Fatty Acid Methyl Ester Biomarkers Research Articles

Effects of traditional field retting of hemp on soil organic carbon and the soil microbial community

AbstractRetting is a process used with bast fiber crops such as industrial hemp (Cannabis sativa L.) to expedite the separation of fibers from the woody core of the stalk. Field retting involves partial decomposition of stalks on the soil surface and is facilitated by soil microorganisms. Effects of field retting on soil C have not been studied, and little information is available on how field retting affects the soil microbial community. We conducted an experiment to investigate effects of field retting on total organic soil C (TOC), permanganate oxidizable soil C (POXC), and relative abundance of microbial fatty acid methyl ester biomarkers (FAMEs). Four treatments were imposed: (a) no retting (NR), (b) low‐density retting (LDR) (2,500 kg stalks ha–1), (c) high‐density retting (HDR) (5,000 kg stalks ha–1), and (d) control (CON). The NR, LDR, and HDR treatments were conducted on plots where hemp was grown, whereas the CON treatment excluded production and retting. Plots under HDR treatment generally had greater TOC and POXC than plots where no retting occurred. Analysis of FAMEs indicated that soil microbial communities were grouped according to retting treatments. Greater fungal abundance and higher fungi to bacteria ratios were associated with soils where retting occurred. Compared with retting methods where harvested stalks are immediately removed from the field, field retting may mitigate soil C losses associated with harvest and may be a useful component of maintaining soil health when used in concert with management practices that build soil C.

Soil biochemical and microbial response to wheat and corn stubble residue management in Louisiana

AbstractThe effects of crop residue on soil conditions depend on the quality and management of the residue. Management practices that do not use physical disturbance (prescribed fire and no‐till) were investigated for their potential impacts on soil chemical and biological properties. Surface soil samples (0–5 cm) were collected across no‐till and prescribed fire treatments of wheat (Triticum spp.) in 2014 and 2015 and in 2014 in corn (Zea mays L.) stubble residue at 0 h (before management) and at 1 h, 6 h, 24 h, 7 d, 1 mo, and 6 mo after management. There was a lack of difference between prescribed fire and no‐till management responses in soil chemical and biological properties. However, similar responses in prescribed fire and no‐till management over sampling time of NO3––N, NH4+–N, enzyme activity, and absolute abundance of ester‐linked fatty acid methyl ester biomarkers suggest that abiotic factors and systems management (i.e., fertilizer applications, crop rotation) had a greater influence in these humid subtropical production systems. Additions of soybean [Glycine max (L.) Merr.] residue and N fertilizers in a wheat (Triticum aestivum L.)–soybean rotation increased NH4+–N concentrations by 153%, N‐acetyl‐β‐d‐glucosaminidase activity by 247%, and relative abundance of Gram‐negative bacteria and saprophytic fungi regardless of residue management. Nitrogen fertilizer applications in corn systems also increased NH4+–N concentrations (322%) along with relative abundance of actinomycetes and saprophytic fungi. These results suggest that no‐till and prescribed fire management are viable residue management options that maintained soil organic matter and inorganic N concentrations; however, further investigation is needed to evaluate the long‐term (>2 yr) impacts on soil health.

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.

Halophyte residue decomposition and microbial community structure in coastal soil

AbstractSaltmarshes are known for higher primary productivity and play a crucial role in carbon‐sequestration, nutrient‐cycling, and ecological services; however, scarce information are available on halophyte residue mineralization and microbial community structure during decomposition. Soil microcosms with residues (1% w/w) of three dominant halophytes (Aeluropus lagopoides, Arthrocnemum indicum, and Suaeda nudiflora) and one control were incubated under laboratory conditions and sampled at 1, 5, 10, 20, 40, and 90 days to link the microbial community structure and residues decomposition in degraded coastal soil. Samples were subjected to identification of active microbial groups and residue mineralization using fatty acid methyl ester (FAME) and CO2 evolution methods, respectively. Biochemical composition of residues was also analyzed. Cumulative CO2 evolution was elevated in residue‐amended soils compared with control, and it was highest in Arthrocnemum followed by Suaeda, Aeluropus, and control soil. The Aeluropus residue decomposed slower than others due to its high C/N ratio and low protein content. The contents of total FAME and biomarker FAMEs of microbial groups (bacterial, fungal, and actinomycetes) responded positively to the residue amendments compared with control, which indicate the improvement in soil microbial biomass. Soils amended with Suaeda had the highest amount of total (76.8 nmol/g) and fungal FAMEs (6.7 nmol/g), and bacterial (28.6 nmol/g) and actinomycete (3.0 nmol/g) FAMEs were elevated in Arthrocnemum amended soil. At the same time, soils amended with Suaeda (6.2%), Arthrocnemum (28.4%), and control (15.4%) had the greatest abundance of fungal, Gram‐negative and Gram‐positive FAME biomarkers, respectively. The present study suggests that residue of halophyte species affected the abundance of fungal and bacterial biomarkers, and the microbial community structure.

Soil properties, microbial communities, and sugarcane yield in paired fields with short- or long-term sugarcane cultivation histories

Abiotic and biotic factors relationship with microbial ecology and yield decline were evaluated in soils under short- and long-term sugarcane cultivation. Sugarcane yields at paired sites were higher in short-term compared to long-term cultivation soils. Evaluation of soil properties confirmed higher levels of soil organic matter and micro- and macro-nutrients interacting with soil pH and texture in soils with newly cultivated sugarcane production capable of affecting microbial ecology. Depletion of micronutrients, including iron, copper, and zinc, was associated with the long-term cultivation of sugarcane. Soil extracellular enzyme activity was affected by soil nutrient concentrations and cultivation history. Endophytic fungal colonization was more extensive in sugarcane roots from plants grown in long-term cultivation soils. Fatty acid methyl ester (FAME) biomarker profiles in bulk soils exhibited clustering for location and paired soils within locations. Similarity was based on relative abundance of biomarkers for different taxonomic groups under the influence of soil pH, texture, organic matter, and nutrients. FAME biomarker profiles revealed greater cultivation history differences for rhizosphere soils than for bulk soils. The observed patterns for short- and long-term sugarcane cultivation soils would likely influence the structure of the microbial community in the rhizosphere and subsequently influence plant growth. However, there was no consistent pattern for the FAME biomarkers distinguishing long-term from short-term sugarcane cultivation soils. The soil chemical and microbial community results highlight differences between recently and continuously cultivated soils associated with detrimental effects on soil health resulting from long-term sugarcane production.

Soil microbial community restoration in Conservation Reserve Program semi-arid grasslands

The Conservation Reserve Program (CRP) in the Southern High Plains (SHP) is known to play a crucial role in maintaining ecosystem health by reducing soil erosion. However, the restoration of soil biological health (biological community and its function) over time under CRP have not been clearly elucidated. The objective of this study was to describe the changes in the soil microbial community composition using a CRP chronosequence. Soil samples (0-10 cm and 10-30 cm) were collected in 2012 and 2014 from 26 fields across seven counties within the SHP and included seven croplands (representing 0 y in CRP), 16 CRP fields of varying ages (8-28 y as of 2014), plus three rangelands (representing no disturbance for > 30 y). Multiple regression analysis was conducted to evaluate the impacts of CRP restoration on soil microbial biomass. Shifts in soil microbial community composition, according to fatty acid methyl ester (FAME) profiles, with increasing CRP restoration years were explored using multivariate ordination. Total microbial biomass (using total FAME content as a proxy) increased with CRP years at 10-30 cm in 2012 and both depths in 2014. Although different environmental conditions were present during the two sampling years (2012 followed a record extreme drought in 2011 with conditions improving in 2014), the physiological stress of microbial community indicated by ratios of saturated to monounsaturated FAME biomarkers consistently decreased with CRP restoration years in both sampling years and both depths. A shift in microbial community composition was measured during CRP restoration at 0-10 cm in both sampling years (and at 10–30 cm in 2012) with an increase in relative fungal abundance through the initial 15 y of CRP and then a decline after 15 y. The overall increase in soil microbial biomass and decrease in microbial physiological stress indicators with increasing years under CRP illustrates how this is a valuable restoration program for building soil health in fragile, sandy SHP soils. The mechanisms underlying the decline in fungal abundance in years 15–28 are unclear and the associated reduction in the fungal to bacterial ratio does not necessarily reflect reduced soil health. Overall, the CRP program is an effective restoration practice in the SHP that can restore overall soil biological attributes including microbial biomass, re-establish the soil microbial community with decreased microbial physiological stress, and improve soil microbial functions related to C sequestration.

Effect of land management and Prosopis juliflora (Sw.) DC trees on soil microbial community and enzymatic activities in intensive silvopastoral systems of Colombia

Livestock production in Latin America has replaced tropical dry forests with conventional monocultures pastures (CP) that have degraded soils. As an alternative to CP, intensive silvopastoral systems (ISS) have been developed with multi-canopied vegetation that mimics native forest (F). The litter inputs and year-round presence of the tree rhizosphere in ISS, contribute to the formation of “fertile islands,” which is expected to impact biological activity and crop productivity. This study, investigated the impact of the conversion of CP to ISS, as well as the effect of canopy of Prosopis juliflora trees in a chronosequence of ISS (3–15years) on soil microbial communities and the physicochemical properties of soil. FAME (fatty acid methyl ester) profiles indicated that soil microbial community structure and composition shifted depending on land management systems. CP promoted the dominance of G− bacteria, while ISS chronosequence and F favored actinomycetes and fungal biomass (total and arbuscular mycorrhizal fungi). In addition, soil microbial community (FAME profiles) of ISS chronosequence and F were more similar than with CP. An increase in the Cy/pre FAME ratio in CP suggested that the microbial community was under higher stress. The advantage of including trees in pasture systems was reinforced by the observation that FAME biomarkers, enzymatic activities and nutrient status were significantly higher beneath the canopy of P. juliflora. The results indicate that ISS are viable alternatives for improving soil quality and metabolic function, which is reflected in the significant increase in microbial biomass, FAME biomarkers and enzyme activities compared with CP.

Microbial activity, community structure and potassium dynamics in rhizosphere soil of soybean plants treated with glyphosate

Abstract With the advent of glyphosate [N-(phosphonomethyl)glycine] tolerant crops, soils have now been receiving repeated applications of the herbicide for over 10 years in the Midwestern USA. There is evidence that long-term use of glyphosate can cause micronutrient deficiency but little is known about plant potassium (K) uptake interactions with glyphosate. The repeated use of glyphosate may create a selection pressure in soil microbial communities that could affect soil K dynamics and ultimately K availability for crops. Therefore, the objectives of this study were to characterize the effect of foliar glyphosate applied to GR (glyphosate resistant) soybeans on: (1) rhizosphere microbial community profiles using ester linked fatty acid methyl ester (EL-FAME) biomarkers, (2) exchangeable, non-exchangeable, and microbial K in the rhizosphere soil, and (3) concentrations of soybean leaf K. A greenhouse study was conducted in a 2 × 2 × 3 factorial design with two soil treatments (with or without long-term field applications of glyphosate), two plant treatments (presence and absence of soybean plants), and three rates of glyphosate treatments (0×, 1× at 0.87, and 2× at 1.74 kg ae ha −1 , the recommended field rate). After each glyphosate application, rhizosphere soils were sampled and analyzed for microbial community structure using ester linked fatty acid methyl ester biomarkers (EL-FAME), and exchangeable, plant tissue and microbial biomass K. Glyphosate application caused a significant decrease in the total microbial biomass in soybean rhizosphere soil that had no previous exposure to glyphosate, at 7 days after glyphosate application. However, no significant changes were observed in the overall microbial community structure. In conclusion, the glyphosate application lowered the total microbial biomass in the GR soybean rhizosphere soil that had no previous exposure to glyphosate, at 7 days after glyphosate application; caused no changes in the microbial community structure; and did not reduce the plant available K (soil exchangeable or plant tissue K).

Effects of Different Potato Cropping System Approaches and Water Management on Soilborne Diseases and Soil Microbial Communities

Four different potato cropping systems, designed to address specific management goals of soil conservation, soil improvement, disease suppression, and a status quo standard rotation control, were evaluated for their effects on soilborne diseases of potato and soil microbial community characteristics. The status quo system (SQ) consisted of barley underseeded with red clover followed by potato (2-year). The soil-conserving system (SC) featured an additional year of forage grass and reduced tillage (3-year, barley/timothy-timothy-potato). The soil-improving system (SI) added yearly compost amendments to the SC rotation, and the disease-suppressive system (DS) featured diverse crops with known disease-suppressive capability (3-year, mustard/rapeseed-sudangrass/rye-potato). Each system was also compared with a continuous potato control (PP) and evaluated under both irrigated and nonirrigated conditions. Data collected over three potato seasons following full rotation cycles demonstrated that all rotations reduced stem canker (10 to 50%) relative to PP. The SQ, SC, and DS systems reduced black scurf (18 to 58%) relative to PP; SI reduced scurf under nonirrigated but not irrigated conditions; and scurf was lower in DS than all other systems. The SQ, SC, and DS systems also reduced common scab (15 to 45%), and scab was lower in DS than all other systems. Irrigation increased black scurf and common scab but also resulted in higher yields for most rotations. SI produced the highest yields under nonirrigated conditions, and DS produced high yields and low disease under both irrigation regimes. Each cropping system resulted in distinctive changes in soil microbial community characteristics as represented by microbial populations, substrate utilization, and fatty acid methyl-ester (FAME) profiles. SI tended to increase soil moisture, microbial populations, and activity, as well result in higher proportions of monounsaturated FAMEs and the FAME biomarker for mycorrhizae (16:1 ω6c) relative to most other rotations. DS resulted in moderate microbial populations and activity but higher substrate richness and diversity in substrate utilization profiles. DS also resulted in relatively higher proportions of FAME biomarkers for fungi (18:2 ω6c), actinomycetes, and gram-positive bacteria than most other systems, whereas PP resulted in the lowest microbial populations and activity; substrate richness and diversity; proportions of monounsaturated and polyunsaturated FAME classes; and fungal, mycorrhizae, and actinomycete FAME biomarkers of all cropping systems. Overall, soil water, soil quality, and soilborne diseases were all important factors affecting productivity, and cropping systems addressing these constraints improved production. Cropping system approaches will need to balance these factors to achieve sustainable production and disease management.

Use of Fatty Acid Methyl Ester Profiles for Discrimination ofBacillus cereusT-Strain Spores Grown on Different Media

The goal of this study was to determine if cellular fatty acid methyl ester (FAME) profiling could be used to distinguish among spore samples from a single species (Bacillus cereus T strain) that were prepared on 10 different medium formulations. To analyze profile differences and identify FAME biomarkers diagnostic for the chemical constituents in each sporulation medium, a variety of statistical techniques were used, including nonmetric multidimensional scaling (nMDS), analysis of similarities (ANOSIM), and discriminant function analysis (DFA). The results showed that one FAME biomarker, oleic acid (18:1 omega9c), was exclusively associated with spores grown on Columbia agar supplemented with sheep blood and was indicative of blood supplements that were present in the sporulation medium. For spores grown in other formulations, multivariate comparisons across several FAME biomarkers were required to discern profile differences. Clustering patterns in nMDS plots and R values from ANOSIM revealed that dissimilarities among FAME profiles were most pronounced when spores grown with disparate sources of complex additives or protein supplements were compared (R > 0.8), although other factors also contributed to FAME differences. DFA indicated that differentiation could be maximized with a targeted subset of FAME variables, and the relative contributions of branched FAME biomarkers to group dissimilarities changed when different media were compared. When taken together, these analyses indicate that B. cereus spore samples grown in different media can be resolved with FAME profiling and that this may be a useful technique for providing intelligence about the production methods of Bacillus organisms in a forensic investigation.

Differentiation of Bacillus endospore species from fatty acid methyl ester biomarkers

A simple method to detect and differentiate Bacillus anthracis (BA), Bacillus thuringiensis (BT), Bacillus atrophaeus (BG), and Bacillus cereus (BC) endospores using biomarker compounds, including dipicolinic acid methyl ester (DPAME) and fatty acid methyl esters (FAMEs), has been developed. The method is based on thermochemolysis methylation (TCM) of the endospores and gas chromatography-mass spectrometry (GC-MS) of the reaction products. A suspension of the sample mixed with sulfuric acid (H2SO4) and tetramethylammonium hydroxide (TMAH) in methanol (MeOH) at room temperature is sampled using a coiled wire filament (CWF) device, which consists of a tiny platinum helical wire coil attached to a retractable plunger that moves the coil in and out of a syringe needle housing. Sampling is accomplished by dipping the CWF in an endospore sample suspension, evaporating the suspension liquid, and then introducing the CWF into the injection port. While DPAME can be used for the general detection of endospores, specific saturated and unsaturated C15, C16, and C17 fatty acid methyl esters provide additional information for differentiating various Bacillus species grown at different temperatures and in different media. DPAME could be detected in samples containing as few as 6000 endospores, and the GC-MS peak area percent reproducibility for FAMEs varied from 3 to 13% (RSD). Better than 97% correct predictability of Bacillus species identity was obtained from a blind experiment consisting of 145 samples.

Effects of Different 3-Year Cropping Systems on Soil Microbial Communities and Rhizoctonia Diseases of Potato

ABSTRACT Eight different 3-year cropping systems, consisting of soybean-canola, soybean-barley, sweet corn-canola, sweet corn-soybean, green bean-sweet corn, canola-sweet corn, barley-clover, and continuous potato (non-rotation control) followed by potato as the third crop in all systems, were established in replicated field plots with two rotation entry points in Presque Isle, ME, in 1998. Cropping system effects on soil microbial community characteristics based on culturable soil microbial populations, single carbon source substrate utilization (SU) profiles, and whole-soil fatty acid methyl ester (FAME) profiles were evaluated in association with the development of soilborne diseases of potato in the 2000 and 2001 field seasons. Soil populations of culturable bacteria and overall microbial activity were highest following barley, canola, and sweet corn crops, and lowest following continuous potato. The SU profiles derived from BIOLOG ECO plates indicated higher substrate richness and diversity and greater utilization of certain carbohydrates, carboxylic acids, and amino acids associated with barley, canola, and some sweet corn rotations, indicating distinct differences in functional attributes of microbial communities among cropping systems. Soil FAME profiles also demonstrated distinct differences among cropping systems in their relative composition of fatty acid types and classes, representing structural attributes of microbial communities. Fatty acids most responsible for differentiation among cropping systems included 12:0, 16:1 omega5c, 16:1 omega7c, 18:1 omega9c, and 18:2omega6c. Based on FAME biomarkers, barley rotations resulted in higher fungi-to-bacteria ratios, sweet corn resulted in greater mycorrhizae populations, and continuous potato produced the lowest amounts of these and other biomarker traits. Incidence and severity of stem and stolon canker and black scurf of potato, caused by Rhizoctonia solani, were reduced for most rotations relative to the continuous potato control. Potato crops following canola, barley, or sweet corn provided the lowest levels of Rhizoctonia disease and best tuber quality, whereas potato crops following clover or soybean resulted in disease problems in some years. Both rotation crop and cropping sequence were important in shaping the microbial characteristics, soilborne disease, and tuber qualities. Several microbial parameters, including microbial populations and SU and FAME profile characteristics, were correlated with potato disease or yield measurements in one or both harvest years. In this study, we have demonstrated distinctive effects of specific rotation crops and cropping sequences on microbial communities and have begun to relate the implications of these changes to crop health and productivity.

Effect of swine and dairy manure amendments on microbial communities in three soils as influenced by environmental conditions

Understanding the impacts of manure amendments on soil microorganisms can provide valuable insight into nutrient availability and potential crop and environmental effects. Soil microbial community characteristics, including microbial populations and activity, substrate utilization (SU) profiles, and fatty acid methyl ester (FAME) profiles, were compared in three soils amended or not amended with dairy or swine manure at two temperatures (18 and 25°C) and two soil water regimes (constant and fluctuating) in laboratory incubation assays. Soil type was the dominant factor determining microbial community characteristics, resulting in distinct differences among all three soil types and some differing effects of manure amendments. Both dairy and swine manures generally increased bacterial populations, substrate diversity, and FAME biomarkers for gram-negative organisms in all soils. Microbial activity was increased by both manures in an Illinois soil but only by dairy manure in two Maine soils. Dairy manure had greater effects than swine manure on SU and FAME parameters such as increased activity, utilization of carbohydrates and amino acids, substrate richness and diversity, and fungal FAME biomarkers. Temperature and water regime effects were relatively minor compared with soil type and amendment, but both significantly affected some microbial responses to manure amendments. Overall, microbial characteristics were more highly correlated with soil physical factors and soil and amendment C content than with N levels. These results indicate the importance of soil type, developmental history, and environmental factors on microbial community characteristics, which may effect nutrient availability from manure amendments and should be considered in amendment evaluations.

Linking Microbial-Scale Findings to Farm-Scale Outcomes in a Dryland Cropping System

Soil biological response to management is best evaluated in field-scale experiments within the context of the soil environment and crop; however, cost-effective methods are lacking to relate these data which span multiple spatial scales. We hypothesized that zones of apparent electrical conductivity (ECa) could be used to integrate soil properties (sampling-site scale), microbial-scale measures of vesicular-arbuscular mycorrhizal (VAM) fungi, and field-scale wheat yields from yield maps. An on-farm dryland experiment (∼250 ha) was established wherein two (∼32-ha) fields were assigned to each phase of a winter wheat (Triticum aestivum L.) – corn (Zea mays L.) – proso millet (Panicum miliaceum L.) – fallow rotation. Each field was mapped and classified into four zones (ranges) of ECa. Soil samples were collected from geo-referenced sites within ECa zones and analyzed for multiple soil properties associated with productivity (0–7.5 and/or 0–30 cm). Additionally, VAM fungi were assessed using C16:1(cis)11 fatty acid methyl ester biomarker (C16vam), glomalin immunoassay, and wet-aggregate stability (WAS) techniques (1–2mm aggregates from 0- to 7.5-cm soil samples). Concentrations of C16vam and WAS increased among cropping treatments as: fallow < wheat < corn < millet. Glomalin across crops and replicates, C16vam and WAS in fallow (crop effect removed), soil properties associated with productivity, and wheat yields were negatively correlated with ECa and different among ECa zones (P ≤ 0.05). Zones of ECa provide a point of reference for relating data collected at different scales. Monitoring cropping system parameters and profitability, over time, may allow linkage of microbial-scale processes to farm-scale economic and ecological outcomes.

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.

Soil microbial community characteristics along an elevation gradient in the Laguna Mountains of Southern California

We sampled soil at four sites in the Laguna Mountains in the western Sonoran Desert to test the effects of site and sample location (between or beneath plants) on fatty acid methyl ester (FAME) and carbon substrate ulilization (Biolog) profiles. The four sites differed in elevation, soil type, plant community composition, and plant percent cover. Soil pH decreased and plant density increased with elevation. Fertile islands, defined as areas beneath plants with greater soil resources than bare areas, are present at all sites, but are most pronounced at lower elevations. Consistent with this pattern, fertile islands had the greatest influence on FAME and Biolog profiles at lower elevations. Based on the use of FAME biomarker and principal components analyses, we found that soil microbial communities between plants at the lowest elevation had proportionally more Gram-negative bacteria than all other soils. At the higher elevation sites there were few differences in FAME profiles of soils sampled between vs. beneath plants. Differences in FAME profiles under plants among the four sites were small, suggesting that the plant influence per se is more important than plant type in controlling FAME profiles. Since microbial biomass carbon was correlated with FAME number (r=0.85, P<0.0001) and with FAME named (r=0.88, P<0.0001) and total areas (r=0.84, P<0.0001), we standardized the FAME data to ensure that differences in FAME profiles among samples were not the result of differences in microbial biomass. Differences in microbial substrate utilization profiles among sampling locations were greatest between samples taken under vs. between plants at the two lower elevation sites. Microbial substrate utilization profiles, therefore, also seem to be influenced more by the presence of plants than by specific plant type.

Soil microbiological properties 20 years after surface mine reclamation: spatial analysis of reclaimed and undisturbed sites

Spatial characteristics of soil microbial community structure and selected soil chemical factors were analyzed in soil surrounding Agropyron smithii (Western wheatgrass) and Artemisia tridentata (Wyoming big sagebrush) plants in sites reclaimed after surface mining and adjacent undisturbed sites in Wyoming. Microbial biomass C (MBC) and fatty acid methyl ester (FAME) biomarkers for total biomass, bacteria, and fungi were used as indicators of soil microbial community abundance and structure. In soil 20 years after reclamation FAME total microbial biomass, bacterial and fungal biomarkers, MBC and soil organic matter (SOM) averaged only 20, 16, 28, 44 and 36% of values found in undisturbed soils. In contrast to undisturbed soils, FAME biomarkers and MBC of reclaimed soils exhibited spatial correlation up to 42 cm. Reclaimed soils also exhibited localized enrichment of bacterial, fungal, and total microbial biomass, as well as depletion of inorganic N concentrations, around plant bases (<10 cm), suggesting relatively poor soil exploration by roots and microorganisms compared to the undisturbed ecosystem. Strong spatial stratification of undisturbed SOM and soil NH 4 + pools was found with highest concentrations on the leeward side of shrubs, likely due to localized changes in microclimate and plant litter deposition. This indicates that shrub cover plays a central role in the establishment of site heterogeneity and regulation of ecological processes, such as C and N mineralization and immobilization, which has important implications for reclamation.