Predation on fungal and bacterial biomass in a soddy-podzolic soil amended with starch,wheat straw and alfalfa meal

The variation in bacterial, fungal and total microbial biomass and activity was studied together with the abundance of soil nematodes and microarthropods after the addition of substrates differing in nitrogen availability to a soddy-podzolic soil. The experiments were carried out in microcosms with native and defaunated soil to evaluate stimulatory and suppressive effects of the microfauna on soil micro-organisms. Predation by microfauna (nematodes) and mesofauna (microarthropods) reduced the microbial biomass and microbial respiration by approximately 25% after addition of nitrogen rich alfalfa meal. When starch and wheat straw were supplied, the microbial biomass and activity were stimulated by up to 30% by grazing. Thus, the effect of predation on the microbiota depended on the composition of the available substrates and available nitrogen seems to be an important factor controlling stimulation or suppression of soil micro-organisms by the soil fauna when fresh organic compounds are accessible. The presence of soil fauna stimulated bacteria and, thus, reduced the fungal/bacterial ratio during the course of decomposition. In contrast, the fungal/bacterial ratio declined due to decreasing fungal biomass in defaunated soil.     

Investigating the influence of transgenic tobacco plants codifying a protease inhibitor on soil microbial community

Serine protease inhibitors (PIs) are involved in several physiological processes, such as regulation of endogenous proteinases and defence against phytophageous insects. Transgenic modifications have enhanced protease inhibitor expression to develop insect resistant cultivars in several important crops. The fate of protease inhibitors released from genetically engineered plants is an important issue because of possible inhibition of soil proteases and effects of the insecticidal protein and its codifying sequence on soil microorganisms. The persistence of transgenic sequence mustard trypsin inhibitor-2 in soil and its hypothetical acquisition by soil microorganisms by horizontal gene transfer and the effect of transgenic plant material on soil microbial community structure and soil protease activity were investigated. With the aim to simulate the effects of plant litter on soil microorganisms, a microcosm experimental model was used. Despite the persistence of transgenic DNA sequences, no recombination event was detected between plant DNA and soil bacteria; molecular analysis of bacterial community also showed no significant influence on the dominant members of the bacterial community and soil protease activity was not inhibited by the release of constitutively over-expressed protease inhibitor.     

Effects of vegetation removal on soil properties and decomposer organisms

The removal of understory vegetation has been a common forest management practice, especially in plantations, but the effects of understory removal on soil physico-chemical properties and decomposer organisms is poorly known. In the present study, the effects of understory vegetation removal and removal of all-plants (i.e. removal of understory vegetation and trees) on soil properties and soil biota were measured in a plantation of mixed native tree species in southern China. During the wet season, understory vegetation removal did not cause significant changes on soil microbial community and major soil faunal groups except for a marked reduction in the density of herbivorous nematodes. However, all-plants removal significantly decreased the fungal biomass, the fungal:bacterial ratio, the density of herbivorous nematodes, the structure of the nematode community, and the density of mites, collembola and total microarthropods. In the dry season, understory vegetation removal resulted in a marked reduction in the density of total and herbivorous nematodes. The effects of plant removal on soil biota were similar to that in dry season. For both seasons, understory removal had no significant effects on soil physico-chemical properties (soil water content, pH, total nitrogen and soil organic carbon) but removal of all-plants significantly decreased soil pH. In general, the effects of understory vegetation removal on soil biota and other soil properties were much less severe than those of all-plants removal. The soil biota did not show significant response to understory removal, suggesting that this part of the vegetation may not be a major governing factor on such biota.     

Effects of oxamyl and chlordane on the activities of nontarget soil organisms

Summary The effect of two pesticides, oxamyl and chlordane, on nontarget soil biota were examined in microcosms. Neither oxamyl nor chlordane had an effect on rates of litter decomposition or soil and litter respiration. There were differences in numbers of nematodes and protozoans and in biomass of bacteria and fungi in microcosms with and without chlordane on some sampling dates. One of the nematodes, Pelodera sp., died out in all of the microcosms within 30 days. Although the pesticide chlordane had no measurable effect on the activities of the soil biota as measured by respiration and mass loss, it did affect the population sizes and biomass of some grazers of soil biota.     

Suppression of nematodes in a coastal grassland soil

The nematophagous fungi Arthrobotrys oligospora and Myzocytiopsis glutinospora increase to large numbers (>10³ propagules/g of soil) when moth larvae killed by entomopathogenic nematodes are added to soil microcosms. In spite of these increases, it is unclear how effective these nematophagous fungi are in suppressing nematodes. We measured nematode mortality in microcosms with small numbers of assay nematodes, and we examined assay nematodes recovered at the end of the experiment for signs of fungal parasites. Because the microcosms did not have a moat or other refuge, the assay nematodes remained vulnerable for the 3 days that they were in the soil. Mortality in this experiment was not substantially increased compared to a previous experiment, which measured the mortality of a larger number of assay nematodes in microcosms surrounded by a moat. Mortality, however, increased from 34 to 50% when recovered assay nematodes were examined and when those with conidia of the nematophagous fungus Hirsutella rhossiliensis were considered dead. The zoosporic fungus M. glutinospora was not detected, perhaps because the soil water potential was too low. Contrary to our expectations, there was no evidence of negative feedback on nematodes (i.e., no evidence of density-dependent mortality) because the addition of dead moth larvae greatly increased numbers of resident nematodes and A. oligospora but did not greatly affect the probability of nematode mortality.     

Effects of two grass species on the composition of soil fungal communities

Many studies have shown effects of plants species on fungal communities, but these are often confounded with soil effects. Thus, the specific role of plant species in structuring rhizospheric and soil fungal communities is poorly described. Our study used microcosms in which plants were grown under artificial conditions to bridge this gap. Two perennial grasses dominating subalpine grasslands, Festuca paniculata and Dactylis glomerata, were grown at two levels of fertilization on standard soil. Fungal communities were determined by 454 pyrosequencing of the internal transcribed spacer 1 region. Among the fungal communities characterized by the primers used, original communities were associated to each plant species and also diverged between rhizosphere and bulk soils within each plant species, though there were no significant fertilization effects. Differences regarded global composition of the fungal communities and abundant molecular operational taxonomic units (MOTUs). Both plant species and location effects were reflected more in the abundance than in the composition of MOTUs. The observed differences in fungal communities coincide with differing strategies of plant root growth, with D. glomerata having greater root mass, length, and area than F. paniculata. Our study, by dissociating soil effects from plant effects, demonstrated that plant species exert a key control on soil fungi. We suggest that such effects may be linked to inter-specific differences in root traits and their consequences on nitrogen uptake.     

A microcosm experiment to evaluate the influence of location and quality of plant residues on residue decomposition and genetic structure of soil microbial communities

The effects of location (soil surface vs. incorporated in soil) and nature of plant residues on degradation processes and indigenous microbial communities were studied by means of soil microcosms incubation in which the different soil zones influenced by decomposition i.e. residues, soil adjacent to residues (detritusphere) and distant soil unaffected by decomposition (bulk soil) were considered. Plant material decomposition, organic carbon assimilation by the soil microbial biomass and soil inorganic N dynamics were studied with ¹³C labelled wheat straw and young rye. The genetic structure of the community in each soil zone were compared between residue locations and type by applying B- and F-ARISA (for bacterial- and fungal-automated ribosomal intergenic spacer analysis) directly to DNA extracts from these different zones at 50% decomposition of each residue. Both location and biochemical quality affected residue decomposition in soil: 21% of incorporated ¹³C wheat straw and 23% left at the soil surface remained undecomposed at the end of incubation, the corresponding values for ¹³C rye being 1% and 8%. Residue decomposition induced a gradient of microbial activity with more labelled C incorporated into the microbial biomass of the detritusphere. The sphere of influence of the decomposing residues on the dynamics of soluble organic C and inorganic N in the different soil zones showed particular patterns which were influenced by both residue location and quality. Residue degradation stimulated particular genetic structure of microbial community with a gradient from residue to bulk soil, and more pronounced spatial heterogeneity for fungal than for bacterial communities. The initial residue quality strongly affected the resulting spatial heterogeneity of bacteria, with a significance between-zone discrimination for rye but weak discrimination between the detritusphere and bulk soil, for wheat straw. Comparison of the different detrituspheres and residue zones (corresponding to different residue type and location), indicated that the genetic structure of the bacterial and fungal communities were specific to a residue type for detritusphere and to its location for residue, leading to conclude that the detritusphere and residue corresponded to distinct trophic and functional niches for microorganisms.     

Fate, tree growth effect and potential impact on soil microbial communities of mycorrhizal and bacterial inoculation in a forest plantation

The knowledge of the survival of inoculated beneficial fungal and bacterial strains in the field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developing. The aim of this study was to monitor, 4 years after plantation into the field site, the effects of Douglas fir (Pseudotsuga menziesii) co-inoculation with the mycorrhiza helper bacterial strain Pseudomonas fluorescens BBc6R8 and/or the fungal strain Laccaria bicolor S238N on seedling growth and on the indigenous bacterial and ectomycorrhizal communities using quantitative and qualitative approaches. The field persistence of the inoculated strains was also monitored. The seedling shoot volume estimate was statistically significantly higher in the fungal inoculated plots in comparison to the non-inoculated plots but no treatment-related changes in the quantitave or qualitative microbial measurements were observed and the inoculated strains could not be detected after 4 years.     

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.     

Effects of plants on net mineralization of nitrogen in forest soil microcosms

Summary The effects of plant roots on net N mineralization were examined by comparing soil microcosms with and without plants. Additionally, inorganic N amendments were used to test for competition for N between plants and microorganisms. Daily watering and the application of suction to microcosms eliminated the effects of transpiration on soil moisture content. Monthly litter collections reduced the influence of the aboveground portions of plants. Plants decreased net N mineralization by 23% during days 0–114 and then increased net mineralization by the same amount during days 144–124. Root-free soil collected from with-plant microcosms on day 244 evolved 24% more CO₂ in laboratory incubations than soil from without-plant microcosms. This indicates that plants had increased substrate availability to soil microorganisms. Inorganic N amendments had no significant effects on the microcosms or on laboratory soil incubations. Evidence is most consistent with the hypothesis that plant roots increased microbial activity due to the increased substrate availability. Different net N mineralization rates probably resulted from changes in the substrate C : N ratio.     

Mechanisms of nematode suppression by organic soil amendments—A review

Application of organic soil amendments is a traditional control method for plant–parasitic nematodes and it is considered a part of nematode-management programs. A variety of organic amendments, such as animal and green manures, compost, nematicidal plants and proteinous wastes, are used for this purpose, but nematode control efficacy is not always satisfactory. Elucidation of nematode-control mechanisms in amended soil may lead to improved efficacy or the development of more effective control techniques, although the effects of organic amendments on nematodes, microbial communities, plants and soil environments are very complex. Possible mechanisms involved in nematode suppression are: (1) release of pre-existing nematicidal compounds in soil amendments, (2) generation of nematicidal compounds, such as ammonia and fatty acids, during degradation, (3) enhancement and/or introduction of antagonistic microorganisms, (4) increase in plant tolerance and resistance, and (5) changes in soil physiology that are unsuitable for nematode behavior. Combinations of these mechanisms, rather than a single one, appear to produce nematode suppression in amended soils.     

Nematode community structure as a sensitive indicator of microbial perturbations induced by a genetically modified Pseudomonas fluorescens strain

The effects of seed inoculation with the Pseudomonas fluorescens strains F113lacZY [a genetically marked biocontrol agent producing the anti-fungal agent 2,4-diacetylphloroglucinol (DAPG)] and F113G22 [a genetically modified (GM) derivative strain of F113lacZY incapable of producing DAPG] on associated nematode communities were investigated over 17 days of plant growth. Plant growth measurements and colony forming unit counts (CFU) derived from rhizosphere soil indicated only small and transient perturbations as a result of introductions of the GM bacteria. Total nematode numbers were increased significantly in the rhizosphere of inoculated plants compared with the non-inoculated control treatments. These increases were mainly due to increases in bacterial feeding nematodes. This indicates that inoculation with the GM P. fluorescens strains induced high bacterial growth rates in the rhizosphere of plants inoculated with these strains. No indication of greater root colonisation by fluorescent Pseudomonas spp. could be found using CFU counts on Pseudomonas-selective media. Numbers of fungal feeding nematodes decreased initially, probably as a result of lack of intact hyphae in the soil. However, inoculation with the two different GM P. fluorescens strains resulted in a rapid recovery of fungal feeding nematode populations, whereas in the non-inoculated control populations of fungal feeding nematodes remained small. This result is surprising as one of the strains (F113lacZY) produces the anti-fungal agent DAPG and it would be expected that this agent would result in a decrease in fungal activity.     

Potential role of polycyclic aromatic hydrocarbons (PAHs) oxidation by fungal laccase in the remediation of an aged contaminated soil

The transformation of PAHs by fungal laccases has been reported but there are no published studies on the direct application of free laccase in the remediation of PAHs-contaminated soil. Here we report a study in which the transformation of PAHs by a fungal laccase was studied both in reaction mixtures and in soil. Anthracene and benzo(a)pyrene were the most degradable of the 15 US Environmental Protection Agency (EPA) priority PAHs tested. Use of a redox mediator greatly enhanced the oxidation of several PAHs in reaction mixtures and the main intermediates were identified as anthraquinone for anthracene and benzo(a)pyrenyl acetate for benzo(a)pyrene as determined by GC–MS analysis. No significant correlation was found between oxidation and ionization potentials of individual PAHs. Soil microcosms were set up to test the potential of laccase to remediate an aged PAHs-contaminated soil. The laccase transformed the PAHs immediately after it was added to the soil and significant dissimilation of benzo(a)pyrene and toxic-equivalent concentration based on benzo(a)pyrene was observed after incubation for 14 days, indicating the potential of laccase to detoxify the soil. Moreover, extractable laccase activity was completely lost and the biomass of the indigenous microorganisms remained constant in the microcosms at the end of the incubation period, suggesting that the enzyme may have potential as an agent for the efficient and safe cleanup of soil contaminated with PAHs.     

Soil sickness of peanuts is attributable to modifications in soil microbes induced by peanut root exudates rather than to direct allelopathy

The quantity and quality of peanut yields are seriously compromised by consecutive monoculture in the subtropical regions of China. Root exudates, which represent a growth regulator in peanut–soil feedback processes, play a principal role in soil sickness. The growth inhibition of a species in an in vitro bioassay enriched with root exudates and allelochemicals is commonly viewed as evidence of an allelopathic interaction. However, for some of these putative examples of allelopathy, the results have not been verified in more natural settings with plants continuously growing in soil. In this study, the phenolic acids in peanut root exudates, their retention characteristics in an Udic Ferrosol, and their effects on rhizosphere soil microbial communities and peanut seedling growth were studied. Phenolic acids from peanut root exudates were quickly metabolized by soil microorganisms and did not accumulate to high levels. The peanut root exudates selectively inhibited or stimulated certain communal bacterial and fungal species, with decreases in the relative abundance of the bacterial taxa Gelria glutamica, Mitsuaria chitosanitabida, and Burkholderia soli and the fungal taxa Mortierella sp. and Geminibasidium hirsutum and increases in the relative abundance of the bacterial taxon Desulfotomaculum ruminis and the fungal taxa Fusarium oxysporum, Bionectria ochroleuca and Phoma macrostoma. The experimental application of phenolic acids to non-sterile and sterile soil revealed that the poor performance of the peanut plants was attributed to changes in the soil microbial communities promoted by phenolic acids. These results suggest that pathogenic fungal accumulation at the expense of such beneficial microorganisms as plant growth promoting rhizobacteria, mycorrhizal fungi induced by root exudates, rather than direct autotoxicity induced by root exudates, might represent the principal cause underlying the soil sickness associated with peanut plants. We hope that our study will motivate researchers to integrate the role of soil microbial communities in allelopathic research, such that their observed significance in soil sickness during continuous monocropping of fields can be further explored.     

Evaluation of soil enzyme activities and microbial communities in tomato continuous cropping soil treated with jerusalem artichoke residues

ABSTRACT

Jerusalem artichoke (JY) (Helianthus tuberosus L.) has been reported to have a strong inhibitory effect on weed growth and root knot nematodes, but little information is available on the effects on soil ecosystems, especially soil microorganisms and soil enzyme activities. Understanding the dynamics of soil microbes and soil enzyme activities in cropping systems can help determine how agricultural practices influence soil processes mediated by JY residues. This study used a pot experiment, with five-year continuous cropping soil of tomato plants as the experimental material and 2% (w/w) JY residue as the treatment material in the soil. The treatment was compared to continuously monocropped tomato soil that was not treated with JY residues. The results of 16S high-throughput sequencing showed that both fungal and bacterial community structure and composition varied significantly at each stage of JY treatment. The analysis showed that the major phyla in the soil fungal community included Ascomycota, Zygomycota and Basidiomycota. Chytridiomycota was dominant in only the JY-treated soil. At the genus level, the abundances of Mortierella, Cephaliophora, Cryptococcus and Fusarium notably changed at each stage of JY treatment. In the bacterial community in the JY-treated group, the abundance of Proteobacteria increased significantly, while that of Firmicutes decreased significantly, compared to the control group. JY enhanced the activity of soil sucrase and urease. In addition, the soil sucrase activity showed a strong negative correlation with Fusarium and Bacillus. Overall, our results revealed that JY residues changed both the soil bacterial and fungal community composition and the soil enzyme activities.     

Liquid laccase production by Phomopsis liquidambari B3 accelerated phenolic acids degradation in long-term cropping soil of peanut

The accumulation of phenolic acids in soil is one of the main problems associated with continuous cropping of peanut. Although laccases secreted by fungi can efficiently transform phenolic acids, there are few reports on the use of these enzymes to bioremediate continuous cropping soil. Food waste and wheat straw are waste products; however, they could be used productively as resources for laccase production by the endophytic fungus Phomopsis liquidambari B3. We cultured Phomopsis liquidambari B3 in medium containing food waste as the main nitrogen source and wheat straw as the main carbon source. In order to study the effects of fermentation liquid on phenolic acid degradation, rhizosphere soil microbial communities and peanut seedling growth, the fermentation product, which had high laccase activity, was added to continuously cropped soil of peanut. The concentration of 4-hydroxybenzoic acid, vanillic acid, and coumaric acid in soil had decreased by 57.4, 52.5, and 49.4%, respectively, compared with no-treatment control during 28 days. Analysis of denaturing gradient gel electrophoresis profiles showed that the bacterial and fungal community structures in rhizosphere soil were affected by changes in the phenolic acids concentration. The biomass of peanut plants and the number of root nodules were increased 68.3% and 5.9-fold, respectively. These results showed that the laccase product reduced the accumulation of phenolic acids in soil, the decrease in phenolic acids concentration and the increase in certain dominant microorganisms promoted peanut seedling growth and nodulation. This technology provides a new strategy for bioremediation of continuous cropping soil, while simultaneously reducing waste and protecting the environment.     

Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches

Background, aim, and scope  Fertilization is an important agricultural practice for increasing crop yields. In order to maintain the soil sustainability, it is important to monitor the effects of fertilizer applications on the shifts of soil microorganisms, which control the cycling of many nutrients in the soil. Here, culture-dependent and culture-independent approaches were used to analyze the soil bacterial and fungal quantities and community structure under seven fertilization treatments, including Control, Manure, Return (harvested peanut straw was returned to the plot), and chemical fertilizers of NPK, NP, NK, and PK. The objective of this study was to examine the effects on soil microbial composition and diversity of long-term organic and chemical fertilizer regimes in a Chinese upland red soil. Materials and methods  Soil samples were collected from a long-term experiment station at Yingtan (28°15′N, 116°55′E), Jiangxi Province of China. The soil samples (0–20 cm) from four individual plots per treatment were collected. The total numbers of culturable bacteria and fungi were determined as colony forming units (CFUs) and selected colonies were identified on agar plates by dilution plate methods. Moreover, soil DNAs were extracted and bacterial 16S rRNA genes and fungal 18S rRNA genes were polymerase chain reaction amplified, and then analyzed by denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. Results  The organic fertilizers, especially manure, induced the least culturable bacterial CFUs, but the highest bacterial diversity ascertained by DGGE banding patterns. Chemical fertilizers, on the other hand, had less effect on the bacterial composition and diversity, with the NK treatment having the lowest CFUs. For the fungal community, the manure treatment had the largest CFUs but much fewer DGGE bands, also with the NK treatment having the lowest CFUs. The conventional identification of representative bacterial and fungal genera showed that long-term fertilization treatments resulted in differences in soil microbial composition and diversity. In particular, 42.4% of the identified bacterial isolates were classified into members of Arthrobacter. For fungi, Aspergillus, Penicillium, and Mucor were the most prevalent three genera, which accounted for 46.6% of the total identified fungi. The long-term fertilization treatments resulted in different bacterial and fungal compositions ascertained by the culture-dependent and also the culture-independent approaches. Discussion  It was evident that more representative fungal genera appeared in organic treatments than other treatments, indicating that culturable fungi were more sensitive to organic than to chemical fertilizers. A very notable finding was that fungal CFUs appeared maximal in organic manure treatments. This was quite different from the bacterial CFUs in the manure, indicating that bacteria and fungi responded differently to the fertilization. Similar to bacteria, the minimum fungal CFUs were also observed in the NK treatment. This result provided evidence that phosphorus could be a key factor for microorganisms in the soil. Thus, despite the fact that culture-dependent techniques are not ideal for studies of the composition of natural microbial communities when used alone, they provide one of the more useful means of understanding the growth habit, development, and potential function of microorganisms from soil habitats. A combination of culture-dependent and culture-independent approaches is likely to reveal more complete information regarding the composition of soil microbial communities. Conclusions  Long-term fertilization had great effects on the soil bacterial and fungal communities. Organic fertilizer applications induced the least culturable bacterial CFUs but the highest bacterial diversity, while chemical fertilizer applications had less impact on soil bacterial community. The largest fungal CFUs were obtained, but much lower diversity was detected in the manure treatment. The lowest bacterial and also fungal CFUs were observed in the NK treatment. The long-term fertilization treatments resulted in different bacterial and fungal compositions ascertained by the culture-dependent and also the culture-independent approaches. Phosphorus fertilizer could be considered as a key factor to control the microbial CFUs and diversity in this Chinese upland red soil. Recommendations and perspectives  Soil fungi seem to be a more sensitive indicator of soil fertility than soil bacteria. Since the major limitation of molecular methods in soil microbial studies is the lack of discrimination between the living and dead, or active and dormant microorganisms, both culture-dependent and culture-independent methods should be used to appropriately characterize soil microbial diversity.     

Spatio-temporal dynamics of bacterial communities associated with two plant species differing in organic acid secretion: A one-year microcosm study on lupin and wheat

Plants are generally assumed to influence the surrounding soil microflora through rhizodeposition. However, the role of rhizodeposits, and especially organic acids, in structuring the bacterial communities is still poorly understood. In this study, we asked the question whether plants differing in organic acid secretion have a different impact on the soil bacterial communities, and if this is the case, to which extent this impact is due to different organic acid concentrations in the rhizosphere. To investigate this question, we compared white lupin and wheat. The former is a high organic acid-secreting species, while the latter secretes only low amounts of carboxylates. We grew the plants in large microcosms including root-free control compartments for one year (replanted every second month) and analyzed the spatio-temporal changes in soil ATP concentrations, as well as in diversity and structure of bacterial communities (using DNA- and RNA-based DGGE) along a root-soil gradient after two, six and twelve month's cultivation. Our results showed: i) that white lupin and wheat differed in their impact on soil ATP concentrations and on the structure of root bacterial communities; ii) that cultivation time was a key factor in explaining the observed differences in all the parameters studied; and iii) that the amounts of organic acids accounted for a significant proportion (15%) of the variability within root active communities. These results indicate that plants influence their associated bacterial communities in a species-specific way and that for communities living in the direct vicinity of roots (rhizoplane-endorhizosphere), a significant part of this influence can be attributed to root-secreted organic acids.     

A comparison of soil food webs beneath C<Subscript>3</Subscript>- and C<Subscript>4</Subscript>-dominated grasslands

Soil food webs influence organic matter mineralization and plant nutrient availability, but the potential for plants to capitalize on these processes by altering soil food webs has received little attention. We compared soil food webs beneath C₃- and C₄-grass plantings by measuring bacterial and fungal biomass and protozoan and nematode abundance repeatedly over 2 years. We tested published expectations that C₃ detritus and root chemistry (low lignin/N) favor bacterial-based food webs and root-feeding nematodes, whereas C₄ detritus (high lignin/N) and greater production favor fungal decomposers and predatory nematodes. We also hypothesized that seasonal differences in plant growth between the two grassland types would generate season-specific differences in soil food webs. In contrast to our expectations, bacterial biomass and ciliate abundance were greater beneath C₄ grasses, and we found no differences in fungi, amoebae, flagellates, or nematodes. Soil food webs varied significantly among sample dates, but differences were unrelated to aboveground plant growth. Our findings, in combination with previous work, suggest that preexisting soil properties moderate the effect of plant inputs on soil food webs. We hypothesize that high levels of soil organic matter provide a stable environment and energy source for soil organisms and thus buffer soil food webs from short-term dynamics of plant communities.     

Methyl-mercury affects microbial activity and biomass,bacterial community structure but rarely the fungal community structure

Monomethyl-mercury is one of the most toxic compounds. Methylation of Hg usually appears under anoxic conditions. In Swiss forest soils, methyl-Hg concentrations of up to 3 μg kg⁻¹ soil dw have been observed, but the impact of methyl-Hg on soil microorganisms have rarely been examined so far. In this study, we investigated the effect of increasing concentrations of methyl-Hg (0, 5, 20, 90 μg kg⁻¹ soil dw) on the microbial communities in various forest soils differing in their physico-chemical properties. Experiments were conducted in microcosms under controlled conditions and the basal respiration (BR), the microbial biomass carbon (MBC) and the bacterial and fungal community structures using T-RFLP-profiling were investigated. BR was significantly affected by methyl-Hg. In general, the BR increased with increasing methyl-Hg concentrations, whereas the MBC was significantly reduced. Bacterial communities were more sensitive to methyl-Hg than fungal communities. In five out of seven soils, the bacterial community structures differed significantly between the treatments whereas the fungal communities did not. The impact of methyl-Hg on the soil bacterial communities was site specific. In one soil, a methyl-Hg concentration of already 5 μg kg⁻¹ soil dw significantly affected the relative abundance of 13% bacterial operational taxonomic units (OTU), whereas in other soils concentrations of even 90 μg kg⁻¹ soil dw rarely affected the abundance of OTUs. In this study, for the first time, the impact of methyl-Hg on soil bacterial and fungal communities in forest soils was assessed. We showed that its impact strongly depends on the physico-chemical conditions of the soil and that bacterial communities were more sensitive to methyl-Hg than fungi.