred in some soils in response to winter cover crops, although effects were not observed until cover crop incorporation. Greater amounts of fungal and protozoan FAME markers were detected in some cover-cropped soils compared to winter fallow soils. Cover crop residues increased FAME diversity at one research station and Biolog diversity at two research stations and the grower fields. Although seasonal and field-dependent factors are major determinants of microbial community structure, shifts can occur as soil physical and chemical properties change in response to alternative practices, as demonstrated by this study.