2-Phenylethylisothiocyanate concentration and microbial community composition in the rhizosphere of canola

Canola crops have been shown to inhibit soil-borne pathogens in following crops. This effect is mainly attributed to the release of low molecular S-containing compounds, such as isothiocyanates, during microbial degradation of the crop residues. We have assessed the effect of low concentrations of phenylethylisothiocyanate (PEITC) on soil microbial communities as well as its rate of degradation in soil and determined the concentration of PEITC and the microbial community structure in the rhizosphere of canola. PEITC was degraded within 96 h by soil microorganisms. PEITC added to the soil daily for 5 d affected both bacterial and eukaryotic community structure, determined by PCR-DGGE. Community structures of bacteria and eukaryotes changed at PEITC concentrations between 1300 and 3790 pmol g⁻¹ soil fresh weight but was unaffected at lower concentrations. The PEITC concentration in the rhizosphere of living canola roots was greater in first order laterals than in second order laterals. The maximal PEITC concentration detected in the rhizosphere was 1827 pmol g⁻¹. Redundancy analysis of the DGGE banding patterns indicated a significant correlation between the PEITC concentration in the rhizosphere and the community structure of the active fraction of eukaryotes and bacteria in the rhizosphere. Other important factors influencing the microbial community structure were soil moisture and plant dry matter. It is concluded that canola may affect the soil microbial community structure not only after incorporation of canola residues but also during active growth of the plants.     

Microbial community composition and rhizodeposit-carbon assimilation in differently managed temperate grassland soils

Rhizodeposit-carbon provides a major energy source for microbial growth in the rhizosphere of grassland soils. However, little is known about the microbial communities that mediate the rhizosphere carbon dynamics, especially how their activity is influenced by changes in soil management. We combined a ¹³CO₂ pulse-labeling experiment with phospholipid fatty acid (PLFA) analysis in differently managed Belgian grasslands to identify the active rhizodeposit-C assimilating microbial communities in these grasslands and to evaluate their response to management practices. Experimental treatments consisted of three mineral N fertilization levels (0, 225 and 450 kg N ha⁻¹ y⁻¹) and two mowing frequencies (3 and 5 times y⁻¹). Phospholipid fatty acids were extracted from surface (0-5 cm) bulk (BU) and root-adhering (RA) soil samples prior to and 24 h after pulse-labeling and were analyzed by gas chromatography-combustion-isotope ratio mass spectrometry (GC-c-IRMS). Soil habitats significantly differed in microbial community structure (as revealed by multivariate analysis of mol% biomarker PLFAs) as well as in gram-positive bacterial rhizodeposit-C uptake (as revealed by greater ¹³C-PLFA enrichment following pulse-labeling in RA compared to BU soil in the 450N/5M treatment). Mowing frequency did not significantly alter the relative abundance (mol%) or activity (¹³C enrichment) of microbial communities. In the non-fertilized treatment, the greatest ¹³C enrichment was seen in all fungal biomarker PLFAs (C16:1ω5, C18:1ω9, C18:2ω6,9 and C18:3ω3,6,9), which demonstrates a prominent contribution of fungi in the processing of new photosynthate-C in non-fertilized grassland soils. In all treatments, the lowest ¹³C enrichment was found in gram-positive bacterial and actinomycetes biomarker PLFAs. Fungal biomarker PLFAs had significantly lower ¹³C enrichment in the fertilized compared to non-fertilized treatments in BU soil (C16:1ω5, C18:1ω9) as well as RA soil (all fungal biomarkers). While these observations clearly indicated a negative effect of N fertilization on fungal assimilation of plant-derived C, the effect of N fertilization on fungal abundance could only be detected for the arbuscular mycorrhizal fungal (AMF) PLFA (C16:1ω5). On the other hand, increases in the relative abundance of gram-positive bacterial PLFAs with N fertilization were found without concomitant increases in ¹³C enrichment following pulse-labeling. We conclude that in situ¹³C pulse-labeling of PLFAs is an effective tool to detect functional changes of those microbial communities that are dominantly involved in the immediate processing of new rhizosphere-C.     

Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils

A number of studies have reported species specific selection of microbial communities in the rhizosphere by plants. It is hypothesised that plants influence microbial community structure in the rhizosphere through rhizodeposition. We examined to what extent the structure of bacterial and fungal communities in the rhizosphere of grasses is determined by the plant species and different soil types. Three grass species were planted in soil from one site, to identify plant-specific influences on rhizosphere microbial communities. To quantify the soil-specific effects on rhizosphere microbial community structure, we planted one grass species (Lolium perenne L.) into soils from three contrasting sites. Rhizosphere, non-rhizosphere (bulk) and control (non-planted) soil samples were collected at regular intervals, to examine the temporal changes in soil microbial communities. Rhizosphere soil samples were collected from both root bases and root tips, to investigate root associated spatial influences. Both fungal and bacterial communities were analysed by terminal restriction fragment length polymorphism (TRFLP). Both bacterial and fungal communities were influenced by the plant growth but there was no evidence for plant species selection of the soil microbial communities in the rhizosphere of the different grass species. For both fungal and bacterial communities, the major determinant of community structure in rhizospheres was soil type. This observation was confirmed by cloning and sequencing analysis of bacterial communities. In control soils, bacterial composition was dominated by Firmicutes and Actinobacteria but in the rhizosphere samples, the majority of bacteria belonged to Proteobacteria and Acidobacteria. Bacterial community compositions of rhizosphere soils from different plants were similar, indicating only a weak influence of plant species on rhizosphere microbial community structure.     

Root exudate effects on the bacterial communities, CO2 evolution, nitrogen transformations and ATP content of rhizosphere and bulk soils

The ATP content, soil respiration, bacterial community composition, and gross N mineralization and immobilization rates were monitored under laboratory condition at 25 °C for 28 d in a model system where low molecular weight root exudates (glucose and oxalic acid) were released by a filter placed on the surface of a forest soil also treated with ¹⁵N, so as to simulate rhizosphere conditions. Periodically, the soil was sampled from two layers, 0-2 and 6-14 mm below the filter's surface, which were indicated as rhizosphere and bulk soils, respectively. The isotope dilution technique was used to determine the effect of these low molecular weight organic compounds (LMWOCs) on gross N mineralization and immobilization rates. From 0 to 3 d both glucose and oxalic acid amended soils showed a rapid evolution of CO₂, more pronunced in the latter treatment together with a decrease in the amount of mineral N of the rhizosphere soil, probably due to N immobilization. Nevertheless, these changes were accompanied by a very small increase in the net ATP content probably because the low C application rate stimulated microbial activity but microbial growth only slightly. A positive ‘priming effect’ probably developed in the oxalic acid amended soil but not in the glucose amended soil. Gross N mineralization and immobilization rates were only observed in the rhizosphere soil, probably due to the greater C and N concentrations and microbial activity, and were a little higher in both amended soils than in the control soil, only between 1 and 7 d. Both glucose and oxalic acid influenced the bacterial communities of the rhizosphere soil, as new bands in the DGGE profiles appeared at 3 and 7 d. Glucose induced lower changes in the bacterial community than oxalic acid, presumably because the former stimulated a larger proportion of soil microorganisms whereas the latter was decomposed by specialized microorganisms. Peaks of net daily soil respiration and net ATP content and the appearence of new dominant bacterial populations were shifted in time, probably because there was less ATP synthesis and DGGE patterns changed after complete substrate mineralization.     

Response of microbial communities to water stress in irrigated and drought-prone tallgrass prairie soils

To better understand how water stress and availability affect the structure of microbial communities in soil, I measured the change in phospholipid fatty acids (PLFA) and the incorporation of ¹³C-labeled glucose into the PLFA following exposure to water stress. Overlaid on the laboratory water stress treatment, samples were collected from drought-prone and irrigated (11 years) tallgrass prairie soil (0-10 cm depth). In the laboratory, soils were either incubated at −250 kPa or dried steadily over a 3-d period to −45 MPa. On the fourth day, the dried samples were brought up to −250 kPa and then all samples received 250 μg of glucose-C (+4000 δ¹³C-PDB) solution that brought them to −33 kPa matric water potential. Samples were then extracted for PLFA following 6 and 24 h of incubation (25 °C). Non-metric multidimensional scaling (NMS) techniques and multi-response permutation procedure (MRPP) showed that the largest effect on the mol% distribution of PLFA was related to the field scale water addition experiment. In response to irrigation, the PLFA 16:1ω5, 18:1+, and 18:2ω6,9 showed increases, and a15:0, a17:0, and cy19:0 showed decreases in their respective mol%. Effects related to the induction of laboratory water stress were predominantly associated with a decrease in the mol% distribution of the putative fungal biomarker (18:2ω6,9) with little to no change in the mol% distribution of the bacterial biomarkers. Interestingly, the flow of C to the microbial community was not strongly related to any single PLFA, and differences were rather subtle, but multivariate MRPP detected change to the community structure related to the laboratory water stress treatment but not related to the 11 years of field irrigation. Our results suggest that both the total and the actively metabolizing bacterial community in soil were generally resistant to the effects of water stress brought by rewetting of dry soil. However, more research is needed to understand the nature of the fungal response to drying and rewetting in soil.     

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.     

Use of an artificial root to examine the influence of 8-hydroxyquinoline on soil microbial activity and bacterial community structure

Invasive plant species have been shown to alter the microbial community composition of the soils they invade and it is suggested that this below-ground perturbation of potential pathogens, decomposers or symbionts may feedback positively to allow invasive success. Whether these perturbations are mediated through specific components of root exudation are not understood. We focussed on 8-hydroxyquinoline, a putative allelochemical of Centaurea diffusa (diffuse knapweed) and used an artificial root system to differentiate the effects of 8-hydroxyquinoline against a background of total rhizodeposition as mimicked through supply of a synthetic exudate solution. In soil proximal (0-10 cm) to the artificial root, synthetic exudates had a highly significant (P < 0.001) influence on dehydrogenase, fluorescein diacetate hydrolysis and urease activity. In addition, 8-hydroxyquinoline was significant (p = 0.003) as a main effect on dehydrogenase activity and interacted with synthetic exudates to affect urease activity (p = 0.09). Hierarchical cluster analysis of 16S rDNA-based DGGE band patterns also identified a primary affect of synthetic exudates and a secondary affect of 8-hydroxyquinoline on bacterial community structure. Thus, we show that the artificial rhizosphere produced by the synthetic exudates was the predominant effect, but, that the influence of the 8-hydroxyquinoline signal on the activity and structure of soil microbial communities could also be detected.     

Profiling of PLFA: Implications for nonlinear spatial gradient of PCP degradation in the vicinity of Lolium perenne L. roots

An investigation was conducted using phospholipid fatty acids (PLFAs) profiles to follow the spatial response of the microbial community at the millimeter scale with the purpose of illustrating the mechanism of nonlinear spatial dependence of PCP degradation on the distance from the root surface in the rhizosphere of Lolium perenne L. A laminar rhizobox was designed to allow the harvest of intact layers of root compartment, near-(1, 2, 3, 4, 5 mm) and far-(>5 mm) rhizosphere soil from root surfaces without the removal of the root material itself. Lolium perenne L. was grown in environmental chambers for 53 days with soil spiked with 8.7 and 18 mg kg⁻¹ PCP. PLFA profiles were found to be affected by the distance from the rhizosphere, indicating a distance-dependent selective enrichment of competent species that may be responsible for efficient PCP degradation. In particular, the five fatty acids 16:1ω5, 16:0, i17:0, a17:0 and 10Me18:0 emerged as microbiological biomarkers that may be used for assessing phytoremediation processes of PCP in soil. Their synergistic effects were shown to be most responsive to the nonlinear spatial patterns of PCP degradation in the vicinity of Lolium perenne L. roots. The results suggest that root exudates induced modifications of microbial communities in the PCP contaminated rhizosphere and spatially modified the dominant species within these communities, resulting in the nonlinear PCP degradation pattern.     

Effects of silver nanoparticles on soil microorganisms and maize biomass are linked in the rhizosphere

Silver nanoparticles hold great promise as effective anti-microbial compounds in a myriad of applications but may also pose a threat to non-target bacteria and fungi in the environment. Because microorganisms are involved in extensive interactions with many other organisms, these partner species are also prone to indirect negative effects from silver nanoparticles.Here, we focus on the effects of nanosilver exposure in the rhizosphere. Specifically, we evaluate the effect of 100 mg kg⁻¹ silver nanoparticles on maize plants, as well as on the bacteria and fungi in the plant's rhizosphere and the surrounding bulk soil. Maize biomass measurements, microbial community fingerprints, an indicator of microbial enzymatic activity, and carbon use diversity profiles are used. Hereby, it is shown that 100 mg kg⁻¹ silver nanoparticles in soil increases maize biomass, and that this effect coincides with significant alterations of the bacterial communities in the rhizosphere. The bacterial community in nanosilver exposed rhizosphere shows less enzymatic activity and significantly altered carbon use and community composition profiles. Fungal communities are less affected by silver nanoparticles, as their composition is only slightly modified by nanosilver exposure. In addition, the microbial changes noted in the rhizosphere were significantly different from those noted in the bulk soil, indicated by different nanosilver-induced alterations of carbon use and community composition profiles in bulk and rhizosphere soil.Overall, microorganisms in the rhizosphere seem to play an important role when evaluating the fate and effects of silver nanoparticle exposure in soil, and not only is the nanosilver response different for bacteria and fungi, but also for bulk and rhizosphere soil. Consequently, assessment of microbial populations should be considered an essential parameter when investigating the impacts of nanoparticle exposure.     

Identification of Metabolically Active Rhizosphere Microorganisms by Stable Isotopic Probing of PLFA in Switchgrass

Root-derived rhizodeposits of recent photosynthetic carbon (C) are the foremost source of energy for microbial growth and development in rhizosphere soil. A substantial amount of photosynthesized C by the plants is translocated to belowground and is released as root exudates that influence the structure and function of soil microbial communities with potential inference in nutrient and C cycling in the ecosystem. We applied the ¹³C pulse chase labeling technique to evaluate the incorporation of rhizodeposit-C into the phospholipid fatty acids (PLFAs) in the bulk and rhizosphere soils of switchgrass (Panicum virgatum L.). Soil samples of bulk and rhizosphere were taken at 1, 5, 10 and 20 days after labeling and analyzed for ¹³C enrichment in the microbial PLFAs. Temporal differences of ¹³C enrichment in PLFAs were more prominent than spatial differences. Among the microbial PLFA biomarkers, fungi and Gram-negative (GM-ve) bacterial PLFAs showed rapid enrichment with ¹³C compared to Gram-positive (GM+ve) and actinomycetes in rhizosphere soil. The ¹³C enrichment of actinomycetes biomarker PLFA significantly increased along with sampling time in both soils. PLFAs indicative to fungi, GM-ve and GM+ve showed a significant decrease in ¹³C enrichment over sampling time in the rhizosphere, but a decrease was also observed in GM-ve (16:1ω5c) and fungal biomarker PLFAs in the bulk soil. The relative ¹³C concentration in fungal PLFA decreased on day 10, whereas those of GM-ve increased on day 5 and GM+ve remained constant in the rhizosphere soil. However, the relative ¹³C concentrations of GM-ve and GM+ve increased on days 5 and 10, respectively, and those of fungal remain constant in the bulk soil. The present study demonstrates the usefulness of ¹³C pulse chase labeling together with PLFA analysis to evaluate the active involvement of microbial community groups for utilizing rhizodeposit-C.     

Elevated enzyme activities in soils under the invasive nitrogen-fixing tree Falcataria moluccana

Like other N-fixing invasive species in Hawaii, Falcataria moluccana dramatically alters forest structure, litterfall quality and quantity, and nutrient dynamics. We hypothesized that these biogeochemical changes would also affect the soil microbial community and the extracellular enzymes responsible for carbon and nutrient mineralization. Across three sites differing in substrate texture and age (50-300 years old), we measured soil enzyme activities and microbial community parameters in native-dominated and Falcataria-invaded plots. Falcataria invasion increased acid phosphatase (AP) activities to >90 μmol g⁻¹ soil h⁻¹ compared to 30-60 μmol g⁻¹ soil h⁻¹ in native-dominated stands. Extracellular enzymes that mineralize carbon and nitrogen also increased significantly under Falcataria on the younger substrates. By contrast, total microbial biomass and mycorrhizal abundance changed little with invasion or substrate. However, fungal:bacterial ratios declined dramatically with invasion, from 2.69 and 1.35 to <0.89 on the 50- and 200-year-old substrates, respectively. These results suggest that Falcataria invasion alters the composition and function of belowground soil communities in addition to forest structure and biogeochemistry. The increased activities of AP and other enzymes that we observed are consistent with a shift toward phosphorus limitation and rapid microbial processing of litterfall C and N following Falcataria invasion.     

Effects of glyphosate on rhizosphere soil microbial communities under two different plant compositions by cultivation-dependent and -independent methodologies

We studied, under two different plant compositions, the short-term effects of glyphosate on rhizosphere soil microbial communities through the utilization of cultivation-dependent and -independent techniques. A short-term pot study was carried out using factorial treatments that included two different compositions of forage plant species (triticale versus a mixture of triticale and pea) and two concentrations of glyphosate (50 and 500 mg active ingredient kg⁻¹ soil, as a commercial formulation, Roundup Plus) arranged in a completely randomized design experiment with four replicates. Control plants (no glyphosate added) were clipped in an attempt to compare two methods of weed control (manual = clipping; chemical = herbicide treatment). Rhizosphere soil was sampled 15 and 30 days after glyphosate treatment and the following soil components were determined: potentially mineralizable nitrogen, ammonium content, community-level physiological profiles using Biolog Ecoplates™, DNA microbial biomass and genotype diversity by means of PCR-DGGE. Fifteen days after herbicide treatment, a glyphosate-induced stimulation of the activity and functional diversity of the cultivable portion of the heterotrophic soil microbial community was observed, most likely due to glyphosate acting as an available source of C, N and P. On the other hand, 30 days after herbicide treatment, both the activity and diversity of the rhizosphere soil microbial communities showed an inconsistent response to glyphosate addition. Apart from its intended effect on plants, glyphosate had non-target effects on the rhizosphere soil microbial community which were, interestingly, more enhanced in triticale than in “triticale + pea” pots. Biolog™ was more sensitive than PCR-DGGE to detect changes in soil microbial communities induced by glyphosate and plant composition.     

Community structure of microeukaryotes in a rice rhizosphere revealed by DNA-based PCR-DGGE

Rice roots provide a specific habitat for microorganisms in the rhizosphere of a submerged field through supply of oxygen and organic matter. Many studies have focused on the microbial community in the rice rhizosphere, but less is still known about the microeukaryotic community structure of rice rhizosphere. This study explored the microeukaryotic community structure of a rice rhizosphere through denaturing gradient gel electrophoresis (DGGE) targeting 18S rRNA gene. The rice roots and the rhizosphere soil samples, which were collected from a field under rice-wheat rotation system, were separately analyzed. To characterize the rice rhizosphere-specific community, the bulk soil of rice field and the wheat rhizosphere samples were also examined. DGGE fingerprints showed that the microeukaryotic community of rice roots were distinct from the community of the bulk soil and showed a temporal shift with the growth stage. The rhizosphere soil community was distinct from the root and bulk soil communities, but this could be explained by that the root and bulk soil communities were shared in the rhizosphere. The rice rhizosphere community was also distinct from those in the wheat rhizosphere. Microeukaryotes that characterized the rice rhizosphere (roots and the rhizosphere soil) community could be affiliated to Polymyxa, flagellates, and oomycetes, which suggested that microeukaryotes with various ecological roles, e.g., parasites, bacterial grazers, and decomposers, inhabit the rice rhizosphere. The results showed that the rice root and its growth stages are key factors shaping the microeukaryotic community structure in the rhizosphere.     

Short-term effects of defoliation on the soil microbial community associated with two contrasting Lolium perenne cultivars

Intra-species variation in response to defoliation and soil amendment has been largely neglected in terms of the soil microbial community (SMC). The influence of defoliation and soil fertiliser amendment on the structure of the SMC was assessed with two Lolium perenne cultivars contrasting in ability to accumulate storage reserves. Plant response to defoliation was cultivar specific and depended on the nutrient amendment of the soil. Results suggested a greater ability to alter plant biomass allocation in the low carbohydrate accumulating cultivar (S23) compared to the high carbohydrate cultivar (AberDove) when grown in improved (IMP), but not in unimproved (UNI), soil. Although differences in plant growth parameters were evident, no treatment effects were detected in the size of the active microbial biomass (total phospholipid fatty acid (PLFA) 313.8 nmol g⁻¹ soil±33.9) or proportions of PLFA signature groups. A lower average well colour development (AWCD) of Biolog sole carbon source utilisation profiles (SCSUPs) in defoliated (D) compared to non-defoliated (ND) treatments may be indicative of lower root exudation 1 week following defoliation, as a consequence of lower root non-structural carbohydrate (NSC) concentrations. Within the bacterial community the lower cyclopropyl-to-precursor ratio of PLFAs, and the trans/cis ratio of 16:1w7, in UNI relative to IMP soil treatments indicates lower physiological stress in UNI soils regardless of L. perenne cultivar. Discrimination of broad scale SMC structure, measured by PLFA analysis, revealed that soil treatment interacted strongly with cultivar and defoliation. In IMP soils the SMCs discriminated between cultivars while defoliation had little effect. Conversely, in UNI soils defoliation caused a common shift in the SMC associated with both cultivars, causing convergence of overall community structure. Separation of SMC structure along the primary canonical axis correlated most strongly (P<0.001) with root:shoot ratio (47.6%), confirming that differences in cultivar C-partitioning between treatments were influential in defining the rhizosphere microbial community.     

Atmospheric nitrate deposition and the microbial degradation of cellobiose and vanillin in a northern hardwood forest

Human activity has increased the amount of N entering terrestrial ecosystems from atmospheric NO₃⁻ deposition. High levels of inorganic N are known to suppress the expression of phenol oxidase, an important lignin-degrading enzyme produced by white-rot fungi. We hypothesized that chronic NO₃⁻ additions would decrease the flow of C through the heterotrophic soil food web by inhibiting phenol oxidase and the depolymerization of lignocellulose. This would likely reduce the availability of C from lignocellulose for metabolism by the microbial community. We tested this hypothesis in a mature northern hardwood forest in northern Michigan, which has received experimental atmospheric N deposition (30 kg NO₃⁻-N ha⁻¹ y⁻¹) for nine years. In a laboratory study, we amended soils with ¹³C-labeled vanillin, a monophenolic product of lignin depolymerization, and ¹³C-labeled cellobiose, a disaccharide product of cellulose degradation. We then traced the flow of ¹³C through the microbial community and into soil organic carbon (SOC), dissolved organic carbon (DOC), and microbial respiration. We simultaneously measured the activity of enzymes responsible for lignin (phenol oxidase and peroxidase) and cellobiose (β-glucosidase) degradation. Nitrogen deposition reduced phenol oxidase activity by 83% and peroxidase activity by 74% when compared to control soils. In addition, soil C increased by 76%, whereas microbial biomass decreased by 68% in NO₃⁻ amended soils. ¹³C cellobiose in bacterial or fungal PLFAs was unaffected by NO₃⁻ deposition; however, the incorporation of ¹³C vanillin in fungal PLFAs extracted from NO₃⁻ amended soil was 82% higher than in the control treatment. The recovery of ¹³C vanillin and ¹³C cellobiose in SOC, DOC, microbial biomass, and respiration was not different between control and NO₃⁻ amended treatments. Chronic NO₃⁻ deposition has stemmed the flow of C through the heterotrophic soil food web by inhibiting the activity of ligninolytic enzymes, but it increased the assimilation of vanillin into fungal PLFAs.     

Is the soil microbial community related to the basal area of trees in a Scots pine stand?

The main energy sources of soil microorganisms are litter fall, root litter and exudation. The amount on these carbon inputs vary according to basal area of the forest stand. We hypothesized that soil microbes utilizing these soil carbon sources relate to the basal area of trees. We measured the amount of soil microbial biomass, soil respiration and microbial community structure as determined by phospholipid fatty acid (PLFA) profiles in the humus layer (FH) of an even-aged stand of Scots pine (Pinus sylvestris L.) with four different basal area levels ranging from 19.9 m² ha⁻¹ in the study plot Kasper 1 to 35.7 m² ha⁻¹ in Kasper 4. Increasing trend in basal respiration, total PLFAs and fungal-to-bacterial ratio was observed from Kasper 1 to Kasper 3 (basal area 29.2 m² ha⁻¹). The soil microbial community structure in Kasper 3 differed from that of the other study plots.     

Microbial activity and hydrolase activities during decomposition of root exudates released by an artificial root surface in Cd-contaminated soils

The aim of this study was to assess the stimulatory effects of different low molecular weight organic compounds commonly present in root exudates on microbial activity and hydrolase activities, and the effects of high Cd concentrations in sandy soils collected from contaminated field plots on the stimulatory effects. Glucose, glutamic acid, citric acid, oxalic acid, or a mixture of all compounds were released by an artificial root surface in a simplified rhizosphere system. The effects were measured at <2 mm (rhizosphere soil layer) and >4 mm (bulk soil layer) distance from the root surface, 7 d after the root exudates release. Results showed that different root exudates were mineralized at different extent and had different stimulatory effects on microbial growth estimated by dsDNA content of soil, and on hydrolase activities, mostly localized in the rhizosphere soil layer. Mineralization of root exudates, microbial growth and stimulation of most of the measured hydrolase activities were drastically reduced by high Cd concentrations in soil.     

Impact of sulfadiazine and chlorotetracycline on soil bacterial community structure and respiratory activity

Veterinary medicines enter agricultural soils by the use of animal excrements as fertilizers. To study their impact on soil bacterial communities, microcosms containing orthic luvisol soil were spiked with the antimicrobial agents sulfadiazine (SDZ) and chlorotetracycline (CTC) at three different concentrations (1, 10, 50 mg kg⁻¹ soil) and incubated for 48 days at 20 °C. The impact on the microbial respiratory activity was measured continuously in a respirometer (Sapromat). Changes in bacterial community structure were visualized by means of PCR-denaturing gradient gel electrophoresis (DGGE) of 16S rDNA derived from soil samples after 1, 7, 11 and 48 days. Additionally, growth inhibitory effects of SDZ and CTC on bacteria previously isolated from the same soil were tested in agar diffusion tests. In microcosms with soil and antibiotics only, no effects could be observed, either on respiratory activity or on bacterial population structure. Therefore, further incubations were conducted in the presence of an additional assimilable carbon source (5 g glucose kg⁻¹ soil). In the presence of glucose, SDZ affected soil respiration as well as the bacterial community structure: Additional bands appeared and some bands already visible at the beginning of incubations increased in intensity. A clear relationship between SDZ concentrations and changes in DGGE patterns became visible. During 48 days of incubation, changes in DGGE patterns were minimal in microcosms with 50 mg SDZ kg⁻¹soil indicating an inhibition of strains, which were capable of growing on glucose in the presence of lower SDZ concentrations. Only a few soil bacterial isolates (5 out of 47 strains tested) were weakly inhibited by SDZ in agar diffusion disk tests. Contrastingly, CTC inhibited growth of 12 soil bacterial isolates significantly in disk tests, but no effects on soil respiration and bacterial community structure could be observed. In the presence of the soil matrix the growth inhibitory potential of CTC decreased due to adsorption or complexation. This was confirmed in growth inhibition experiments with soil suspensions and time-dependent sampling.     

Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition

The relative importance of specific plant properties versus soil characteristics in shaping the bacterial community structure of the rhizosphere is a topic of considerable debate. Here, we report the results of a study on the bacterial composition of the rhizosphere of the wild plant Carex arenaria (sand sedge) growing at 10 natural sites in The Netherlands. The soil properties of the sandy soils at these sites were highly disparate, most notably in pH, chloride and organic matter content. Rhizosphere and bulk soil bacterial communities were examined by culture-independent means, namely, 16S rDNA-directed PCR-DGGE profiling. Large differences were observed between the bacterial communities of the different sites for both bulk and rhizosphere soil. Cluster analysis of bacterial profiles revealed that the rhizosphere community of each site was generally more closely related to the bulk soil community of that site rather than to rhizosphere communities of other sites. Hence, bacterial community structure within the rhizosphere of C. arenaria appeared to be determined to a large extent by the bulk soil community composition. This conclusion was supported by a reciprocal planting experiment, where C. arenaria shoots of different sites yielded highly similar rhizosphere communities when planted in the same soil.     

Influence of Glomus etunicatum/Zea mays mycorrhiza on atrazine degradation, soil phosphatase and dehydrogenase activities, and soil microbial community structure

The effects of an arbuscular mycorrhizal (AM) fungus (Glomus etunicatum) on atrazine dissipation, soil phosphatase and dehydrogenase activities and soil microbial community structure were investigated. A compartmented side-arm (‘cross-pot’) system was used for plant cultivation. Maize was cultivated in the main root compartment and atrazine-contaminated soil was added to the side-arms and between them 650 or 37 μm nylon mesh was inserted which allowed mycorrhizal roots or extraradical mycelium to access atrazine in soil in the side-arms. Mycorrhizal roots and extraradical mycelium increased the degradation of atrazine in soil and modified the soil enzyme activities and total soil phospholipid fatty acids (PLFAs). Atrazine declined more and there was greater stimulation of phosphatase and dehydrogenase activities and total PLFAs in soil in the extraradical mycelium compartment than in the mycorrhizal root compartment when the atrazine addition rate to soil was 5.0 mg kg⁻¹. Mycelium had a more important influence than mycorrhizal roots on atrazine degradation. However, when the atrazine addition rate was 50.0 mg kg⁻¹, atrazine declined more in the mycorrhizal root compartment than in the extraradical mycelium compartment, perhaps due to inhibition of bacterial activity and higher toxicity to AM mycelium by atrazine at higher concentration. Soil PLFA profiles indicated that the AM fungus exerted a pronounced effect on soil microbial community structure.