Differences in the activity and bacterial community structure of drained grassland and forest peat soils

The microbial activity and bacterial community structure were investigated in two types of peat soil in a temperate marsh. The first, a drained grassland fen soil, has a neutral pH with partially degraded peat in the upper oxic soil horizons (16% soil organic carbon). The second, a bog soil, was sampled in a swampy forest and has a very high soil organic carbon content (45%), a low pH (4.5), and has occasional anoxic conditions in the upper soil horizons due to the high water table level. The microbial activity in the two soils was measured as the basal and substrate-induced respiration (SIR). Unexpectedly, the SIR (μl CO₂ g⁻¹ dry soil) was higher in the bog than in the fen soil, but lower when CO₂ production was expressed per volume of soil. This may be explained by the notable difference in the bulk densities of the two soils. The bacterial communities were assessed by terminal restriction fragment length polymorphism (T-RFLP) profiling of 16S rRNA genes and indicated differences between the two soils. The differences were determined by the soil characteristics rather than the season in which the soil was sampled. The 16S rRNA gene libraries, constructed from the two soils, revealed high proportions of sequences assigned to the Acidobacteria phylum. Each library contained a distinct set of phylogenetic subgroups of this important group of bacteria.     

Species-specific effects of plants colonising cutover peatlands on patterns of carbon source utilisation by soil microorganisms

Root exudates and litter are the main sources of inputs of labile carbon into the microbial pool in successional ecosystems. Here we studied whether typical pioneer species (Eriophorum vaginatum, Eriophorum angustifolium and Calluna vulgaris) alter the functional response of the microbial community of a previously cutover peatland. Peat was sampled at three depths (0–5, 20–25 and 40–45 cm) from beneath these species and from bare soil areas. MicroResp analysis using ecologically relevant, radiolabelled, carbon sources showed significant separation in community level physiological profiles (CLPP) of soil microorganisms according to peat depth. This effect was also reflected in microbial biomass carbon, which also decreased with increasing depth. Furthermore, distinct differences in CLPP were observed between the three plant species and the bare soil in the absence of an effect on microbial biomass carbon or total soil carbon. The plant species effects were driven by differential utilisation of xylose, glutamic acid, lysine and phenylethylamine. The data suggest that ‘new’ carbon inputs from plants colonising abandoned cutover peatland may support communities of microorganisms that have functionally distinct roles in carbon turnover.     

Influence of cold storage on soil microbial community level physiological profiles and implications for soil quality monitoring

Following collection of soil, storage prior to analyses is often required where the microbial community is unlikely to remain stable. We assessed the change in microbial community level physiological profiles (CLPP) during cold storage at 4 °C between 3 and 101 days. We hypothesized that the microbial community in soils containing less carbon would be affected more rapidly by storage. In particular we wanted to ascertain whether variability in CLPP through time masked inherent differences between soils derived from different ecosystems. Results illustrated that whilst total CO₂ evolution did vary with incubation time, significant differences in microbial community structure were detected between ecosystems for all times. Thus storage time did not mask intrinsic differences in microbial community structure between ecosystems.     

退化喀斯特植被恢复与土壤微生物特征的关系

The mechanism of vegetation restoration on degraded karst regions has been a research focus of soil science and ecology for the last decade.In an attempt to preferably interpret the soil microbiological characteristic variation associated with vegetation restoration and further to explore the role of soil microbiology in vegetation restoration mechanism of degraded karst regions,we measured microbial biomass C and basal respiration in soils during vegetation restoration in Zhenfeng County of southwestern Guizhou Province,China.The community level physiological profiles(CLPP) of the soil microbial community to were estimated determine if vegetation changes were accompanied by changes in functioning of soil microbial communities.The results showed that soil microbial biomass C and microbial quotient(microbial biomass C/organic C) tended to increase with vegetation restoration,being in the order arboreal community stage > shrubby community stage > herbaceous community stage > bare land stage.Similar trend was found in the change of basal respiration(BR).The metabolic quotient(the ratio of basal respiration to microbial biomass,qCO 2) decreased with vegetation restoration,and remained at a constantly low level in the arboreal community stage.Analyses of the CLPP data indicated that vegetation restoration tended to result in higher average well color development,substrate richness,and functional diversity.Average utilization of specific substrate guilds was highest in the arboreal community stage.Principle component analysis of the CLPP data further indicated that the arboreal community stage was distinctly different from the other three stages.In conclusion,vegetation restoration improved soil microbial biomass C,respiration,and utilization of carbon sources,and decreased qCO 2,thus creating better soil conditions,which in turn could promote the restoration of vegetation on degraded karst regions.     

Response of soil microbial communities to compost amendments

Soil organic matter is considered as a major component of soil quality because it contributes directly or indirectly to many physical, chemical and biological properties. Thus, soil amendment with composts is an agricultural practice commonly used to improve soil quality and also to manage organic wastes. We evaluated in laboratory scale experiments the response of the soilborne microflora to the newly created soil environments resulting from the addition of three different composts in two different agricultural soils under controlled conditions. At a global level, total microbial densities were determined by classical plate count methods and global microbial activities were assessed by measuring basal respiration and substrate induced respiration (SIR). Soil suppressiveness to Rhizoctonia solani diseases was measured through bioassays performed in greenhouses. At a community level, the modifications of the metabolic and molecular structures of bacterial and fungal communities were assessed. Bacterial community level physiological profiles (CLPP) were determined using Biolog™ GN microtiter plates. Bacterial and fungal community structures were investigated using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Data sets were analyzed using analysis of variance and ordination methods of multivariate data. The impact of organic amendments on soil characteristics differed with the nature of the composts and the soil types. French and English spent mushroom composts altered all the biological parameters evaluated in the clayey soil and/or in the sandy silty clay soil, while green waste compost did not modify either bacterial and fungal densities, SIR values nor soil suppressiveness in any of the soils. The changes in bacterial T-RFLP fingerprints caused by compost amendments were not related to the changes in CLPP, suggesting the functional redundancy of soil microorganisms. Assessing the density, the activity and the structure of the soil microflora allowed us not only to detect the impact of compost amendment on soil microorganisms, but also to evaluate its effect at a functional level through the variation of soil disease suppressiveness. Differences in disease suppressiveness were related to differences in chemical composition, in availability of nutrients at short term and in microbial composition due to both incorporation and stimulation of microorganisms by the compost amendments.     

Rhizosphere effects on functional stability of microbial communities in conventional and organic soils following elevated temperature treatment

The resistance and resilience of soil function may be increased through selection of crops and organic matter inputs. Soil from paired organic or conventional plots was left unplanted or used to grow barley. Substrate induced respiration (SIR) and community level physiological profiles (CLPP) were significantly different in both planted and unplanted systems and in conventional and organically-managed farming systems with no interaction; planted and organic systems had higher SIR. Following heat treatment (30 min at 70 °C), CLPP of planted and unplanted soils in both farming systems changed; a small short-lived decline in SIR only occurred in the planted soils. Differences in the response of these microbial communities to stress may be related to the relative proportions of active and dormant organisms; an increase in functional diversity did not necessarily reflect changed soil function.     

Comparison of two methods that assess soil community level physiological profiles in a forest ecosystem

There are currently two approaches that use whole soil to determine community level physiological profiles (CLPP) based on C-substrate utilization. We assessed the Degens and Harris and MicroResp™ approaches for their ability to distinguish between previously mined and non-mined forest soils that are characterized by gradients in biological, chemical and physical properties. Surface soils (0-5 cm) were collected from two ages of forest rehabilitation (3- and 16-years post mining), within mounds and furrows (caused by contour ripping) and from adjacent non-mined forest soil. Microbial respiration response to individual substrates was six times greater from the Degens and Harris (1.84 μg CO₂-C g soil h⁻¹) than the MicroResp™ (0.31 μg CO₂-C g soil h⁻¹) approach. The MicroResp™ approach was able to distinguish between CLPP of the two ages of rehabilitation (P=0.05), whereas the Degens and Harris approach did not. Neither approach identified an overall difference between the CLPP of mined and adjacent non-mined forest. The MicroResp™ approach revealed a significant difference (P=0.03) in CLPP from mounds of the two rehabilitation ages but no differences between the furrows. In addition there was a difference (P=0.03) in CLPP between the mounds and furrows within the 3-year old rehabilitation but no difference between the mounds and furrows within the 16-year-old rehabilitation. However, the CLPP of mounds of the 3-year old rehabilitation were different (P=0.059) to adjacent non-mined forest, while the furrows were not. There was no difference in CLPP between the mounds or the furrows of the 16-year-old rehabilitation and adjacent non-mined forest. These results suggest that the aspect of microbial heterotrophic function measured in this study takes up to 3 years to re-establish in the furrows and between 3-16 years in the mounds of post-mined rehabilitation soils. Our results also indicated that the MicroResp™ was substantially better than the Degens and Harris approach in distinguishing between treatments; this is likely to be due to differences in substrate concentrations and soil water potentials between approaches. Testing of a more comprehensive range of organic compounds would likely provide greater ecological interpretation of the CLPP data.     

CLPP and EEA profiles of microbial communities in salt marsh sediments

Objective  Microbial communities are a central component of trophic dynamics and biogeochemical processes on coastal systems, since most of the processes in sediments are mediated by microorganisms and carried out by enzymes. Microorganisms play a key role in decomposition processes in salt marsh sediments, although the significance of microbial dynamics is largely unexplored. A culture-dependent (Ecoplate) and a culture-independent (extracellular enzyme activity [EEA]) approaches were evaluated in their ability to distinguish the catabolic potential among sediments from Tagus estuary salt marshes with different proximities to anthropogenic sources. Methods  Ecoplate was used to analyse the salt marsh community-level physiological profiles (CLPPs). Results were expressed as the net area under the curve for each of the 31 response wells over a 3-day incubation period in two sediment horizons. The catabolic profiles for salt marsh samples were analysed by Principal Component Analysis (PCA) and hierarchic clustering methods. EEA was analysed by fluorescein diacetate (FDA) hydrolysis in two sediment horizons. The FDA is catalysed by extracellular enzymes, i.e. esterases, lipases and partially by proteases. Results were expressed as μg g⁻¹d wt h⁻¹. Results and Discussion  In this study the CLPP and EEA data were not generally correlated. In Corroios salt marsh only in surface sediments higher net areas corresponded to higher extracellular enzymatic activity, and in Alcochete deep sediments lower net areas corresponded to lower enzymatic activity. Although EEA profiles more directly reflect the inherent activity of resident community in each salt marsh sample, the CLPP profiles provide better assessments of diversity. ESS-Submission Editor: Prof. Dr. Peter Schroeder, Institute of Soil Ecology, Department of Rhizosphere Biology, GSF — National Research Center for Environment & Health, Ingolstaedter Landstrasse 1, 85758 Neuherberg, Germany (peter.schroeder@gsf.de)     

Assessing CLPPs using MicroResp™

Background, Aims and Scope  Soil microbial community diversity has been suggested as a way of assessing the ‘health’ or ‘quality’ of soils. While molecular (genetic) or biochemical (phenotypic) measurements of microbial diversity have their place, functional diversity is popular in that it relates to the activity of the soil microflora, particularly in the carbon cycle. Community Level Physiological Profiles (CLPPs) are usually assessed by carbon substrate utilization. The aim here is to review the various methods available for CLPP assessment. Main Features  The original method for CLPP determination was based upon the Biolog plate with its range of 95 carbon substrates and many studies have been employing this over the past 15 years. However, a number of criticisms have been leveled at the method, principally that it relies upon the growth of an extracted microbial population, which may not represent the true functioning of the whole soil. A multiple carbon-source, substrate induced respiration method (multi-SIR) was developed that did measure the response of the whole soil community without the need for growth but it did not have the convenience of the microtitre plate format. MicroResp™ was designed to overcome the deficiencies in both methods and we have applied it to a range of media including mineral and organic soils, sediments and litter. In addition we have adapted the method to the testing of a wide range of carbon substrates such as hydrocarbons, terpenes and pesticides. Results  The MicroResp™ technique covers the middle road of relevance and convenience, being a ‘whole soil’ method in a flexible microtitre plate format. It also has the advantage that it can be adapted for the use of radiolabelled (¹⁴C) substrates, which increases the specificity and sensitivity of the assay. A few direct comparisons between MicroResp™ have been made. We have found that its discriminatory ability compares favourably with Biolog while other users have reported it to be superior to the multiple SIR approach. A number of laboratories around the world are now utilizing MicroResp™ and reporting good sensitivity to changes to the microbial community due to such varied factors as age of forest rehabilitation, heavy metal treatment, hydrocarbon exposure, salinity, peatland vegetation, cropping system and tree clone type. Discussion  A comparison of the available methods reveals that each has its advantages and drawbacks. The choice of method may depend upon the particular hypotheses or questions. Conclusions  MicroResp™ offers a convenient, rapid and sensitive method for the determination of Community Level Physiological Profiles. Its application in a number of case studies has demonstrated its utility and advantages over other methods though its full potential for characterizing soil activity is yet to be realized. Perspectives  Increasing awareness of the environmental pressures on soils and the need to monitor soil health has resulted in a range of potential indicators. Microbial functional diversity is one such indicator that seeks to characterize a core soil attribute. The availability of rapid methods for its assessment will aid our understanding of such pressures on basic soil functioning. ESS-Submission Editor: Jizheng (Jim) He, PhD (jzhe@rcees.ac.cn)     

13C标记磷脂脂肪酸分析在土壤微生物生态 研究中的应用

磷脂脂肪酸(PLFA)是微生物细胞膜的重要组成成分,不同微生物群落可通过不同生化途径合成不同的PLFA,因此可选择某些PLFA作为微生物群落结构变化的生物标志物。PLFA与稳定性同位素~(13)C标记(~(13)C-PLFA)技术结合,不仅能够确定原位土壤环境中微生物群落组成,而且能够定向发掘土壤生态系统中参与碳源代谢过程的微生物群落,提供复杂群落中土壤微生物相互作用的信息,具有广阔的应用前景。其基本原理为:将富集~(13)C稳定同位素的基质加入土壤中,土壤中的某些微生物群落利用基质~(13)C合成PLFA,提取并纯化土壤微生物的PLFA,利用气相色谱-燃烧-同位素比例质谱(GC-C-IRMS)测定其~(13)C丰度,通过对比分析,从而获取微生物群落组成与其功能的直接信息。本文在介绍了~(13)C-PLFA原理的基础上,综述了该技术在光合同化碳的根际微生物利用、土壤有机质分解的激发效应、甲烷氧化、有机污染物降解、外源简单碳源和外源复杂碳源的微生物利用等方面的应用,对此项技术的优缺点进行了分析并展望了其未来应用。     

Controls on soil nitrogen cycling and microbial community composition across land use and incubation temperature

We conducted a laboratory incubation of forest (Scots pine (Pinus sylvestris) or beech (Fagus sylvatica)), grassland (Trifolium repens/Lolium perenne) and arable (organic and conventional) soils at 5 and 25 °C. We aimed to clarify the mechanisms of short-term (2-weeks) nitrogen (N) cycling processes and microbial community composition in relation to dissolved organic carbon (DOC) and N (DON) availability and selected soil properties. N cycling was measured by ¹⁵N pool dilution and microbial community composition by denaturing gradient gel electrophoresis (DGGE), phospholipid fatty acid (PLFA) and community level physiological profiles (CLPP). Soil DOC increased in the order of arable<grassland<forest soil while DON and gross N fluxes increased in the order of forest<arable<grassland soil; land use had no affect on respiration rate. Soil DOC was lower, while respiration, DON and gross N fluxes were higher at 25 than 5 °C. Gross N fluxes, respiration and bacterial biomass were all positively correlated with each other. Gross N fluxes were positively correlated with pH and DON, and negatively correlated with organic matter, fungal biomass, DOC and DOC/DON ratio. Respiration rate was positively correlated with bacterial biomass, DON and DOC/DON ratio. Multiple linear modelling indicated that soil pH, organic matter, bacterial biomass, DON and DOC/DON ratio were important in predicting gross N mineralization. Incubation temperature, pH and total-C were important in predicting gross nitrification, while gross N mineralization, gross nitrification and pH were important in predicting gross N immobilization. Permutation multivariate analysis of variance indicated that DGGE, CLPP and PLFA profiles were all significantly (P<0.05) affected by land use and incubation temperature. Multivariate regressions indicated that incubation temperature, pH and organic matter content were important in predicting DGGE, CLPP and PLFA profiles. PLFA and CLPP were also related to DON, DOC, ammonium and nitrate contents. Canonical correlation analysis showed that PLFA and CLPP were related to differences in the rates of gross N mineralization, gross nitrification and soil respiration. Our study indicates that vegetation type and/or management practices which control soil pH and mediate dissolved organic matter availability were important predictors of gross N fluxes and microbial composition in this short-term experiment.     

Changes in microbial community structure and function following Sphagnum peatland restoration

This study examines the recovery of the microbial compartment following active restoration of a North American ombrotrophic peatland extracted for horticultural peat-based substrates and restored by the Sphagnum moss transfer method. We used phospholipid fatty acids (PLFAs) to portrait the microbial community structure and Community Level Physiological Profiles (CLPP) to describe the functional diversity of the microbial communities. Our results indicate that the PLFA profiles were different between the beginning and the end of the growing season, but that it was impossible to distinguish five different vegetation classes found along the disturbance-recovery gradient on the basis of the microbial community structure. The pH, the cover of mosses, Ledum groenlandicum and Eriophorum vaginatum var. spissum were the best environmental predictors for the PLFA composition. The newly formed peat found in aerobic conditions beneath restored Sphagnum carpets had the highest decomposition capacity, whereas the lowest rates were found in the surface samples of non-restored conditions or in the deepest horizons of the natural samples. A large proportion of the variation in the physiological profiles was explained with variables related to the vegetation cover, the physicochemical environment and the microbial structure of the community, which is very promising for future monitoring studies. Overall, this study demonstrates that the recovery of particular plant groups, namely mosses and shrubs in restored peatlands might be the driver of changes occurring in the structure of the microbial communities in restored peatlands.     

An evaluation of the functional significance of peat microorganisms using a reciprocal transplant approach

Our current knowledge on the relevance of microbial diversity and composition for the recovery and maintenance of soil biological processes is rudimentary, partly because experimental substantiation of the importance of community composition to function is scarce. Guided by this gap, we devised a reciprocal transplant experiment to examine the functional behaviour of different microbial communities exposed to two structurally distinct peats. Sterile peat samples representing two types, one humified (sedge) and the other dominated by coarse plant material (fibric), were inoculated with a 10⁻¹, 10⁻³, 10⁻⁵, or 10⁻⁸ dilution of either the same or reciprocal peats. After 5 months of incubation, we used a nucleotide-analog technique to label the active bacterial taxa in samples receiving the 10⁻¹ and 10⁻⁸ dilutions. We assessed both the peats' functional potential (respiration and nutrient-acquiring and lignin-degrading enzyme activities) and the structures of active and total bacterial communities (PCR-DGGE). In general, we found a decline in respiration rates and increase in enzyme activities with increasing dilution level, but the effect of dilution on bacterial richness was weak. The bacterial community structure and richness depended on both the inoculum source and the peat type. The activity of enzymes involved in nutrient acquisition depended mainly on the soil type, while the lignin-degrading activity was influenced by differences in community composition between peat types. Neither active bacterial populations nor respiration were significantly influenced by peat type or inoculum source. Our results suggest that the relationship between microbial community composition and function is not only related to the taxonomic breadth of the taxa that perform a given function, but may also be shaped by interactions between microorganisms in the inoculum source and the substrate being colonized.     

Choice of methods for soil microbial community analysis: PLFA maximizes power compared to CLPP and PCR-based approaches

Polyphasic studies that used phospholipid fatty acid analysis (PLFA) in conjunction with community level physiological profiling (CLPP) or PCR-based molecular methods were analyzed in order to evaluate the power of each strategy to detect treatment effects on soil microbial community structure (MCS). We found no studies where CLPP or PCR-based methods differentiated treatments that were not also differentiated by PLFA. In 14 of 32 studies (44%), PLFA differentiated treatments that were not resolved by CLPP analysis. In 5 of 25 studies (20%), PLFA differentiated treatments that were not resolved by PCR-based methods. We discuss PLFA, CLPP, and PCR-based methods with respect to power to discriminate change in MCS versus potential for characterization of underlying population level changes.     

Effect of long-term fertilizers and manure application on microbial biomass and microbial activity of a tropical agricultural soil

We investigated some aspects of soil quality and community-level physiological profiles (CLPP) of bacteria in soil under a long-term (37 years) trial with either exclusive inorganic fertilizers or fertilizers combined with farmyard manure cultivated with jute–rice–wheat system. The treatments consisted of 100% recommended dose (RD) of NPK, 150% RD of NPK, 100% RD of N, 100% RD of NPK + FYM (10 t ha⁻¹ year⁻¹), and untreated control. Long-term application of 150% RD of NPK lowered the soil pH considerably while the soils in the other treatments remained near neutral. The 100% RD of NPK + FYM treated plot showed significantly highest accumulation of organic carbon, total nitrogen, microbial biomass carbon, basal soil respiration, and fluorescein diacetate hydrolyzing activity among the treatments. CLPP analysis in Biolog Ecoplates revealed that utilization of carbohydrates was enhanced in all input treated regimes, while the same for polymers, carboxylic acids, amino acids, and amines/amides were similar or less than the untreated control. However, within these groups of carbon sources, heterogeneity of individual substrate utilization between treatments was also noted. Taken together, addition of organic supplements showed significantly increased microbial biomass carbon and microbial activity, but input of nutrient supplements, both inorganic and organic, only marginally affected the overall substrate utilization pattern of soil microorganisms.     

Direct comparison of individual substrate utilization from a CLPP study: A new analysis for metabolic diversity data

For over a decade, community level physiological profile (CLPP) assays, which assess a microbial community's capacity to metabolize specific sole carbon sources under defined laboratory conditions, have been popular for study of environmental soil samples. One such assay, BiOLOG™ allows for the colorimetric measurement of metabolism through the reduction of a tetrazolium dye, which yields optical density (OD) data for each substrate. Bacterial communities are extracted from soil and 150 μL of this extract is inoculated directly into each well of the microtitre plate. The combined metabolic data obtained are most often analyzed with multivariate statistical analyses, such as principal component analysis (PCA). The objectives of this study were (1) to develop a simple, visual, statistically valid method of determining community capabilities to utilize specific substrates in CLPP studies and (2) to test the number of samples needed for such discrimination to be reliable. This was done by direct comparison of the OD values obtained for two closely related microbial communities (surface and subsurface soil), plotted against a one-to-one (y=x) line. Due to variability in the portion of the soil microbial community inoculated into the individual test wells, the accuracy of the method was dependent on the number of replicates analyzed. A variety of data set sizes were tested, from n=3 samples/soil depth to n=40 samples/depth. The method was statistically valid for all data sets tested. Those substrates that deviated from the one-to-one line consistently had F values greater than 1. Additionally, data sets of n=30,35 and 40 samples/depth consistently allowed identification of the eight substrates whose metabolism varied significantly between the two test soil communities. In conclusion, this one-to-one comparison has been shown to be a statistically valid analytical method to compare individual substrate usage between soils.     

Rock fragments in soil support a different microbial community from the fine earth

Two sandstone-derived soils under pure stands of silver fir (Abies alba Mill.) and European beech (Fagus sylvatica L.) were studied to determine if the fine earth (<2 mm material) and two size-classes of porous rock fragments (>2 mm material) supported different microbial communities. Samples from three soil horizons (A, Bw, and BC) were analysed under both optical and scanning electron microscopes. Small stones (2-10 mm in average diameter) appeared more altered than larger ones (40-60 mm) and the effects of weathering became more obvious with shallower depth. In both soils, numerous hyphae and other living forms were observed on the surface of the stones from the A and Bw horizons; this contrasted with the stones from the BC horizon, which showed little or no colonisation. The microbial community of each fraction was characterised using Biolog-Community Level Physiological Profiles (CLPP) and phospholipid fatty acid analyses (PLFA) for samples in the A and B horizons. Significant potential microbial activity (C source utilisation) was associated with rock fragments, from the A horizon and, to a lesser extent, the B, although this was lower than for the equivalent fine earth fraction. The microbial colonisation of the stones appeared inversely related with their size and sampling depth. The PLFA analysis showed not only quantitative differences in the microbial biomass between horizons and size-fractions but also highlighted that the communities differed between soils, horizons (for the sole beech soil) and fractions. These findings demonstrate that by considering rock fragments as a microbiologically inert fraction and discarding them before analysis, as usually is done, can lead to an incomplete picture of both the total amount and, perhaps more importantly, the structure of soil microbial community.     

Changes in soil bacterial community structure and microbial function caused by straw retention in the North China Plain

ABSTRACT

The effects of straw retention on soil bacterial community structure, microbial function, and biochemical properties were assessed. Terminal restriction fragment length polymorphism (T-RFLP) and community-level physiological profile (CLPP) assays were used to assess the bacteria community structure and microbial function respectively. Treatments included straw removal with conventional tillage (CT), straw retention with conventional tillage (SRCT) and straw retention with no tillage (SRNT). SRCT and SRNT significantly (p < 0.05) increased soil organic carbon by 8.9% and 9.7%, and microbial biomass carbon by 44.7% and 330.8%, respectively, compared with CT. T-RFLP analysis indicated that straw retention had no favourable effect on soil bacterial diversity, and SRCT significantly (p < 0.05) decreased bacterial diversity compared to CT. Among the three treatments, SRNT had the highest activity of urease, invertase, cellulase, and β-glucosidase. SRCT significantly (p < 0.05) increased the activity of invertase and β-glucosidase compared to CT treatment. CLPP analysis showed that microbial functional diversity was significantly (p < 0.05) increased by straw retention. Enzyme activity and microbial functional diversity were not correlated with bacterial diversity. Therefore, according to this study, SRNT is a better farming practice because it improves soil fertility and biological quality.     

Microbial activity and functional composition among northern peatland ecosystems

The extent to which complex interrelationships between plants and microorganisms influence organic matter dynamics is critical to our understanding of global C cycles in changing environments. We examined the hypothesis that patterns of soil microbial activity and functional composition differ among vegetation types in northern peatland ecosystems. Microbial characteristics were compared among peatlands differing in plant growth form (tree, shrub/moss, sedge) in two regions (New York State and West Virginia). Microbial activity (basal respiration) was greater in surface (0-15 cm) than subsurface (15-30 cm) peat and from sites dominated by shrubs and Sphagnum moss (3.9±0.65 μg C g⁻¹ h⁻¹) compared to forested (1.8±0.20 μg C g⁻¹ h⁻¹) or sedge-dominated sites (1.9±0.38 μg C g⁻¹ h⁻¹). Microbial activity was not related to decomposability of peat organic matter among vegetation types, and activity was unexpectedly higher in sites with lower peat pH and higher water table level. Substrate-induced respiration (SIR) did not show a clear pattern among vegetation types, but was greater in surface than subsurface peat. Microbial responsiveness to added glucose was very low. The ratio of basal respiration to SIR varied between 0.39 and 0.72 and, like activity, was highest in shrub/Sphagnum sites. Microbial substrate utilization patterns (assayed with BIOLOG^® GN plates) also differed between shrub/Sphagnum sites and forest or sedge sites, suggesting that C fluxes were mediated by different assemblages of microorganisms in shrub/Sphagnum peatlands. Principal component (PC) scores indicated more utilization of N-containing compounds and carboxylic acids, and less utilization of carbohydrates by microbial communities in shrub/Sphagnum sites. PC scores were much more variable both within and among vegetation types for sites in West Virginia than in New York State, and a greater diversity of C sources were utilized in WV (57±3) than NYS (47±2) peat. Our results suggest a link between microbial respiratory activity and microbial functional composition as they vary among these peatland vegetation types.     

Effects of sulfamethoxazole on soil microbial communities after adding substrate

The effect of the antibiotic sulfamethoxazole (SMX) on soil bacteria was studied using two methods (leucine incorporation and Biolog plates) of estimating pollution-induced community tolerance (PICT). SMX was added to an agricultural soil in a microcosm setup. The addition of different substrates (manure and alfalfa), and a non-amended soil, were also studied over 5 weeks. PICT measurements were validated by comparison with other measurements. Community structure was assessed using phospholipid fatty acid (PLFA) analysis and community-level physiological profiling (CLPP), and bacterial growth was estimated using leucine incorporation. Increased PICT was found at SMX concentrations of 20 and 500 mg SMX kg⁻¹ soil in samples containing manure and alfalfa, and at 500 mg SMX kg⁻¹ soil in non-amended soil (only concentration tested) using leucine incorporation. No effect was seen at 1 mg SMX kg⁻¹ soil. It was not necessary to add any substrate to increase the microbial activity in order to detect the effects of a bacteriostatic toxicant such as SMX when using measures based on bacterial growth. Direct inhibition of bacterial growth 2 days after SMX addition was correlated to PICT. No major changes in PICT due to SMX addition were found when using Biolog plates. However, there was a tendency towards increased PICT at the higher SMX concentrations in the manure-amended soil. Thus, different methods of detecting PICT have different sensitivities in detecting the toxic effects of SMX. The effects of substrate amendment were reflected by changes in the microbial community, estimated using both PLFA and CLPP. SMX was found to have a clear effect at the two highest levels of SMX in the manure- and alfalfa-amended soils, with an increase in fungal and a decrease in bacterial PLFAs. Little difference in the PLFA composition was found in the non-amended soil. CLPP was only affected at the highest SMX concentration. Although different variables showed different sensitivities to the effects of SMX, the results were consistent with an initial decrease in bacterial growth rates of sensitive species, which eventually transformed into more tolerant species, altering the community composition.