Catabolic response and phospholipid fatty acid profiles as microbial tools to assess soil functioning

Microbial properties may help to provide an integrated view of changes in soil functioning associated with soil management or soil status. The fatty acid profiles of membrane phospholipids (PLFA) can give the composition of ecophysiological groups of soil microbial communities, while catabolic response profiles (CRP) estimate the heterotrophic functional diversity in soils, both relevant to the understanding of the role of micro‐organisms in the functioning of the soil. The objectives of this study were (i) to evaluate the CRP and PLFA as microbial tools to characterize changes in soil functioning and (ii) clarify the relation among these microbial measurements, with other physical, chemical and biochemical soil properties. We compare the same soil subjected to different managements and degrees of erosion. An undisturbed soil (UN), an old pasture soil (OP) and soils under continuous cultivation (NT) with four different depth of A horizon: 25 cm (NT 25), 23 cm (NT 23), 19 cm (NT 19) and 14 cm (NT 14) were tested. Substrate‐induced respiration of most substrates diminished when cropping pressure increased (UN > OP > NT), and soil catabolic evenness, as a diversity index, decreased by increasing production pressure and soil erosion. The correlation found among most of the measured physical, chemical and biochemical soil properties with the catabolic evenness showed the potential of this measurement to provide an integrated view of soil functioning. The PLFA analysis showed that the composition of microbial community denoting a partial recovery after 10 yr under grazed grassland. The stress indicators showed that farming practices increased microbial stress with the highest values found in the most eroded soils.     

The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil

The cell content of 12 bacterial phospholipid fatty acids (PLFA) was determined in bacteria extracted from soil by homogenization/centrifugation. The bacteria were enumerated using acridine orange direct counts. An average of 1.40×10^-17 mol bacterial PLFA cell^-1 was found in bacteria extracted from 15 soils covering a wide range of pH and organic matter contents. With this factor, the bacterial biomass based on PLFA analyses of whole soil samples was calculated as 1.0–4.8 mg bacterial C g^-1 soil C. The corresponding range based on microscopical counts was 0.3–3.0 mg bacterial C g^-1 soil C. The recovery of bacteria from the soils using homogenization/centrifugation was 2.6–16% (mean 8.7%) measured by PLFA analysis, and 12–61% (mean 26%) measured as microscopical counts. The soil content of the PLFA 18:26 was correlated with the ergosterol content (r=0.92), which supports the use of this PLFA as an indicator of fungal biomass. The ratio 18:26 to bacterial PLFA is therefore suggested as an index of the fungal:bacterial biomass ratio in soil. An advantage with the method based on PLFA analyses is that the same technique and even the same sample is used to determine both fungi and bacteria. The fungal:bacterial biomass ratio calculated in this way was positively correlated with the organic matter content of the soils (r=0.94).     

Characterization of cider apples on the basis of their fatty acid profiles

In the current study, the fatty acids composition of 30 monovarietal apple juices from six cider apple varieties belonging to two categories was analyzed. The different apple juices were obtained from three consecutive harvests (1997, 1998, and 1999). The fatty acids concentration in apple juice together with chemometric techniques such as principal components analysis (PCA), soft independent modeling of class analogy (SIMCA), and linear discriminant analysis (LDA), allowed us to differentiate apple juices on the basis of the sweet or sharp category to which the cider apple variety belongs. Fatty acids such as the unsaturated oleic and linoleic acids, and saturated caprylic, capric, stearic, and palmitic acids were related to the sweet cider apple category, while pentadecanoic acid is related to the sharp class.     

Effect of added caffeic acid and tyrosol on the fatty acid and volatile profiles of camellia oil following heating

Camellia oil is widely used in some parts of the world partly because of its high oxidative stability. The effect of heating a refined camellia oil for 1 h at 120 degrees C or 2 h at 170 degrees C with exogenous antioxidant, namely, caffeic acid and tyrosol, was studied. Parameters used to assess the effect of heating were peroxide and K values, volatile formation, and fatty acid profile. Of these, volatile formation was the most sensitive index of change as seen in the number of volatiles and the total area count of volatiles in gas chromatograms. Hexanal was generally the dominant volatile in treated and untreated samples with a concentration of 2.13 and 5.34 mg kg(-1) in untreated oils heated at 120 and 170 degrees C, respectively. The hexanal content was significantly reduced in heated oils to which tyrosol and/or caffeic acid had been added. Using volatile formation as an index of oxidation, tyrosol was the more effective antioxidant of these compounds. This is contradictory to generally accepted antioxidant structure-activity relationships. Changes in fatty acid profiles after heating for up to 24 h at 180 degrees C were not significant.     

Differentiation of Enterobacter sakazakii from closely related Enterobacter and Citrobacter species using fatty acid profiles

Capillary gas chromatography with flame ionization detection (GC-FID) was used to determine the cellular fatty acid (CFA) profiles of 134 Enterobacter sakazakii strains, and these were compared to the CFA profiles of other closely related Enterobacter and Citrobacter species. For GC-FID analysis, whole cell fatty acid methyl esters (FAMEs) from cells cultured on brain heart infusion (BHI) agar at 37 degrees C for 24 h were obtained by saponification, methylation, and extraction into hexane/methyl tert-butyl ether. A database for E. sakazakii was prepared using fatty acid profiles from the 134 strains. Major fatty acids of E. sakazakii strains evaluated in this study were straight-chain 12:0, 14:0, and 16:0, unsaturated 18:1 omega7c, and 17:0 omegacyclo 7-8. Principal component analysis (PCA) based on CFA profiles for E. sakazakii strains shows separation of E. sakazakii subgroups A and B. The CFA profiles for E. sakazakii and Enterobacter cloacae show that there are several fatty acids, 14:0, 17:0 omegacyclo 7-8, 18:1 omega7c, and summed 16:1 omega6c/16:1 omega7c, that differ significantly between these two species. A PCA model based on CFA profiles for E. sakazakii strains clearly shows separation of E. sakazakii from closely related Enterobacter and Citrobacter species. Analysis of FAMEs from E. sakazakii strains grown on BHI agar by a rapid GC-FID method can provide a sensitive procedure for the identification of this organism, and this analytical method provides a confirmatory procedure for the differentiation of E. sakazakii strains from closely related Enterobacter and Citrobacter species.     

Soil bacterial and fungal communities along a soil chronosequence assessed by fatty acid profiling

Microbial communities are important components of terrestrial ecosystems. The importance of their diversity and functions for natural systems is well recognized. However, a better understanding of successional changes of microbial communities over long time scales is still required. In this work, the size and composition of microbial communities in soils of a deglaciation chronosequence at the Damma glacier forefield were studied by fatty acid profiling. Soil fatty acid concentrations clearly increased with soil age. The abundances of arbuscular mycorrhizal fungi (AMF), bacteria and other soil fungi, however, were more affected by abiotic soil parameters like carbon content and pH than by soil age. Analysis of ratios of the different microbial groups (AMF, fungi, bacteria) along the soil chronosequence indicated that: i) the ratios of AMF to bacteria and AMF to fungi decreased with soil age; and ii) the ratio of fungi to bacteria remained unchanged along the soil chronosequence. These two pieces of evidence suggest that the evolution of this ecosystem proceeds at an uneven pace over time and that the role of AMF is less important in older, more organic and acidified soils than in mineral soils. In contrast to other studies, no successional replacement of bacteria with fungi in more acidified and organic soil was observed.     

不同肥力水平和利用历史的红壤磷脂脂肪酸图谱

Analysis of phospholipid fatty acids(PLFAs) was used to estimate the microbial community structures of eight Chinese red soils with different fertility levels and land use histories.The total amounts of PLFAs in the soils were significantly correltaed with soil organic carbon, total nitrogen,microbial biomass C and basal respiration,indicating that total PLFA was closely related to fertility and sustainbility in these highly weathered soils.Soils of the eroded wastelan were rich in Gram-positive species .When the eroded soils were planted with citrus trees,the soil microbial population had changed little in 4 years but took up to 8-12 yearss before it reached a significantly different population,Multivariate analysis of PLFAs demonstrated that land use history and plant cover type had a significant impact on microbial community structure.Howver,the difference of soil microbial community structure in the paddy field compared to other land uses was not larger than expected in this experiment.     

Use of GC-olfactometry to identify the hop aromatic compounds in beer

This paper describes a sensorial aroma extract dilution analysis (AEDA) approach to the analysis of beer aromas derived from hops. To obtain an extract with an odor representative of the original product, the XAD extraction procedure was applied and the experimental conditions were optimized. The aromagrams of three beers were compared: one brewed without hops, one brewed with Saaz hop pellets, and one brewed with Challenger hop pellets. One spicy/hoppy compound, unmodified from hop to beer, proved responsible for the most intense odor in both hopped beer extracts. Another flavoring compound in hops, linalool, also survives through the process to the final beer. Other compounds such as gamma-nonalactone and humuladienone, although not found in our extracts of hop, significantly modify beer aromagrams after hopping. Sulfur compounds characteristic of Challenger hops proved to be at least partially responsible for the unpleasant flavor found in the corresponding beer.     

Changes in fatty acid composition with age and environment in different types of peat profiles in Japan

Fatty acid composition of the crude lipid fraction of peat was investigated using several typical peat profiles in Japan. Fatty acid composition varied with the peat layers accumulated in a peat profile since 32,000 years BP. Deposition of long-range transported volcanic ash tephras also affected the composition remarkably due to the acceleration of decomposition. Fatty acid composition differed among high moor, transitional moor, and low moor peat profiles sampled in several locations in Hokkaido, Japan. The difference in the plants involved in the formation of peat was considered to be a very important factor determining the fatty acid composition. For example, arachidic acid was considered to be a good indicator for the presence of reed, while the percentage of stearic acid tended to be high in the high moor peat profiles dominated by sphagnum. As the fatty acids with a longer chain length were more stable than those with a shorter chain length, the percentage of longer fatty acids (C24 and C26) tended to increase and that of shorter fatty acids (CI4 and CI6) to decrease in the lower peat profiles. The drying of peatland also exerted a similar effect on the fatty acid composition.     

Zinc effects on a soil bacterial flora characterized by fatty acid composition of the isolates

Summary Effects of zinc (zinc chloride) added to a sandy clay loam soil on its bacterial flora were investigated by the study of cellular fatty acid composition of the isolates. The soil amended with glucose (carbon source) and ammonium sulfate (nitrogen source) was incubated in the presence (1.0 mg/g) or absence of zinc for 96 h. Bacterial strains were isolated on albumin agar from the incubated soils every 24 h. Their cellular fatty acid composition was analyzed and the strains were classified according to the percentage distribution pattern of the fatty acid composition.Two and four dominant patterns of the fatty acid composition were obtained in the isolates from the control soil and the soil with zinc added, respectively. They were different from one another. Most of the dominant strains isolated from the soil with added zinc were zinc-tolerant, and it was suggested that the selection for zinc tolerance readily proceeded.     

Changes in the fatty acid profiles through the digestive tract of the earthworm Lumbricus terrestris L.

The gut of many soil arthropods contains a complex and mutualistic microbial community that usually assists the host with digestion. The same is probably true for earthworms, but the nature and function of the microbiota inhabiting their gut are virtually unknown. In this paper, we studied the microbial community in the gut content of the earthworm Lumbricus terrestris L. and in the bulk soil by assessing their fatty acid (FA) profiles. Our results indicated that the total FA concentration in the earthworm gut was about two orders of magnitude greater than in bulk soil, with higher concentration of bacteria (up to 500-fold), fungal and metazoan-derived FAs. Several FAs appearing in the gut were not present in bulk soil. PCA analysis revealed that the microbial community in the gut was different from that in the bulk soil, and that significant changes occurred between midgut, hindgut and proctodeum. Cluster analysis of bacterial and fungal-derived FA profiles grouped the bulk soil samples apart from the gut samples, where the hindgut profiles were more closely related to those from the proctodeum than those from the midgut. We showed important changes in the FA concentration and composition occurring at very small spatial scales inside the gut of the earthworm L. terrestris. These results have implications for understanding earthworm digestion, and they suggest that the microbial community in the earthworm gut is not a casual combination of microorganisms already present in the soil. Further study is needed to determine how these gut microbial communities are involved in earthworm digestion processes.     

Changes in the fatty acid and triacylglycerol profiles in the subcutaneous fat of Iberian ham during the dry-curing process

In this study, we have evaluated the changes that occur in the profiles of total fatty acids and triacylglycerols during the dry-curing process (730 days) of Iberian ham. The subcutaneous adipose tissues of six hams obtained from three Iberian pigs fed on acorns were analyzed periodically during the processing time (from the raw to the dry-cured samples), including postsalting, drying, and ripening stages. The environmental conditions were also registered. The curing process significantly decreased (p < 0.01) the relative percentages of total polyunsaturated fatty acids, including C18:2n-6 and C18:3n-3 and, therefore, significantly increased (p < 0.05) the level of monounsaturated fatty acids. The triglycerides containing 0-2 double bonds showed an increase during the curing process. On the contrary, the more unsaturated ones (3-5 double bonds) suffered a significant decrease. We have postulated that these changes could also be due to polymerization and oxidation reactions that affect the triacylglycerols and besides the fatty acids. In general, most fatty acids and triacylglycerols reversed the trend by about 500-600 days of processing.     

Crop rotation and seasonal effects on fatty acid profiles of neutral and phospholipids extracted from no‐till agricultural soils

Analysis of phospholipids (PLFA) and neutral lipids fatty acids (NLFA) was used to characterize no‐till productive agricultural soils associated with different crop rotation levels, replicated across a 400 km transect in the Argentinean pampas, during two sampling seasons, summer and winter. High rotation (HR) management consisted in maize–wheat–soybean intense rotation including cover crops. Low rotation (LR) management trend to soybean monocultures. Soils from nearby natural environments (NEs) were used as references. Fatty acids concentration in soils (nmol/g) decreased c.a. 50% from summer to winter differentially according to soil treatment being the smallest decrease in HR management 35%. Both PLFA and NLFA profiles showed strong potential to discriminate between different land uses. In winter samples, some rare or unknown fatty acids were relevant for the discrimination of agricultural practices while NLFA 20:0 appears to be a good marker of HR soils despite season or location. The PLFA‐based taxonomic biomarkers for total bacteria, Gram‐negative bacteria and arbuscular mycorrhiza showed a significant trend NE>HR>LR in the winter sampling. HR management was also characterized by high levels of NLFA in winter samples as if high crop rotation improves lipids reserves in soil during winter more than in monocropping soil management. In conclusion, PLFA and particularly NLFA profiles appear to provide useful and complementary information to obtain a footprint of different soil use and managements, improving soil biochemistry characterization tools.     

Ergosterol profiles, fatty acid composition, and antioxidant activities of button mushrooms as affected by tissue part and developmental stage

This article investigated the mycochemical profiles and the antioxidant activities of the lipophilic extracts of the white and brown button mushrooms. We found that only free ergosterols were present in both mushrooms at 2.04-4.82 mg/g dry matter (DM). Ergosterol concentration was higher in early growth stages but decreased as the mushrooms grew, and it distributed evenly between the caps and stems during early developmental stages but accumulated more in the caps after maturation. The photochemiluminescence (PCL) values of the two mushrooms were 5.49-10.48 nmol trolox equivalent/mg DM, and the EC50 values of 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay ranged 20.19-41.49 mg DM/μg DPPH. The ergosterol content positively correlated with the antioxidant activities (r2>0.89). The total fatty acid content was 8.7 mg/g DM in the white and 5.1 mg/g DM in the brown button mushroom and contained mainly linoleic, palmitic, and stearic acids. Our data provide guidance for optimized harvesting time of mushrooms and maximized health benefits.     

Direct methylation procedure for converting fatty amides to fatty acid methyl esters in feed and digesta samples

Two direct methylation procedures often used for the analysis of total fatty acids in biological samples were evaluated for their application to samples containing fatty amides. Methylation of 5 mg of oleamide (cis-9-octadecenamide) in a one-step (methanolic HCl for 2 h at 70 degrees C) or a two-step (sodium methoxide for 10 min at 50 degrees C followed by methanolic HCl for 10 min at 80 degrees C) procedure gave 59 and 16% conversions of oleamide to oleic acid, respectively. Oleic acid recovery from oleamide was increased to 100% when the incubation in methanolic HCl was lengthened to 16 h and increased to 103% when the incubation in methoxide was modified to 24 h at 100 degrees C. However, conversion of oleamide to oleic acid in an animal feed sample was incomplete for the modified (24 h) two-step procedure but complete for the modified (16 h) one-step procedure. Unsaturated fatty amides in feed and digesta samples can be converted to fatty acid methyl esters by incubation in methanolic HCl if the time of exposure to the acid catalyst is extended from 2 to 16 h.     

Characterization of soil microbial communities under different potato cropping systems by microbial population dynamics, substrate utilization, and fatty acid profiles

The effects of 11 different 2- and 3-yr potato crop rotations on soil microbial communities were characterized over three field seasons using several techniques. Assessments included microbial populations determined by soil dilution plate counts on various general and selective culture media, microbial activity by fluorescein diacetate (FDA) hydrolysis, single carbon source substrate utilization (SU) profiles, and fatty acid methyl ester (FAME) profiles. Potato rotation crops evaluated in research plots at Newport, ME, included barley/clover, canola, green bean, millet, soybean, sweet corn, and a continuous potato control. Soil populations of culturable bacteria and overall microbial activity tended to be highest following barley, canola, and sweet corn rotations, and lowest with continuous potato. Differences among rotations were less apparent during the potato phase of the rotations. Populations of actinomycetes and fluorescent pseudomonads tended to be greater in barley rotations than in most other rotations. SU profiles derived from BIOLOG GN2 plates indicated that certain rotations, including barley, canola, and sweet corn tended to have higher overall microbial activity, and barley and sweet corn rotations averaged higher substrate richness and diversity. Soybean and potato rotations tended to have lower substrate richness and diversity. Principal component analyses of SU data revealed differences among rotation soil communities in their utilization of individual carbon sources and substrate guilds, including carbohydrates, carboxylic acids, amines/amides, and amino acids. Analyses of soil FAME profiles demonstrated distinct differences among all the rotation soils in their relative composition of fatty acids, indicating differences in their microbial community structure. Fatty acids most responsible for differentiation among rotation soils included 16:1 ω5c, 16:1 ω7c, 18:2 ω6c, 18:1 ω9c, 12:0, and 13:0 anteiso, with 16:1 ω5c being the single greatest determinant. Overall, monounsaturated fatty acids, particularly 16:1 ω5c, were most prevalent in sweet corn rotations and polyunsaturates were highest in barley and millet rotations. Straight chain saturated fatty acids comprised the greatest proportion of fatty acids in soils under continuous potato. FAME biomarkers for microorganism groups indicated barley and millet rotations had the highest ratio of fungi to bacteria, and soybean and continuous potato had the lowest ratio. This research has demonstrated that different crop rotations have distinctive effects on soil microbial communities that are detectable using a variety of techniques. Further studies will identify more specific changes associated with particular rotations and relate these changes to potential effects on disease management, crop health, and crop productivity.     

Capacity of fatty acid profiles and substrate utilization patterns to describe differences in soil microbial communities associated with increased salinity or alkalinity at three locations in South Australia

 Fatty acid methyl ester (FAME) profiles, together with Biolog substrate utilization patterns, were used in conjunction with measurements of other soil chemical and microbiological properties to describe differences in soil microbial communities induced by increased salinity and alkalinity in grass/legume pastures at three sites in SE South Australia. Total ester-linked FAMEs (EL-FAMEs) and phospholipid-linked FAMEs (PL-FAMEs), were also compared for their ability to detect differences between the soil microbial communities. The level of salinity and alkalinity in affected areas of the pastures showed seasonal variation, being greater in summer than in winter. At the time of sampling for the chemical and microbiological measurements (winter) only the affected soil at site 1 was significantly saline. The affected soils at all three sites had lower organic C and total N concentrations than the corresponding non-affected soils. At site 1 microbial biomass, CO₂-C respiration and the rate of cellulose decomposition was also lower in the affected soil compared to the non-affected soil. Biomarker fatty acids present in both the EL- and PL-FAME profiles indicated a lower ratio of fungal to bacterial fatty acids in the saline affected soil at site 1. Analysis of Biolog substrate utilization patterns indicated that the bacterial community in the affected soil at site 1 utilized fewer carbon substrates and had lower functional diversity than the corresponding community in the non-affected soil. In contrast, increased alkalinity, of major importance at sites 2 and 3, had no effect on microbial biomass, the rate of cellulose decomposition or functional diversity but was associated with significant differences in the relative amounts of several fatty acids in the PL-FAME profiles indicative of a shift towards a bacterial dominated community. Despite differences in the number and relative amounts of fatty acids detected, principal component analysis of the EL- and PL-FAME profiles were equally capable of separating the affected and non-affected soils at all three sites. Redundancy analysis of the FAME data showed that organic C, microbial biomass, electrical conductivity and bicarbonate-extractable P were significantly correlated with variation in the EL-FAME profiles, whereas pH, electrical conductivity, NH₄-N, CO₂-C respiration and the microbial quotient were significantly correlated with variation in the PL-FAME profiles. Redundancy analysis of the Biolog data indicated that cation exchange capacity and bicarbonate-extractable K were significantly correlated with the variation in Biolog substrate utilization patterns. Received: 8 March 2000     

Estimation of the root colonization of soybean by an arbuscular mycorrhizal fungus,Gigaspora rosea,based on specific fatty acid profiles

Root colonization by arbuscular mycorrhizal (AM) fungi has traditionally been analyzed by microscopy. However, this method is time consuming and it is often difficult to distinguish between AM and non-AM fungi. In this study, we analyzed the fatty acid profiles in soybean roots colonized by AM fungi to determine if specific fatty acids derived from AM fungi can be used as markers for the intensity of the AM fungal colonization. The wild-type Enrei and hypernodulating Kanto100 soybean cultivars were inoculated with an AM fungus (Gigaspora rosea) alone or with Bradyrhizobium diazoefficiens, which nodulates soybean roots. Fatty acids 20:1ω9, 20:4ω6, and 20:5ω3 were specifically detected in the lateral roots of AM fungus-inoculated and dual-inoculated soybean plants. In the second lateral roots, the percentage of AM-specific fatty acids (i.e., 20:1ω9, 20:4ω6, and 20:5ω3) derived from AM fungi was closely correlated with the intensity of the AM fungal colonization. We propose that the AM-specific fatty acids represent useful markers for estimating the degree of AM fungal colonization. The percentage of AM-specific fatty acids was more than twofold higher in the second lateral roots than in the first lateral roots. Thus, the degree of AM fungal colonization is probably twofold higher in the second lateral roots than in the first lateral roots.