The impacts of individual plant species on rhizosphere microbial communities in soils of different fertility

To investigate the effects of individual plant species on microbial community properties in soils of differing fertility, a microcosm experiment was carried out using plant species representative of the dominant flora in semi-fertile temperate grasslands of northern England. Soil microbial biomass and activity were found to be significantly greater in the more fertile, agriculturally improved soil than in the less productive unimproved meadow soil. Differences in microbial community structure were also evident between the two soils, with fungal abundance being greater in the unimproved soil type. Individual plant species effects significantly differed between the two soils. Holcus lanatus and Anthoxanthum odoratum stimulated microbial biomass in the improved soil type, but negatively affected this measure in the unimproved soil. In both soil types, herb species generally had negative effects on microbial biomass. Patterns for microbial activity were less consistent, but as with microbial biomass, A. odoratum and H. lanatus promoted respiration, whereas the herbs negatively affected this measure. All plant species grown in the improved soil increased the abundance of fatty acids synthesised by bacteria (bacterial phospholipid fatty acid analysis) relative to bare soil, but they negatively impacted on this group of fatty acids in unimproved soil. Similarly, the abundance of the fungal fatty acid 18:26 was increased by all plants in the more fertile improved soil only, albeit non-significantly. Our data indicate that effects of plant species on microbial properties differ markedly in soils of differing fertility, making general predictions about how individual plants impact on soil properties difficult to make.     

Changes in soil microbial community structure following the abandonment of agricultural terraces in mountainous areas of Eastern Spain

In Eastern Spain, almond trees have been cultivated in terraced orchards for centuries, forming an integral part of the Mediterranean forest scene. In the last decades, orchards have been abandoned due to changes in society. This study investigates effects of changes in land use from forest to agricultural land and the posterior land abandonment on soil microbial community, and the influence of soil physico-chemical properties on the microbial community composition (assessed as abundances of phospholipids fatty acids, PLFA). For this purpose, three land uses (forest, agricultural and abandoned agricultural) at four locations in SE Spain were selected. Multivariate analysis showed a substantial level of differentiation in microbial community structure according to land use. The microbial communities of forest soils were highly associated with soil organic matter content. However, we have not found any physical or chemical soil property capable of explaining the differences between agricultural and abandoned agricultural soils. Thus, it was suggested that the cessation of the perturbation caused by agriculture and shifts in vegetation may have led to changes in the microbial community structure. PLFAs indicative of fungi and ratio of fungal to bacterial PLFAs were higher in abandoned agricultural soils, whereas the relative abundance of bacteria was higher in agricultural soils. Actinomycetes were generally lower in abandoned agricultural soils, while the proportions of vesicular–arbuscular mycorrhyzal fungi were, as a general trend, higher in agricultural and abandoned agricultural soils than in forests. Total microbial biomass and richness increased as agricultural < abandoned agricultural < forest soils.     

Response of soil microbial communities to the herbicide mesotrione: A dose-effect microcosm approach

Mesotrione is a new selective herbicide used for maize crops. The responses of microbial communities of a chernozem soil (Limagne basin, France) to pure or formulated (Callisto^®) mesotrione, applied at three different doses [one fold field rate (1 × FR), 10 × FR and 100 × FR], were studied using a laboratory microcosm approach. The effects were assessed on the prokaryotic cell abundance, the overall microbial activities (substrate-induced respiration (SIR) and dehydrogenase activity (DHA)) and the genetic structure of the bacterial and fungal communities (temporal temperature/denaturing gradient gel electrophoresis (TT/DGGE)). Mesotrione dissipation was similar whatever the formulation applied and the amounts dissipated were positively correlated to application rates. Several biodegradation products including the metabolites 4-methylsulfonyl-2-nitrobenzoic acid (MNBA) and 2-amino-4-methylsulfonylbenzoic acid (AMBA) were detected from day 42 post-treatment, in 10 × FR and 100 × FR treated soils. No response of the soil microbial communities was detected in soil spread with both the 1 × FR applications. Overall soil microbial activity was stimulated from day 6 by 10 × FR of Callisto^® and more strongly by 100 × FR of pure mesotrione and Callisto^®, whereas prokaryote abundance did not increase before day 95 in both the 100 × FR treatments. Genetic structural shifts recorded from day 42 in the bacterial and fungal communities were small and mainly attributable to variations in band intensity. Maximum dissimilarity of the bacterial and fungal genetic structures between control and 100 × FR treated soils did not exceed 12% and 28%, respectively. The general pattern was that more consistent effects occurred with increasing exposure times, especially in both the 100 × FR treated soils. These microbial responses could be due to the stimulation of (i) adapted mesotrione-degrading microorganisms and (ii) the activity of resistant heterotrophic microbial groups promoted by dead biomass from sensitive organisms. In addition, at 100 × FR doses, pure mesotrione seemed to induce stronger microbial responses than Callisto^®, formulation which contains adjuvants with potential side-effects on some microbial populations. This experimental approach indicated that pure mesotrione and Callisto^® affected soil microbial communities, but the effects were only detected at doses far exceeding the recommended field rates.     

Microbial colonisation of roots as a function of plant species

Fifteen plants species were grown in the greenhouse on the same soil and sampled at flowering to obtain rhizosphere soil and root material. In both fractions, the data on fungal and bacterial tissue obtained by amino sugar analysis were compared with the total microbial biomass based on fumigation-extraction and ergosterol data. The available literature on glucosamine concentrations in fungi and on muramic acid concentrations in bacteria was reviewed to prove the possibility of generating conversion values for general use in root material. All microbial properties analysed revealed strong species-specific differences in microbial colonisation of plant roots. The root material contained considerable amounts of microbial biomass C and biomass N, reaching mean levels of 10.9 and 1.4 mg g⁻¹ dry weight, respectively. However, the majority of CHCl₃ labile C and N, i.e. 89 and 55% was root derived. The average amount of ergosterol was 13 μg g⁻¹ dry weight and varied between 0.0 for Phacelia roots and 45.5 μg g⁻¹ dry weight for Vicia roots. The ergosterol content in root material of mycorrhizal and non-mycorrhizal plant species did not differ significantly. Fungal glucosamine was converted to fungal C by multiplication by 9 giving a range of 7.1-25.9 mg g⁻¹ dry weight in the root material. Fungal C and ergosterol were significantly correlated. Bacterial C was calculated by multiplying muramic acid by 45 giving a range from 1.7 to 21.6 mg g⁻¹ dry weight in the root material. In the root material of the 15 plant species, the ratio of fungal C-to-bacterial C ranged from 1.0 in mycorrhizal Trifolium roots to 9.5 in non-mycorrhizal Lupinus roots and it was on average 3.1. These figures mean that the microbial tissue in the root material consists on average of 76% fungal C and 24% bacterial C. The differences in microbial colonisation of the roots were reflected by differences in microbial indices found in the rhizosphere soil, most strongly for microbial biomass C and ergosterol, but to some extent also for glucosamine and muramic acid.     

Soil microbial communities under different soybean cropping systems: Characterization of microbial population dynamics, soil microbial activity, microbial biomass, and fatty acid profiles

This work analyzes the direct effect of soil management practices on soil microbial communities, which may affect soil productivity and sustainability. The experimental design consisted of two tillage treatments: reduced tillage (RT) and zero tillage (ZT), and three crop rotation treatments: continuous soybean (SS), corn–soybean (CS), and soybean–corn (SC). Soil samples were taken at soybean planting and harvest. The following quantifications were performed: soil microbial populations by soil dilution plate technique on selective and semi-selective culture media; microbial respiration and microbial biomass by chloroform fumigation-extraction; microbial activity by fluorescein diacetate hydrolysis; and fatty acid methyl ester (FAME) profiles. Soil chemical parameters were also quantified. Soil organic matter content was significantly lower in RT and SS sequence crops, whereas soil pH and total N were significantly higher in CS and SC sequence crops. Trichoderma and Gliocladium populations were lower under RTSS and ZTSS treatments. Except in a few cases, soil microbial respiration, biomass and activity were higher under zero tillage than under reduced tillage, both at planting and harvest sampling times. Multivariate analyses of FAMEs clearly separated both RT and ZT management practices at each sampling time; however, separation of sequence crops was less evident. In our experiments ZT treatment had highest proportion of 10Me 16:0, an actinomycetes biomarker, and 16:1ω9 and 18:1ω7, two fatty acids associated with organic matter content and substrate availability. In contrast, RT treatment had highest content of branched biomarkers (i15:0 and i16:0) and of cy19:0, fatty acids associated with cell stasis and/or stress. As cultural practices can influence soil microbial populations, it is important to analyze the effect that they produce on biological parameters, with the aim of conserving soil richness over time. Thus, in a soybean-based cropping system, appropriate crop management is necessary for a sustainable productivity without reducing soil quality.     

Reclamation of lignite mine areas with Triticum aestivum: The dynamics of soil functions and microbial communities

In this paper is studied the dynamics of the soil microbial structure and function, and enzymatic activities during a chronosequence (0, 5, 10, 15 and 20 years) after reclamation of coal mine areas with wheat (Triticum aestivum). Due to the homogeneity induced by monoculture all over the sites, similarity in the dynamics of structural and functional soil attributes was expected. Moreover, the idea of Whisenant (2002) claiming non monotonic succession unfolding during the reclamation process was checked. Soil samples were collected from the upper 12 cm of cultivated fields differing in their post-reclamation age, and they were analyzed for physicochemical variables, microbial community structure (PLFAs), catabolic profiles (Biolog Ecoplates) and enzymatic activities (β-glucosidase, urease and alkaline phosphatase). Fields outside the mine area, cultivated with the same species were used as controls. Exhibiting rapid growth from 0 to 4–5 years after reclamation, slow decline from 5 to 10 years and stabilization after 10 years, the abundances of the microbial groups (Gram⁺, Gram⁻, fungi, protozoa) showed similar dynamics. Similar dynamics displayed also the activity of alkaline phosphatase and β-glucosidase, which increased gradually from 0 to 10 years and stabilized afterwards. By contrast, the activity of urease showed an inverse temporal pattern. After 15 years, the microbial abundances, the functional diversity (Shannon index), and the soil enzymatic activities of the reclaimed soils converged to values recorded in the controls fields. Significant shifts in the microbial community structure were not detected, probably because of the type of reclamation (agricultural use). However, when the overall PLFA and carbon utilization data sets were analyzed, it was revealed that the microbial community structure changed non monotonically in the transition between 0 and 5 years after reclamation, while the carbon utilization profiles exhibited more complex successional patterns. Above findings support the idea of non monotonic successional processes in soil microbial communities.     

Soil microbial communities under conventional-till and no-till continuous cotton systems

Soil management practices affect soil microbial communities, which in turn influence soil ecosystem processes. In this study, the effects of conventional- (fall disking, chiseling and spring disking, field cultivation) and no-tillage practices on soil microbial communities were examined under long-term continuous cotton (Gossypium hirsutum L.) systems on a Decatur silt loam soil. Soil samples were taken in February, May, and October of 2000 at depths of 0-3, 3-6, 6-12, and 12-24 cm. Compared to the conventional-till treatment, the no-till treatment increased soil organic carbon and total nitrogen contents in the surface layer by 130 and 70%, respectively. Microbial biomass C content under no-till treatment was 60, 140, and 75% greater than under conventional-till treatment in February, May, and October, respectively. Principal components analysis of phospholipid ester-linked fatty acid (PLFA) profile indicated soil microbial communities shifted over time and with soil depth. This change appeared to be driven primarily by soil bacterial populations as indicated by the major PLFA contributors (i.e. fatty acids 16:0, 10Me16:0, cy19:0, 16:1 2OH, and i15:0) to the first two principal components. Tillage treatment differences were revealed by analysis of variance on the first principal components (PC 1), which accounted for 62% of the total sample variance, and by the relative abundance of selected PLFAs and PLFA ratios. The impact of tillage practices was significant in February and May, but not in October. During the growing season, changes in the microbial community may be primarily determined by soil conditions responding to cotton growth and environmental variables such as moisture and temperature; during fallow or prior to cotton establishment, community changes associated with tillage practices become more pronounced. These findings have implications for understanding how conservation tillage practices improve soil quality and sustainability in a cotton cropping system.     

Alteration of soil microbial communities and water quality in restored wetlands

Land usage is a strong determinant of soil microbial community composition and activity, which in turn determine organic matter decomposition rates and decomposition products in soils. Microbial communities in permanently flooded wetlands, such as those created by wetland restoration on Sacramento-San Joaquin Delta islands in California, function under restricted aeration conditions that result in increasing anaerobiosis with depth. It was hypothesized that the change from agricultural management to permanently flooded wetland would alter microbial community composition, increase the amount and reactivity of dissolved organic carbon (DOC) compounds in Delta waters; and have a predominant impact on microbial communities as compared with the effects of other environmental factors including soil type and agricultural management. Based on phospholipid fatty acid (PLFA) analysis, active microbial communities of the restored wetlands were changed significantly from those of the agricultural fields, and wetland microbial communities varied widely with soil depth. The relative abundance of monounsaturated fatty acids decreased with increasing soil depth in both wetland and agricultural profiles, whereas branched fatty acids were relatively more abundant at all soil depths in wetlands as compared to agricultural fields. Decomposition conditions were linked to DOC quantity and quality using fatty acid functional groups to conclude that restricted aeration conditions found in the wetlands were strongly related to production of reactive carbon compounds. But current vegetation may have had an equally important role in determining DOC quality in restored wetlands. In a larger scale analysis, that included data from wetland and agricultural sites on Delta islands and data from two previous studies from the Sacramento Valley, an aeration gradient was defined as the predominant determinant of active microbial communities across soil types and land usage.     

Temperature and substrate controls on microbial phospholipid fatty acid composition during incubation of grassland soils contrasting in organic matter quality

Soil incubations are often used to investigate soil organic matter (SOM) decomposition and its response to increased temperature, but changes in the activity and community composition of the decomposers have rarely been included. As part of an integrated investigation into the responses of SOM components in laboratory incubations at elevated temperatures, fungal and bacterial phospholipid fatty acids (PLFAs) were measured in two grassland soils contrasting in SOM quality (i.e. SOM composition), and changes in the microbial biomass and community composition were monitored. Whilst easily-degradable SOM and necromass released from soil preparation may have fuelled microbial activity at the start of the incubation, the overall activity and biomass of soil microorganisms were relatively constant during the subsequent one-year soil incubation, as indicated by the abundance of soil PLFAs, microbial respiration rate (r), and metabolic quotient (qCO₂). PLFAs relating to fungi and Gram-negative bacteria declined relative to Gram-positive bacteria in soils incubated at higher temperatures, presumably due to their vulnerability to disturbance and substrate constraints induced by faster exhaustion of available nutrient sources at higher temperatures. A linear correlation was found between incubation temperatures and the microbial stress ratios of cyclopropane PLFA-to-monoenoic precursor (cy17:0/16:1ω7c and cy19:0/18:1ω7c) and monoenoic-to-saturated PLFAs (mono/sat), as a combined effect of temperature and temperature-induced substrate constraints. The microbial PLFA decay patterns and ratios suggest that SOM quality intimately controls microbial responses to global warming.     

Soil microbial communities in (sub)alpine grasslands indicate a moderate shift towards new environmental conditions 11 years after soil translocation

A change in environmental conditions may result in altered soil microbial communities in alpine grasslands but the extent and direction of the change is largely unknown. The aim of our study was to investigate (i) differences in soil microbial communities across an elevation gradient of (sub)alpine grassland soils in the Swiss Alps, and (ii) the long-term effect of translocation of soil cores from a higher to a lower elevation site. The translocation of undisturbed soil cores from a high alpine site (2525 m asl) to a subalpine site near the timberline (1895 m asl) induced an effective artificial warming of 3.3 °C. We hypothesized that after longer than a decade, soil microbial community in translocated cores would differ from that at the original site but resemble the community at the new site. Results from soil phospholipid fatty acid (PLFA) analysis confirm significant differences in microbial communities between sites and a shift in total microbial biomass (TMB) and proportional distribution of structural groups in the translocated cores towards the lower elevation community. Patterns related to translocation were also observed as shifts in the fractional biomass of ectomycorrhizal and arbuscular fungi, and in relative contents of several structural groups. Hence, soil microbial community activity and diversity indicate a moderate shift towards new site conditions after 11 years and therefore, our data suggest slow responses of microbial communities to environmental changes in alpine soils.     

Changes in the succession and diversity of protozoan and microbial populations in soil spiked with a range of copper concentrations

We studied microbial and protozoan activity, diversity and abundance as affected by Cu²⁺ amendments ranging from 0 to 1000 μg g⁻¹ over a 70-day period. At the end of the experiment the microbial population size, as indicated by substrate-induced respiration, had normalized for all Cu²⁺ concentrations, but 1000 μg g⁻¹. Protozoan abundance was negatively affected by Cu²⁺, although, only in the first few weeks. A more detailed analysis of the individual components that make up the microbial and micro-faunal populations (phospholipid fatty acid (PLFA) profile and protozoan morphotypes), however, yielded a somewhat more complex picture. For the three highest Cu²⁺ amendments (160, 400 and 1000 μg g⁻¹), there still was a significant reduction in number of differentiable protozoan morphotypes. The bacterial PLFA pattern suggested a shift from Gram-negative towards Gram-positive bacteria for the high amendments, a process where protozoan grazing most likely played a significant role. The ratio of the trans/cis isomers of the 16:1ω7 fatty acid indicated that Cu²⁺, even at low and medium concentrations, induced physiological changes in the microbial population. The relatively slight changes in total microbial and micro-faunal abundance and activity, also at the highest Cu²⁺ concentrations, probably reflected the ability of the community to compensate for loss of taxa by functional substitution.     

Functional resilience of soil microbial communities depends on both soil structure and microbial community composition

The effects of soil structure and microbial community composition on microbial resistance and resilience to stress were found to be interrelated in a series of experiments. The initial ability of Pseudomonas fluorescens to decompose added plant residues immediately after a copper or heat stress (resistance) depended significantly on which of 26 sterile soils it was inoculated into. Subsequent studies showed that both the resistance and subsequent recovery in the ability of P. fluorescens to decompose added plant residues over 28 days after stress (resilience) varied significantly between a sandy and a clay-loam soil. Sterile, sandy and clay-loam soil was then inoculated with a complex microbial community extracted from either of the soils. The resulting microbial community structure depended on soil type rather than the source of inoculum, whilst the resistance and resilience of decomposition was similarly governed by the soil and not the inoculum source. Resilience of the clay-loam soil to heat stress did not depend on the water content of the soil at the time of stress, although the physical condition of the soil when decomposition was measured did affect the outcome. We propose that soil functional resilience is governed by the physico-chemical structure of the soil through its effect on microbial community composition and microbial physiology.     

Rapid effects of plant species diversity and identity on soil microbial communities in experimental grassland ecosystems

Changes in plant community structure, including the loss of plant diversity may affect soil microbial communities. To test this hypothesis, plant diversity and composition were experimentally varied in grassland plots cultivated with monocultures or mixtures of 2, 3 or 4 species. We tested the effects of monocultures versus mixtures and of plant species composition on culturable soil bacterial activity, number of substrates used and catabolic diversity, microbial biomass N, microbial respiration, and root biomass. These properties were all measured 10 months after seeding the experiment. Soil bacterial activity, number of substrates used and catabolic diversity were measured in the different plant communities using BIOLOG GN and GP microplates, which are redox-based tests measuring capacity of soil culturable bacteria to use a variety of organic substrates. Microbial biomass N, microbial respiration, and root biomass were insensitive to plant diversity. Culturable soil microbial activity, substrates used and diversity declined with declining plant diversity. Their activity, number of substrates used and diversity were significantly higher in plots with 3 and 4 plant species than in monocultures and in plots with 2 species. There was also an effect of plant species composition. Culturable soil microbial activity and diversity was higher in the four-species plant community than in any of the plant monocultures suggesting that the effect of plant diversity could not be explained by the presence of a particular plant species. Our results showed that changes in plant diversity and composition in grassland ecosystems lead to a rapid response of bacterial activity and diversity.     

Response of the chitinolytic microbial community to chitin amendments of dune soils

 The dynamics of culturable chitin-degrading microorganisms were studied during a 16-week incubation of chitin-amended coastal dune soils that differed in acidity. Soil samples were incubated at normal (5% w/w) and high (15% w/w) moisture levels. More than half of the added chitin was decomposed within 4 weeks of incubation in most soils. This rapid degradation was most likely due to fast-growing chitinolytic fungi (mainly Mortierella spp. and Fusarium spp.) at both moisture levels, as dense hyphal networks of these fungi were observed during the first 4 weeks of incubation. Chitin N mineralization was inhibited by cycloheximide, and fast-growing fungal isolates were capable of rapid chitin decomposition in sterile sand, further suggesting that these fungi play an important role in initial chitin degradation. The strong increase in fast-growing fungi in chitin-amended dune soils was only detected by direct observation. Plate counts and microscopic quantification of stained hyphae failed to reveal such an increase. During the first part of the incubation, numbers of unicellular chitinolytic bacteria also increased, but their contribution to chitin degradation was indicated to be of minor importance. During prolonged incubation, colony forming units (CFU) of chitinolytic streptomycetes and/or slow-growing fungi increased strongly in several soils, especially at the 5% moisture level. Hence, the general trend observed was a succession from fast-growing fungi and unicellular bacteria to actinomycetes and slow-growing fungi. Yet, the composition of chitinolytic CFU over time differed strongly between chitin-amended dune soils, and also between the two moisture levels. These differences could not be attributed to pH, organic matter or initial microbial composition. The possible consequence of such unpredictable variation in microbial community composition for the use of chitin-amendments as a biocontrol measure is discussed. Received: 10 March 1998     

Relationships between microbial community structure and soil environmental conditions in a recently burned system

Most wildfires, even the most severe, burn at mixed intensities across a landscape, depending on local fuel loads, fuel moistures, and wind strength and direction. This heterogeneous patchwork of fire effects can influence the patterns of above- and belowground biotic recovery through altered environmental conditions, nutrient availability, and biotic sources for microbial and vegetative re-colonization. We quantified the effects of low- and high-severity fire 14 months post-burn on key environmental variables typically limiting to microbial activity. We characterized the soil microbial community structure through ester-linked fatty acid analysis (EL-FAME) and identified the soil environmental factors that best explain the pattern of microbial community profiles through canonical correspondence analysis (CCA). Low-severity burning caused no change in soil moisture, pH or temperature while high-severity burning caused an increase in soil moisture, temperature, and a decrease in pH levels, relative to the unburned sites. Soil respiration rates were significantly lower in both the low- and high-severity burn sites, relative to unburned sites, likely due to initial root and microbial death. Overall microbial biomass did not change with either low- or high-severity burning, but the microbial community ordination biplots showed separation of communities by fire, and slight separation by fire severity along three axes. This community separation was driven primarily by a decrease in fungal biomarkers (18:2ω6c, 18:3ω6c) with both low- and high-severity fire. Only 23% of the variation in the microbial community distribution could be explained by three environmental variables: soil pH, temperature, and carbon. These results suggest that the microbial communities in both the low- and high-severity burn sites are structurally different from the populations in the unburned sites.     

Soil microbial communities changed with a continuously monocropped processing tomato system

To reveal the regulatory mechanisms underlying the productivity of long-term continuous cropping of processing tomato, a multi-year study was carried out to understand the effects of long-term continuous cropping on the community structures of the root zone microbes. Soil samples collected from continuous cropping of processing tomato after 3, 5 and 7 years were used for this study. Results showed that soil microbial biomass C (SMBC), N (SMBN) and microbial quotient (qMB) significantly decreased with longer cropping. After seven years of continuous cropping, the SMBC and SMBN contents, and qMB respectively significantly decreased by 52.3%, 78.8% and 48.2% (p?相似文献   

Experimental analysis of the effect of exotic and native plant species on the structure and function of soil microbial communities

Invasions of exotic plant species are among the most pervasive and important threats to natural ecosystems, however, the effects of plant invasions on soil processes and the soil biota have rarely been investigated. We grew two exotic and a native under-story plant species in the same mineral soil from a non-invaded forest stand in order to test whether observed differences in the field could be experimentally produced in the greenhouse. We characterized changes in the soil microbial community structure (as indexed by PLFAs) and function (as indexed by enzyme activities and SIR), as well as changes in potential nitrogen mineralization rates. We found that the invasion of two very dissimilar exotic species into the under-story of deciduous forests in eastern North America can rapidly cause changes in most of the studied soil properties. At the end of the three-month incubation, soils under the exotic species had significantly different PLFA, enzyme and SIR profiles than both initial soils and soils where native shrubs had been grown. We also observed a significant increase in pH and nitrification rates under one of the exotic plants. Such changes in the soil are potentially long-term (e.g. changes in soil pH) and are therefore likely to promote the re-invasion of these and other exotics. Both management of exotic plant invasions and the restoration of native communities must take into account exotic species effects on the soil.     

Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review

 This review discusses the analysis of whole-community phospholipid fatty acid (PLFA) profiles and the composition of lipopolysaccharides in order to assess the microbial biomass and the community structure in soils. For the determination of soil microbial biomass a good correlation was obtained between the total amount of PLFAs and the microbial biomass measured with methods commonly used for determinations such as total adenylate content and substrate-induced respiration. Generally, after the application of multivariate statistical analyses, whole-community fatty acid profiles indicate which communities are similar or different. However, in most cases, the organisms accounting for similarity or difference cannot be determined, and therefore artefacts could not be excluded. The fatty acids used to determine the biomass vary from those which determine the community structure. Specific attention has to be paid when choosing extraction methods in order to avoid the liberation of fatty acids from non-living organic material and deposits, and to exclude the non-target selection of lipids from living organisms, as well. By excluding the fatty acids which were presumed to be common and widespread prior to multivariate statistical analysis, estimates were improved considerably. Results from principal component analysis showed that determining the levels of fatty acids present in both low and high concentrations is essential in order to correctly identify microorganisms and accurately classify them into taxonomically defined groups. The PLFA technique has been used to elucidate different strategies employed by microorganisms to adapt to changed environmental conditions under wide ranges of soil types, management practices, climatic origins and different perturbations. It has been proposed that the classification of PLFAs into a number of chemically different subgroups should simplify the evaluating procedure and improve the assessment of soil microbial communities, since then only the subgroups assumed to be involved in key processes would be investigated. Received: 24 August 1998     

Culture-based and culture-independent assessment of the impact of mixed and single plant treatments on rhizosphere microbial communities in hydrocarbon contaminated flare-pit soil

Phytoremediation is a novel treatment option for weathered, hydrocarbon contaminated, flare-pit soil in prairie ecosystems. The remediation potential of six different naturalized prairie plants was assessed by examining their impact on the degradation potential of indigenous bacterial communities. Culture-based and culture-independent microbiological methods were used to determine if mixed plant treatments stimulate different microbial communities and catabolic genotypes in comparison to individual plant species that comprise the mix. DGGE analysis of PCR-amplified 16S rRNA genes revealed that alfalfa (Medicago sativa) had a dominant effect on the structure of rhizosphere microbial communities in mixed plant treatments, stimulating relative increases in specific Bacteroidetes and Proteobacteria populations. Alfalfa and mixes containing alfalfa, while supporting 100 times more culturable PAH degraders than other treatments, exhibited only 10% TPH reduction, less than all planted treatments except perennial rye grass (Lolium perenne). Total petroleum hydrocarbon (TPH) reduction was greatest in single-species grass treatments, with creeping red fescue (Festuca rubra) reducing the TPH concentration by 50% after 4.5 months. Overall TPH reduction throughout the study was positively correlated (p<0.001) to culturable n-hexadecane degraders.