Applied Soil Ecology

Published by Elsevier
Online ISSN: 0929-1393
Publications
Article
In Eastern Spain, almond trees have been cultivated in terraced orchards for centuries, forming an integral part of the Mediterranean forest scene. In the last decades, orchards have been abandoned due to changes in society. This study investigates effects of changes in land use from forest to agricultural land and the posterior land abandonment on soil microbial community, and the influence of soil physico-chemical properties on the microbial community composition (assessed as abundances of phospholipids fatty acids, PLFA). For this purpose, three land uses (forest, agricultural and abandoned agricultural) at four locations in SE Spain were selected. Multivariate analysis showed a substantial level of differentiation in microbial community structure according to land use. The microbial communities of forest soils were highly associated with soil organic matter content. However, we have not found any physical or chemical soil property capable of explaining the differences between agricultural and abandoned agricultural soils. Thus, it was suggested that the cessation of the perturbation caused by agriculture and shifts in vegetation may have led to changes in the microbial community structure. PLFAs indicative of fungi and ratio of fungal to bacterial PLFAs were higher in abandoned agricultural soils, whereas the relative abundance of bacteria was higher in agricultural soils. Actinomycetes were generally lower in abandoned agricultural soils, while the proportions of vesicular-arbuscular mycorrhyzal fungi were, as a general trend, higher in agricultural and abandoned agricultural soils than in forests. Total microbial biomass and richness increased as agricultural < abandoned agricultural < forest soils.
 
Article
A symposium during the 16th Congress of Soil Science, held in Montpellier, France, 20–26 August 1998, was entitled `Biodiversity and Soil Functioning'. This viewpoint paper highlights some of the issues presented and discussed.
 
Article
A comparative study of organic and conventional arable farming systems was conducted in The Netherlands to determine the effect of management practices on chemical and biological soil properties and soil health. Soils from thirteen accredited organic farms and conventionally managed neighboring farms were analyzed using a polyphasic approach combining traditional soil analysis, culture-dependent and independent microbiological analyses, a nematode community analysis and an enquiry about different management practices among the farmers. Organic management, known primarily for the abstinence of artificial fertilizers and pesticides, resulted in significantly lower levels of both nitrate and total soluble nitrogen in the soil, higher numbers of bacteria of different trophic groups, as well as larger species richness in both bacteria and nematode communities and more resilience to a drying–rewetting disturbance in the soil. The organic farmers plough their fields less deeply and tend to apply more organic carbon to their fields, but this did not result in a significantly higher organic carbon content in their soils. The levels of ammonium, organic nitrogen, phosphate and total phosphorus did not differ, significantly between the soils under different management. Fifty percent of the conventional Dutch farmers also used organic fertilizers and the numbers of farmers using a green crop fertilizer did not differ between the two management types. Soil type – clayey or sandy soil – in general had a much stronger effect on the soil characteristics than management type. The soil type influenced pH, nitrate, ammonium, phosphate and organic carbon levels as well as numbers of oligotrophic bacteria and of different groups of nematodes, and different diversity indices. With the collected data set certain soil characteristics could also be attributed to the use of different management practices like plow depth, crop or cover crop type or to the management history of the soil.
 
Article
Research in low biodiversity extreme environments allows separation of the climatic, soil and biological interactions that determine soil biodiversity and community structure. Studies focused on the response of low diversity communities in soils of the Antarctic Dry Valleys and the Chihuahuan Desert of the southwestern USA, to manipulations of soil resources and climate, offer the best opportunity to learn about the environmental controls on soil biodiversity and the role of biodiversity in soil functioning. We propose that insights based on research in these extreme environments should be applicable to understanding soil biodiversity in more complex, temperate and tropical ecosystems. The study of extreme soil ecosystems may also provide information on the response of soil biodiversity to increasing occurrences of environmental extremes that are predicted to occur from global change models. Studies from hot and cold deserts show that decomposition-based food webs can be very simple, that aridity produces similar mechanisms for survival and dispersal of organisms in temperate and polar systems, that suitable soil habitats are patchily distributed in arid environments, and the low biodiversity of extreme soil ecosystems creates little or no functional redundancy making these systems susceptible to disturbance. We suggest that species within the same functional group can have small differences in ecology that are sufficient to affect ecosystem processes. When this occurs, differential responses of species to disturbance within a functional group will not stabilise the soil ecosystem, but rather lead to dramatic changes in community composition and ecosystem process rates.
 
Article
Physical changes caused by forest management practices can have a dramatic effect on the soil biota in a forest ecosystem. The effects of soil compaction associated with harvesting on earthworm populations and selected soil properties were measured in a hardwood (oak-hickory) forest in Missouri. Soils in this region of Missouri are characterized by a cherty residuum that is primarily of the Clarksville series (Loamy-skeletal, mixed, mesic Typic Paledults). Earthworms were collected from a 0–15 cm depth each spring and fall for 2 years by handsorting and their populations determined on a per square meter basis. Two native earthworm species, Diplocardia omata and Diplocardia smithii, were identified at this site. Regardless of species, juvenile populations accounted for a major portion of the earthworms found in spring or fall. In 1995, Diplocardia ornata was the dominant species present and most affected by soil compaction. In 1996, soil compaction seemed to have a less restrictive effect on earthworms. Harvesting had no effect on either earthworm populations or biomass but had a significant effect on selected soil properties. Harvest levels had a significant negative correlation with soil moisture, soil inorganic N, and soil microbial biomass C and N. When above-ground biomass like logs and forest floor litter were removed and the soil was compacted, the standing soil microbial biomass along with soil moisture content and nutrients were reduced. Time (season of the year) had a significant effect on earthworm populations and biomass and all soil properties that were measured in both 1995–1996. Future studies at this site might include a seasonal study on the ecology and reproduction of these native earthworm species.
 
Ratio of CFUs of copiotrophic bacteria to total microscopic counts of bacteria 1 day before, 1 day after and 1, 2, 3, 5, and 7 weeks after incorporation of a vetch/oats cover crop (‘Cover crop’) or the same amount of vetch/oats cover crop foliage (‘Fallow + debris’) into soil, or after leaving the soil unamended (‘Unamended’). 
Ratio of CFUs of copiotrophic to oligotrophic bacteria 1 day before, 1 day after and 1, 2, 3, 5, and 7 weeks after incorporation of a vetch/oats cover crop (‘Cover crop’) or the same amount of vetch/oats cover crop foliage (‘Fallow + debris’) into soil, or after leaving the soil unamended (‘Unamended’). 
Number of corky root ( Pyrenochaeta lycopersici ) lesions per tomato root (A), and percentage of root tips with softrot ( Phytophthora or Pythium sp.) (B) in organic 4-year rotation, low-input 4-year rotation, conventional 4-year rotation, and conventional 2-year rotation plots at the sustainable agriculture farming systems (SAFS) field site at UC Davis in 1997 and 1998. 
Damping-off of tomato seedlings caused by Pythium ultimum and Pythium aphanidermatum naturally occurring in soil collected 1 day before, 1 day after and 1, 2, 3, and 5 weeks after incorporation of a vetch/oats cover crop (‘Cover crop’) or the same amount of vetch/oats cover crop foliage (‘Fallow + debris’) into soil, or after leaving the soil unamended (‘Unamended’) (no soil collected 7 weeks after incorporation, compare with Figs. 1 and 2). 
Article
While soil quality encompasses physical and chemical besides biological characteristics, soil health is primarily an ecological characteristic. Ecosystem health has been defined in terms of ecosystem stability and resilience in response to a disturbance or stress. We therefore, suggest that indicators for soil health could be found by monitoring responses of the soil microbial community to the application of different stress factors at various intensities. The amplitude of a response and time to return to the current state before application of stress could serve as measures of soil health. Root pathogens are an integral part of soil microbial communities, and the occurrence of epiphytotics forms an indication of an ecosystem in distress. Disease suppression can be viewed as a manifestation of ecosystem stability and health. Thus, indicators for soil health could possibly also function as indicators for disease suppressiveness. Previously suggested indicators for soil health and disease suppression have mainly been lists of variables that were correlated to more or less disturbed soils (ranging from conventional to organic agricultural soils, grassland and forest soils) or to conduciveness to disease. We suggest a systematic ecological approach to the search for indicators for soil health and disease suppression, namely, measuring biological responses to various stress factors and the time needed to return to the current state.
 
Article
Differences in food resource use by earthworms (Megascolecidae) were studied at three Japanese forest sites with different latitude in cool-temperate (TOEF), temperate (MFF) and subtropical (Yona) zones. The vertical distribution and the fractionation of gut contents of earthworms were analysed to determine ecological categories. At TOEF and MFF, earthworm communities were composed of species living mainly in litter and topsoil layers. At TOEF, Amynthas vittatus (Goto and Hatai, 1898), Metaphire hilgendorfi (Michaelsen, 1892) and Eisenia japonica (Michaelsen, 1891) (Lumbricidae) were dominant, the former two species being mainly observed in the litter layer whereas the latter was in soil layers. At MFF, ‘Metaphire’ soulensis (Kobayashi, 1938), Amynthas purpuratus (Ishizuka, 1999), A. vittatus and Amynthas distichus (Ishizuka, 2000) were dominant and the former three species were observed in the litter layer whereas the latter one occurred in soil. The gut contents of those living in the litter layer had more organic fractions, whereas the latter had more inorganic fractions. Therefore these species were regarded as epigeic species and polyhumic-endogeic species, respectively. At Yona, Amynthas yambaruensis (Ishizuka and Azama, 2000) had burrows through 20 cm depth with casts and middens on the forest floor, and their fraction ratio of gut content was intermediate between the epigeic and endogeic earthworms at TOEF and MFF. Therefore A. yambaruensis was classified as anecic. In addition, at Yona, there were two unidentified Amynthas spp.; one epigeic species in the midden of A. yambaruenesis, and one endogeic species found in B-layer soil. Natural abundances of the stable isotope pairs and ( and ) were measured in soil organic matter and earthworm tissue. values showed epigeic < polyhumic-endogeic at TOEF and MFF, whereas at Yona, values were in the order anecic < epigeic < endogeic. The observed enrichments thus appear to indicate that the functional niches of earthworm species are due to resources available to them in the decomposition process from fresh litter to humus. values showed similar trends, but the differences between ecological group was smaller compared to .
 
Article
The main findings of research into carbon (C) fluxes from plants to soil micro-organisms using in situ 13CO2 pulse-labelling on upland grassland at the NERC Soil Biodiversity Thematic Programme field site in Southern Scotland are reviewed. From 1999 to 2003 the site was the focus of a unique and intensive programme of stable isotope tracing of C flux through rhizodeposition to soil microbiota and stable isotope probing of microbial biomarker compounds. We review the findings published to date, and highlight the novel ways in which the pulse-labelling approach has been applied to further understand C fluxes in the rhizosphere and mycorrhizophere in this grassland. The most important achievements from these studies, many of which are the first field measurements of their kind, include: (1) quantification of C flux from recent photosynthate into roots, soil microbial populations and soil respiration over time periods of hours to months; (2) analysis of diurnal control of root exudation and respiration linked to photoperiod and photosynthetic activity; (3) measurements of C flux from plants directed through mycorrhizal fungal networks; (4) establishing the importance C flow from recent photosynthate into soil fungi, revealed by 13C enrichment of phospholipid fatty acid biomarker molecules (PLFA); (5) detection of the disruptive effects of fungal-feeding microarthropods on 13CO2 respiration in the mycorrhizosphere; (6) measurement of 13C enrichment into soil microbial DNA and RNA and the rates of turnover of RNA; (7) identification of soil micro-organisms most enriched with 13C by sequence analysis of ‘heavy’ RNA separated by density-gradient centrifugation; and (8) estimates of the effects of liming on C flux into and through upland grassland, and its effects on C cycling by soil micro-organisms. In reviewing all these findings we highlight the strengths and limitations of the in situ 13C technique. We also explain how the new insights gained from these studies emphasise the complex temporal dynamics of recent photosynthate entering the soil through different pathways and the role of multi-trophic interactions between soil biota in determining the fate of recently fixed carbon in grasslands.
 
Article
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 (Loliumperenne 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.
 
Article
A simple method for assessing the effects of a chemical on the degradation of -labeled grass tissue was developed for future ecotoxicology studies. Grass was grown for several weeks in a simple soil microcosm amended with -glucose to generate a atmosphere. The resulting grass tissue (4 μCi g−1) was placed in two soils (Cohoctah loam from a grassy field and Pipestone sand from a pine woods) within specialized biometer flasks. Production of was 47.1% (s = 2.3%) after 4 weeks, and was similar for both soils sampled in April and July. Production of in Cohoctah soil amended with 3,5-dichlorophenol showed a hormesis response curve with slight stimulation at 80 mg kg−1, followed by inhibition at 400 mg kg−1. Finally, when -grass tissue stored frozen for a year was added to soil stored refrigerated for 10 months, production was nearly identical to experiments with fresh materials. Our technique combines the sensitivity and accuracy of 14C methods with simplicity, low cost, and a minimum of 14C waste to allow evaluation of a chemical on the soil's litter degradation system.
 
Article
Rice plants were grown in a temperature-controlled greenhouse in 1.2 L glass fleakers. The rooting media were inoculated with either the parent strain or a nitrogenase-derepressed mutant strain (which excreted NH44+ produced by nitrogenase) of the cyanobacterium Anabaena variabilis and exposed to 15N2. Dry matter and total N accumulated in the roots and shoots of plants inoculated with the mutant strain were significantly greater than from plants inoculated with the parent strain. Significantly higher levels of 15N2 accumulated in the roots and shoots of plants inoculated with the mutant strain, which indicated that more fixed N was readily available for root uptake and assimilation. Roots and shoots of uninoculated plants exposed to 15N2 had a small, consistent but nonsignificant increase in levels of 15N compared with treatments that were exposed only to the natural atmospheric abundance of the isotope. These results show that the NH4+-excreting mutant strain of A. variabilis has the potential to increase N input for plant growth in rice production systems.
 
Article
Brassicaceae seed meals (BSMs) average 6% N by weight and produce biologically active glucosinolate (GLS) degradation products. Little is known about N mineralization in BSM-amended soils or how the specific composition of secondary compounds, which varies by species, influences microbially mediated N cycling. We performed a laboratory incubation using 15N-labeled BSMs with different GLS concentrations to determine how mineralization and nitrification of BSM N is influenced by GLS hydrolysis products. Seed meals were added to soil at a 2% rate (wt. meal:wt. soil) and the amended soil incubated at 25 °C and 60% water-holding capacity for 45 d. Relative to the low-GLS Brassica napus treatment, modeled peak CO2 efflux was 44–68% lower and delayed by 0.9–1.5 d in the high-GLS Brassica juncea and Sinapis alba treatments, respectively. Mineralization of N in all BSMs was rapid initially, with 41–46% of the mineralized seed meal N recovered in the inorganic N pool on day 15. On day 45, 34–49% of the seed meal N mineralized was recovered in the total inorganic N pool. Between days 15 and 45, 78% of the total inorganic N pool was NH4+ in the S. alba treatment, whereas total inorganic N was 31% and 41% NH4+ in the B. napus and B. juncea treatments, respectively. We suggest that the GLS-degradation products 2-propenyl isothiocyanate (ITC) and ionic thiocyanate (SCN) released from B. juncea and S. alba BSMs were responsible for inhibited microbial respiration in the early period of the incubation (<3 d), and that nitrification inhibition in the S. alba treatment was caused by SCN− release. Our results indicate that BSMs can be used to increase inorganic N in soil and that GLS-degradation products have different short-term effects on the microbially mediated soil N cycle.
 
Total amount of 15 N contained in whole tomato tissues. All (%) reflected 
Article
Harmful environmental effects resulting from fertilizer use have spurred research into integrated nutrient management strategies which can include the use of specific micro-organisms to enhance nutrient use efficiency by plants. Some strains of plant growth-promoting rhizobacteria (PGPR) have been reported to enhance nutrient uptake by plants, but no studies with PGPR have used 15N isotope techniques to prove that the increased N in plant tissues came from the N applied as fertilizer. The current study was conducted to demonstrate that a model PGPR system can enhance plant uptake of fertilizer N applied to the soil using different rates of 15N-depleted ammonium sulfate. The experiments were conducted in the greenhouse with tomato using a mixture of PGPR strains Bacillus amyloliquefaciens IN937a and Bacillus pumilus T4. Results showed that PGPR together with reduced amounts of fertilizer promoted tomato growth compared to fertilizer without PGPR. In addition, atom% 15N per gram of plant tissue decreased as the amount of fertilizer increased, and PGPR inoculation resulted in a further decrease of the atom% 15N values. The atom% 15N abundance in plants that received 80% fertilizer plus PGPR was 0.1146, which was significantly lower than 0.1441 for plants that received 80% fertilizer without PGPR and statistically equivalent to 0.1184 for plants that received 100% fertilizer without PGPR. The results demonstrate that increased plant uptake of N applied in fertilizer could be achieved with PGPR as indicated by the differences in 15N uptake. Strains of PGPR that lead to increased nutrient uptake by plants should be evaluated further as components in integrated nutrient management systems.
 
Article
The aim of this experiment was to study the effect of the most frequently used preservation media for soil invertebrates on the concentration in Folsomia candida (Collembola) during extraction and storage. Two stocks of F. candida were fed with food containing either a low or a high quantity of for at least 2 months. Specimens from both stocks were stored in different preservatives for 1, 5 and 27 weeks. Specimens were preserved in eleven different solutions during the first week: 70% ethyl alcohol, 70% ethyl alcohol with 5% glycerin, 1% picric acid, distilled water, tap water, 70% isopropanol, 0.5% salicylic acid, saturated NaCl, 0.5% sodium benzoate, 25% ethyl glycol, and 10% formalin. Some specimens were killed immediately using heat (60°C). Another group of animals was kept frozen at −18°C. The specimens for the 5- and 27-week experiments were kept in 70% ethyl alcohol for the first week and subsequently one group was transferred into 90% ethyl alcohol, a second into 4% formalin and a third group was frozen. The results show that the different preservatives influenced the concentration. The alcohols did not change the concentration while picric acid and sodium benzoate led to reduced amounts of the isotope. The other liquids had modest effects. Freezing or preservation in ethyl alcohol or formalin proved to be reliable methods of storage for the purpose of a analysis.
 
Article
Three mesocosms were studied to evaluate the effect of wetland plants on the methanotrophic bacterial populations in the sediments of a full-scale constructed wetland. Cores were collected from two vegetated mesocosms and one unvegetated mesocosm from fall 2002 through summer 2003. Competitive quantitative PCR revealed no significant differences in the quantities of either Type I or Type II methanotrophic bacteria between the vegetated and unvegetated mesocosms. Type I methanotroph-biased nested PCR-DGGE resulted in the detection of 23 different populations related to Methylococcus, Methylomonas, Methylobacter, Methylocaldum, and Methylosarcina spp. Type II methanotroph-biased nested PCR-DGGE resulted in the detection of 5 different populations, more than 90% of which were related to previously uncultivated Type II methanotrophs. While wetland vegetation did not affect the structure of either the Type I or Type II methanotrophic communities, the Type I methanotrophic community structure was observed to vary seasonally. This work suggests that wetland plants neither enhanced nor adversely affected the size or structure of methanotrophic communities in our constructed wetland. Substantial quantities of both Type I and Type II methanotrophic populations were detected in both planted and unplanted mesocosms, suggesting that the constructed wetland had substantial potential for xenobiotic bioremediation whether or not plants were present.
 
Article
Organic mulches such as recycled, ground wood pallets and composted yard waste are widely used in landscapes to suppress weeds, and improve plant health. However, little is known about how mulches affect soil or rhizosphere microbial communities. In a field microcosm study, we compared effects of mulching with composted yard waste, ground wood pallets, or a bare soil control, with or without chemical fertilizer on soil mineral, chemical, biological, and rhizosphere bacterial community properties. Both mulch treatments had significant effects on organic matter content, soil respiration, microbial biomass N, soil pH, cation-exchange capacity, and concentrations of essential plant nutrients. Microbial respiration rate was highest in soils mulched with composted yard wastes (17.2 and 15.3 mg CO2 kg−1 per day for non-fertilized and fertilized plots, respectively) and lowest in bare soil plots (5.0 and 9.4 mg CO2 kg−1 per day for non-fertilized and fertilized plots, respectively). In general, the other parameters were highest in plots mulched with composted yard waste and not affected by fertilization. Bacterial communities in the rhizosphere of cucumber (Cucumis sativus L. Straight Light) seedlings grown in the microcosms were analyzed using most probable number (MPN) analysis of culturable heterotrophic fluorescent pseudomonads in King’s B medium as well as by analysis of terminal restriction fragment length polymorphisms (TRFLPs) of PCR amplified 16S rRNA genes. Populations of culturable heterotrophic bacteria and fluorescent pseudomonads in the rhizosphere were significantly greater in the composted yard waste plots than the bare soil fertilized mulched plots. TRFLP analysis of PCR amplified bacterial 16S rRNA genes from triplicate root tips grown in each treatment and digested with HhaI, MspI, and RsaI revealed that the TRFLP similarity was 0.81–0.91 among triplicate samples and 0.48–0.86 among different treatments. The TRFLP pattern of rhizosphere communities from the bare soil treatment were more similar (54–82%) to plots mulched with ground wood than to plots mulched with compost. Only 48–71% of TRFLP peaks detected in samples from the compost treatment were also detected in the bare soil control. The similarity in TRFLPs between the compost and ground wood pallet treatments was 56–80%. Although the community profiles showed differences in bacterial diversity, no significant difference in TRFLP-based diversity indices were observed. Unique TRF peaks detected among treatments suggest that specific subcomponents of the microbial communities differed. A higher number of TRFs corresponding with biocontrol organisms such as Pseudomonas and Pantoea spp. were observed in plots mulched with compost. However, the mulch treatments had more pronounced effects on soil chemical and microbial properties than on TRFLP based bacterial community structure on cucumber roots. Nonetheless, the data show clearly that mulching with compost strongly influenced the structure of the microbial rhizophere community.
 
Article
Labile soil organic matter pools (LSOMs) are the fine indicators of soil quality which are influenced by changes in management practices. The suitability of forest tree species is essential for soil quality improvement of a nutrient deficient calciorthent with very high percentage of free CaCO3 (34%). Six multipurpose tree species were selected to investigate the effect of afforestation after 18 years of plantations on size and dynamics of LSOMs, e.g. dissolved organic carbon (DOC), microbial biomass carbon (MBC) and light fraction carbon (LFC) and also on soil respiration. LSOMs were estimated during four seasons: summer (June), autumn (September), winter (December) and spring (March) in 0–15 cm and 15–30 cm soil depths and in situ soil respiration was also measured during the corresponding periods. Afforestation by Eucalyptus tereticornis (Smith) increased soil organic carbon (SOC) of the surface 30 cm soil layer by 142% which was at par with Terminalia arjuna Bedd. and Albizia procera (Roxb.) Benth while 63% increase was found by Pongamia pinnata (Linn.) over control plot (3.10 kg ha−1 SOC). Soil under T. arjuna had the highest increase in the mean annual concentration of DOC (by 201%), MBC (by 413%) and LFC (by 263%) over control in the 30 cm soil layer followed by E. tereticornis. Among the LSOMs, LFC had the maximum contribution to SOC (9.61–11.71%) in the afforested plots up to 30 cm soil layer. The relationships among the three labile pools were highly significant. Mean annual soil respiration was highest in E. tereticornis plot which was at par with Acacia lenticularis (L.) Willd and A. procera, while it was lowest in T. arjuna plot. Thus, MBC was the most sensitive to afforestation and LFC was the largest reservoir of carbon among the three LSOMs. The results suggest that afforestation by the six multipurpose tree species had increased the LSOMs and soil respiration to different magnitudes. T. arjuna was found to be the most suitable plantation with highest increase in LSOMs and lowest respiration among the different plantations.
 
– Design of soil microcosms experiments 
Article
The intensive use of herbicides in agricultural soils of the Pampas region (Argentina) is a matter of environmental concern. We investigated the impacts of three widely used, post-emergence herbicides, glyphosate, 2,4-dicholorophenoxyacetic acid (2,4-D) and metsulfuron-methyl, on soil microbial communities by an integrated approach using short-term soil incubations. The key structural and functional parameters were estimated by culturable aerobic heterotrophic bacterial (AHB) density, substrate-induced respiration (SIR), dehydrogenase activity (DHA), fluorescein diacetate (FDA) hydrolysis, and functional richness. Functional richness was evaluated as the proportion of carbon sources utilized in microplates containing various carbohydrates, carboxylic acids, amino acids and aromatic compounds, and 1,3,5-triphenyiltetrazolium chloride (TTC) as redox dye. Three different soil types (Typic Argiudoll, Typic Haplustoll and Petrocalcic Paleustoll) were collected from agricultural fields with reported history of herbicide application. Soil microcosms were treated with one herbicide at a time at a dose 10 times higher than the recommended field application rates (glyphosate, 150 mg a.i. kg−1; 2,4-D, 5 mg a.i. kg−1; metsulfuron-methyl, 1 mg a.i. kg−1 soil) and incubated for up to 3 weeks. Metsulfuron-methyl had the least pronounced effects on soil microbial community. 2,4-D showed transient effects on soils, inhibiting either SIR or FDA and stimulating DHA. Several short-term effects of glyphosate on microbial activities and bacterial density were observed: (1) early stimulation of SIR and AHB; (2) dissimilar response in the soils for FDA and DHA; (3) transient increase in functional richness. To conclude, the addition of these herbicides at a dose 10 times higher than the normal field application rates caused minor changes to soil microbial activity, bacterial density and functional richness. The specific changes varied among herbicides, with the effects of glyphosate most pronounced.
 
Article
The addition of nonindigenous microorganisms to soil can alter the structure of the soil foodweb and, consequently, the manner in which nutrients cycle through soil. Alterations in the cycling of nutrients through soil may, in turn, affect the growth, reproduction, and competitive ability of the vegetative community. To assess the effectsof introduced organisms on soil foodwbs, a xeric soil was amended with 500 μg g−1 of the herbicide 2,4-D and inoculated with either the genetically engineered organisms (GEM) Pseudomonas putida PP0301(pRO103) or P. putida PP0301 (the wild-type strain), as well as controls where no 2,4-D was added. Plasmid pRO103 contains constitutively expressed genes that encode for the mineralization of phenoxyacetate and the partial degradation of 2,4-D. Soil for this study was collected from the same site as the soil used in previous studies, but was not amended with glucose. Degradation of 2,4-D was not detected during the course of this study, although isolates of P. putida PPO301(pRO103) obtained from soil amended with 2,4-D at the end of of the study were able to catabolize phenoxyacetate in pure culture, suggesting that they retained the constitutive pathway for the partial degradation of 2,4-D. In all treatments amended with 2,4-D (with or without added PP0301(pRO103) or PP0301), active fungal biomass, active bacterial biomass, plate count estimates of bacteria, numbers of nitrifying bacteria, and numbers of flagellates and amoebae decreased. In soil without 2,4-D treatment and inoculated with the GEM, PP0301(pRO103) , active fungal biomass and total fungal biomass was reduced relative to that inoculated with PP0301. Increases in protozoan biomass were clearly evident in unamended soil inoculated with either PP0301(pRO103) or PP0301. The GEM had no continuing effects on the structure and function of the soil foodweb relative to the wild-type strain, in contrast to previous studies where 2,4-D was degraded and the fungal community was affected throughout the experiment.
 
Article
Effects of grazing by a common collembolan, Onychiurus subtenuis, and a common oribatid mite, Oppiella nova, singly and in combination, at a variety of densities, on lodgepole pine needle litter fungal biomass and microbial respiration were assessed in microcosms. At 3 weeks the numbers of O. subtenuis did not affect respiration. Increasing numbers of immature O. nova increased microbial respiration, accounting for 25% (p<0.001) of the variation in respiration. At 6 weeks, respiration was not affected by numbers of either animal, but was significantly and positively affected by moisture content which accounted for 49% (p<0.0001) of the variation. Increasing total numbers of fauna had a negative effect on fungal biomass, accounting for 24% (p<0.002) of the variation in fungal biomass. Gut content data showed that both O. subtenuis and O. nova consumed far more dark hyphae than hyaline hyphae. It appears that densities of the two most abundant mesofaunal species in lodgepole pine needle litter have a statistically significant effect on fungal biomass and respiration. However, their effects account for only about 25% of the variation in fungal biomass and respiration.
 
Article
3,3′-Diaminobenzidine was applied at doses of 5, 10, 25, and 50 mg kg−1 of soil and their effects were evaluated on indigenous soil microbial communities (viable aerobic bacteria, fungal populations, aerobic N2-fixing bacteria, denitrifying, and nitrifying bacteria), and soil enzymatic activities (acid and alkaline phosphatases, arylsulfatase, and dehydrogenase). At doses of 5 or 10 mg kg−1, 3,3′-diaminobenzidine increased the numbers of culturable soil bacteria, including Azotobacter spp., nitrifying and denitrifying bacteria. Higher doses (25–50 mg kg−1) enhanced growth of aerobic nitrogen fixers too, but negatively affected denitrifying and nitrifying bacterial groups, altering the natural balance of populations involved in N cycling. Fungi were not strongly affected by any doses tested. All enzymatic activities in soil were enhanced by application of 3,3′-diaminobenzidine.
 
Article
Insight is needed into how management influences soil biota when sustainable grassland systems are developed. A crop rotation of grass and maize can be sustainable in terms of efficient nutrient use. However, there is lack of information on the effect of such a crop rotation on soil biological quality. Earthworms, nematodes, bacteria and fungi were sampled over three years in a 36 years old experiment. Permanent arable land was compared with permanent grassland and with a ley-arable crop rotation. In the rotation, a period of three years of grassland (temporary grassland) was followed by a period of three years of arable land (temporary arable land) and vice versa. In the first year of arable cropping in the rotation, the number of earthworms was already low and not different from continuous cropping. In the three-year grass ley, the abundance of earthworms returned to the level of permanent grassland in the second year. However, the restoration of earthworm biomass took a minimum of three years. Furthermore, the anecic species did not recover the dominance they had in the permanent grassland. The numbers of herbivorous and microbivorous nematodes in the ley-crop rotation reached similar levels to those in the permanent treatments within one to two years. Although the same holds for the nematode genera composition, the Maturity Index and the proportion of omnivorous nematodes in the temporary treatments remained significantly lower than in their permanent counterparts. Differences in recovery were also found among microbial parameters. In the temporary treatments, bacterial growth rate and the capacity to degrade a suite of substrates recovered in the second year. However, the Community-Level Physiological Profiles in the permanent grassland remained different from the other treatments. Our results suggest that many functions of soil biota that are well established in permanent grassland, are restored in a ley-arable crop rotation. However, due to a reduction in certain species, specific functions of these soil biota could be reduced or lost. The ley-arable crop rotations were intermediate to permanent grassland and continuous arable land in terms of functioning of soil biota (e.g., N-mineralization). In terms of the functional aspects of the soil biota, permanent grassland might be preferable wherever possible. For maize cultivation, a ley-arable crop rotation is preferable to continuous arable land. However, a ley-arable crop rotation is only preferable to continuous arable cropping if it is not practised at the expense of permanent grassland at farm level.
 
Article
The effect of inoculation with PGPR belonging to the genus Bacillus (Bacillus licheniformis CECT 5106 and B. pumilus CECT 5105) in enhancing growth of Pinus pinea plants, and the changes that occur in rhizosphere microbial communities were evaluated. Both Bacillus strains promoted the growth of P. pinea seedlings (probably by gibberellin production), but this biological effect was not found with both strains in combination, which implies a possible competition effect. The introduction of both inoculants caused an alteration in the microbial rhizosphere composition, despite the low levels of inoculants which were found at the end of the assay.
 
Article
In laboratory experiments, earthworms (Eisenia foetida) exhibited no assimilation of radioactive 60Co from mineral soil, but did assimilate small quantities (about 7% of ingestion) of 60Co from manure. This study supports earlier work suggesting that earthworms assimilate only small amounts of inorganic elements from mineral soil, and that any assimilation of metals must be from the organic fraction of soils. Thus, assimilation rates are a function of substrate quality. When fed to earthworms, gamma-emitting radioactive elements can provide measurement of assimilation efficiency, gut passage time and feeding rate.
 
Article
Adsorption and mineralisation of the herbicide glyphosate in five contrasting Danish surface soils were investigated using labelled glyphosate. A comparison was made to several chemical and microbiological soil characteristics to identify their role in regulating the fate of glyphosate in these soils. Glyphosate was rapidly adsorbed to iron and aluminium oxides, but were later released from these pools during mineralisation. In soils with high mineralisation rates the metabolite AMPA was formed and adsorbed. Of all the soil factors tested, the rate of mineralisation was best correlated with the population size of Pseudomonas spp. bacteria in the soils. Phosphate addition had a stimulating effect on glyphosate degradation in soils with low mineralisation rates, but no effect or a negative effect on mineralisation in soils with high mineralisation rates. Finally, mineralisation rates were higher in soils from organically managed soils than in soils from conventional farming. The results indicate that the activity of glyphosate mineralising bacteria (e.g. Pseudomonas spp.) was a major factor controlling the fate of glyphosate in the soils.
 
Article
Prior to the onset of extensive grazing and clearing for agriculture, riparian floodplains of southeastern Arizona, USA, historically supported large grassland communities dominated by Sporobolus wrightii Munro ex Scribn., big sacaton grass. Large-scale abandonment of agricultural operations has occurred in this region in the past 50 years, but natural re-establishment of big sacaton into abandoned fields has typically been slow. This study assesses whether arbuscular mycorrhizal fungi (AMF) may be one factor in recovery rates of abandoned fields within three riparian areas in southeastern Arizona (San Pedro river, the Babocomari river and Cienega creek). In each riparian area, soil samples were collected along paired 100 m transects, one in an extant grassland and one in a neighboring abandoned agricultural field. At one site (San Pedro), a third transect was established in a second adjoining abandoned agricultural field to enable comparisons between fields showing differing rates of recovery at a single site. Roots were assessed for mycorrhizal colonization using the modified intercept method and the modified mean infection percentage (MIP) method was used to determine inoculum potential of each soil sample. No significant differences were found between the levels of mycorrhizal colonization in roots collected from the grassland and those collected from the abandoned field for any of the sample sites. Levels of colonization did differ among the three sample sites, with higher levels seen at the San Pedro site than at the Babocomari and Cienega sites. With one exception, MIPs were greater in the soil from the abandoned agricultural field than in the soil from the nearby grassland. In the exception, no difference was detected in inoculum potentials at the San Pedro site between the paired grassland and the abandoned field that had the lower level of sacaton recovery. MIPs were also greater in the soil from the abandoned agricultural field at Babocomari, where Salsola tragus L. growth for cattle feed was promoted by discing every 3–4 years. These results indicate that higher inoculum potentials in abandoned fields were not always linked to the high levels of recovery of native vegetation.
 
Distribution of trees and sampling points along the belt transect. Circles, trees (symbol size corresponds to tree diameter at breast height); small diamonds, vegetation plots; large diamonds, vegetation plots used for the Biolog assay.
Redundancy analysis of soil microbial data: functional groups positions and significant environmental variables which passed the forward selection. The diagram explains 21% of the total variance. Arrow tips show the positions of functional microbial groups (metabolizing specific substrates): s2, b -methyl- D - 
Redundancy analysis of soil microbial data (percentages of variance in microbial data explained by environmental variables).
Article
The impact of secondary succession of grassland communities towards a Norway spruce forest on soil microbial community was studied on a belt transect established in the Pol’ana Mts., Central Europe. Data on understory vegetation, light availability, soil properties and microbial activity were collected on 147 plots distributed over regular grid. Moreover, distributions of functional groups of microorganisms were assessed using BIOLOG analysis on a subset of 27 plots. Mantel partial correlations between microbial community indicators and environmental variables showed that microbial activity generally decreased with increasing tree density and size, whereas it increased with increasing radiation at the soil surface, soil temperature, and cover and diversity of understory vegetation. Functional richness and diversity of microorganisms were positively correlated with solar radiation, but also with plant species richness and diversity. Abundance of several functional groups correlated closely with succession-related variables. Redundance analysis of microbial data provided slightly different outcomes. Forward selection yielded only two environmental variables significantly influencing the composition of the microbial community: tree influence potential and organic carbon content. Abundances of several functional microbial groups correlated with tree influence, documenting that microbial community changes are at least partially driven by the colonization of grassland by trees. Nevertheless, the relative importance of abiotic environment change and plant community succession on microbial community dynamics remains unresolved.
 
– Soil food web diagram. Arrows represent feeding links and points at the predator. TL = trophic level, R = recalcitrant organic matter, L = labile organic matter, S = water soluble sugars and cr = cryptostigmatic.  
– Biomass for (A) trophic level (TL) 0, (B) TL 1, (C) TL 2 and (D) TL 3 in the young, mid-aged and old field, and in the heathland (mean W standard error). Different letters denote significant differences between fields at the p < 0.05 level.  
Article
The re-establishment of natural species rich heathlands on abandoned agricultural land is a common land use change in North-West Europe. However, it can take several decades to re-establish natural species rich heathland vegetation. The development rate has found to depend both on soil food web composition and on soil processes.We measured the soil food web composition in three ex-arable fields abandoned 2, 9 and 22 years ago and in a heathland. To characterize food structure, we defined four trophic levels and a root, fungal and bacterial energy channel. We hypothesized that with increasing time since abandonment, i.e. field age, (1) the basic resource level biomass, i.e. soil organic matter (SOM) and roots, will increase and thereby also that of biomasses at higher trophic levels, (2a) the root energy channel biomass will decrease, (2b) the fungal energy channel biomass will increase, and (2c) the bacterial energy channel biomass will not change.The results showed that biomasses at the basic resource level and at the first trophic level indeed increased with field age, but not the biomasses at higher trophic levels. It is not clear what the cause of the lack of increase in higher trophic levels was, possibly top-down or bottom-up forces played a role.The root energy channel biomass decreased and the fungal channel increased as hypothesized, but the bacterial channel biomass also increased with field age. The increase of the bacterial channel biomass contradicted the hypothesis, but agreed with the observed increase in SOM quantity and lack of decrease in SOM quality.On overall, results show that changes in belowground food webs lag behind changes of the aboveground vegetation. Such time lags may hamper secondary vegetation succession. Understanding those time lags may therefore help to develop management schemes improving land conversion processes.
 
Article
The importance of the soil microbial community for plant mineral nutrition and nutrient cycling has long been recognized. One of the most important interactions is the symbiosis of plants with mycorrhizas. In contrast, the effects of soil microfauna on plant performance have so far received little attention, although soil protozoa in particular, have been shown to beneficially affect plant growth. We investigated in a laboratory experiment the impact of mycorrhiza and protozoa and their interaction on plant performance. Spruce seedlings with or without the ectomycorrhizal fungus Paxillusinvolutus (Batsch) Fr. were grown in microcosm chambers with defaunated forest soil with naked amoebae (Acanthamoeba sp.) or without protozoa for 10 months. The presence of protozoa resulted in the development of a more complex root system by increasing root length (51%), length of fine roots (64%) and number of root tips (43%). The effects of protozoa were more pronounced in the absence of mycorrhiza. In contrast to protozoa, the presence of mycorrhiza resulted in a less complex root system, i.e. root length, length of fine roots and number of root tips were reduced by 47, 47 and 40%, respectively. Shoot height, and stem, shoot and needle mass were at a maximum in the combined treatment with both mycorrhiza and protozoa. The presence of mycorrhiza and protozoa also affected plant nutrient concentrations. In treatments with protozoa shoots of spruce seedlings contained less nitrogen, leading, e.g. to an increased C/N ratio in needles. Conversely, in treatments with mycorrhiza concentrations of phosphorus in needles were increased by a factor of almost two. Mycorrhiza and protozoa also affected rhizosphere microorganisms. Microbial biomass was reduced in the presence of mycorrhiza, mainly due to a reduction in bacterial numbers. Conversely, in the presence of protozoa the length of hyphae in the rhizosphere was reduced. It is concluded that the plant–mycorrhiza mutualism and the bacteria-mediated mutualism between plants and protozoa (microbial loop) complement each other; plant resources presumably are allocated to optimize simultaneous exploitation of both mutualistic relationships.
 
Article
Actinomycete strains originating from Moroccan phosphate mines (MPM) were selected for their ability to use the insoluble ground hydroxyapatite called rock phosphate (RP), present in their biotope, as sole phosphate (P) source. Physiological studies carried out with these strains and with the reference strains, Streptomyces lividans and Streptomyces griseus, demonstrated that all strains were able to grown in a synthetic minimal medium (SMM) containing either soluble (SP) or insoluble (RP) phosphate as sole P source. The MPM strains and S. griseus took up glucose much more actively and exhaustively than S. lividans, constituting more abundant glycogen reserves than the latter. All strains took up soluble P at comparable rates, storing it as polyphosphates. In SMM + RP, a sharp increase in the concentration of soluble P was detected in the culture broths of all MPM strains and S. griseus, at stationary phase, but not in that of S. lividans. The P peak detected in the supernatant of these strains correlated with the successive appearance of two compounds absorbing at 320 nm and 430 nm, respectively. These compounds are thought to be strong ion chelators involved in the destruction of the hydroxyapatite structure leading to soluble P release. The good growth of S. lividans in SMM + RP indicated that this strain was also able to release P from RP but consummed it as soon as it was released, unlike the other strains. Our study is expected to lead to the development of a novel type of slow release bio-phosphate fertilizer constituted by the association of the MPM strains and ground RP. This novel product would precisely supply plant needs and thus limit the pollution of the environment.
 
Article
The ability of a few soil microorganisms to convert insoluble forms of phosphorus to an accessible form is an important trait in plant growth-promoting bacteria for increasing plant yields. The use of phosphate solubilizing bacteria as inoculants increases the P uptake by plants. In this study, isolation, screening and characterization of 36 strains of phosphate solubilizing bacteria (PSB) from Central Taiwan were carried out. Mineral phosphate solubilizing (MPS) activities of all isolates were tested on tricalcium phosphate medium by analyzing the soluble-P content after 72 h of incubation at 30 °C. Identification and phylogenetic analysis of 36 isolates were carried out by 16S rDNA sequencing. Ten isolates belonged to genus Bacillus, nine to genus Rhodococcus, seven to genus Arthrobacter, six to genus Serratia and one each to genera Chryseobacterium, Delftia, Gordonia and Phyllobacterium. In addition, four strains namely, Arthrobacter ureafaciens, Phyllobacterium myrsinacearum, Rhodococcus erythropolis and Delftia sp. are being reported for the first time as phosphate solubilizing bacteria (PSB) after confirming their capacity to solubilize considerable amount of tricalcium phosphate in the medium by secreting organic acids. P-solubilizing activity of these strains was associated with the release of organic acids and a drop in the pH of the medium. HPLC analysis detected eight different kinds of organic acids, namely: citric acid, gluconic acid, lactic acid, succinic acid, propionic acid and three unknown organic acids from the cultures of these isolates. An inverse relationship between pH and P solubilized was apparent from this study. Identification and characterization of soil PSB for the effective plant growth-promotion broadens the spectrum of phosphate solubilizers available for field application.
 
Article
Increases in UV-B radiation have been shown to slow the rate of litter decomposition in ecosystems. However, it is unclear if this is a result of direct UV-B effects on saprobic microorganisms, or a result of UV-B-induced changes in litter quality that indirectly affect decay by saprobes. In this study, we evaluated the magnitude of direct and indirect effects on litter decomposition of Brassica napus by soil fungi, under growth chamber conditions. We found that, both, direct and indirect UV-B negatively influenced litter decomposition, however, direct effects were much more pronounced. We then tested whether UV-B radiation would have species-specific effects on fungal colonization and competitive ability, rather than influencing all fungal species equally. We predicted that darkly pigmented fungi would increase their relative competitive ability under high UV-B. The test fungi were all isolated from field soil under Brassica napus. Two fungi were hyaline (Aspergillus terreus, Trichoderma koningii), two were darkly-pigmented (Cladosporium sphaerospermum, Epicoccum purpurascens) and one had a hyaline mycelium but darkly-pigmented conidia (Aspergillus niger). Elevated UV-B radiation had differential direct and indirect effects on fungal growth, and caused shifts in the competitive balances between pigmented and non-pigmented fungi. However, in only two of six pair-wise challenges did the pigmented species increase their relative competitive ability under UV-B conditions. It is clear that UV-B profoundly influence fungal community structure in soil, but the direction of such effects remains unpredictable.
 
Article
Any study of the fate of genetically modified microorganisms (GMMs), released into the environment, must examine how far they can disperse from their release site. The likelihood of dispersal will depend on two key factors: 1.1. . Speed and distance of dispersal.2.2. . Survival and/or reproduction, enabling them to reach new environments or hosts in a viable state.This paper reviews factors influencing the speed and distance of dispersal of soil microbes. These will depend on soil management practices, soil physico-chemical properties, and on the activities and movement of members of the soil biota acting as vectors.Models of viral and bacterial dispersal are evaluated. Their limited relevance to natural soils, with their inherent heterogeneity, and applicability to actinomycete and fungal dispersal is discussed. Cultivation practices cause physical disturbance of the soil by ploughing, tyning and hoeing. The movement of soil during these activities can disperse microorganisms within 20–30 cm of the plough depth and several metres horizontally. Ploughing and tyning increase porosity, but heavy traffic compacts the soil and destroys macropores. The former thus aid dispersal and the latter retards it. Plant roots can act as food for microorganisms, and their growth will disperse the microorganisms deeper into the soil. Dispersal may be further increased as root death creates new macropores. As dispersal models have been mainly developed from studies of homogenised soils, many of these factors have not been adequately incorporated in predictions of microbial dispersal.Their are few studies directly pertaining to faunal movement of GMMs. This review highlights our current knowledge in identifying potential key faunal groups which may be influential in enhancing GMM transport in soil. The soil faunal community present a range of species diversity and function. The potential importance of the major soil faunal groups in dispersal of microorganisms is discussed. Larger, mobile animals, such as lumbricids are the main agents of vertical and horizontal dispersal of GMMs. Large epigeic fauna such as diplopods and isopods may be important in horizontal dispersal at the soil surface but information on their abundance in different ecosystems is limited. Geographic distribution of faunal groups inflences their importance at any one location. Generally, the more numerically abundant, but smaller-sized protozoa and nematodes play an insignificant part. The dispersal of microorganisms by soil fauna may be of greater importance than abiotic factors in soils of high clay content or impeded drainage. Models based on artificial microcosms have shown the importance of soil particle size in downward movement of the drainage water which will carry the microbial propagules.This review highlights two major areas where our understanding of interactions of soil structure, biotic components and microbial dispersal is lacking. Firstly, soil heterogeneity is not included as a factor in model systems of abiotic dispersal of microbes. This is a major drawback for their use as predictive tools in natural field soils. Secondly, our lack of knowledge of the interactions between many soil faunal taxa and the microbial community requires further attention.We recommend that further studies should be conducted in intact systems (natural, undisturbed sites or intact soil cores) to improve the predictive power of models of movement of microorganisms in soil.
 
Article
We examined the effects of decreasing plant diversity and functional group identity on root biomass, soil bulk density, soil nitrate and ammonium concentrations, microbial basal respiration, density of predaceous and non-predaceous nematodes, earthworm biomass and density and Shannon–Wiener indices of earthworm diversity in a temperate grassland. Plant species and functional group diversity did not have significant effects on any of these measured variables. However, functional group identity of the plants did significantly affect root biomass and soil abiotic factors. In addition, root biomass, Shannon–Wiener indices of earthworm diversity and density of epigeic earthworms were significantly higher in the presence of legumes, while we found no correlation between functional group identity and other groups of soil biota. We also found several significant relationships among root biomass density, soil microbial basal respiration, nematodes and earthworms.
 
Article
Using ordinations techniques, we investigated the effects of different types of plant cover on the relationship between soil structure and invertebrate communities in an Amazonian savanna. Vegetation islands were chosen where four selected shrubs species were present on sandy and clayey soils. For each sample under a selected shrub within the clump, another sample was taken in the grass-tuft and extracted in Berlese-Tullgren. Classifying at higher taxonomic levels, we detected 27 zoological categories. The mean number of individuals was generally higher on shrubs. Acari and Collembola were the dominant groups. Non-Oribatid mites dominated in the savanna, in contrary with what occurs in most Amazonian ecosystems, where the dominance of Oribatida is always higher than others Acari. The level of taxonomic resolution utilized was sufficient to show the main differences of the spatial variation in community structure. We detected effects of soil type, vegetation structure and plant specie identity on the composition of the communities. The mesofauna have a mosaic distribution in the savanna dependent on the soil-food web structure of the vegetation. Shrubs and grass-tuft generate different ecosystems. Therefore, studies with better taxonomic resolution will be necessary to assess the magnitude of the effect of biotic and abiotic factors.
 
Article
Relationships between soil characteristics, various forms of soil organic matter, microbial biomass and the structure of phytoparasitic nematode populations were investigated in six fallow fields aged from 1 to 26 years in the West African Savanna (WAS) belt in southern Senegal. Soil sampling was performed along two transects in each field. Herbaceous biomass and soil physical, chemical and biological characteristics were studied with principal component analysis (PCA) and the relationships between the parameters were extracted with co-inertia analysis. Soil properties (mainly calcium, magnesium and total carbon content, and cation exchange capacity) slightly improved in the upper soil layer (0-5 cm) during the succession of vegetation. In contrast, in the 0-10 cm soil layer, microbial biomass and total soil organic carbon content showed no clear pattern of change over time, while highest charcoal stocks were found in older fallows where bush fires are frequent. In the 0-40 cm layer, living root biomass increased and herbaceous biomass decreased through the chronosequence. Evidence is presented here for particular relationships between some of the carbon components and the structure of the nematode community. #Pratylenchus$ and #Ditylenchus$ species were associated with the grass vegetation of the youngest fallows. In contrast #Helicotylenchus$ and #Scutellonema$ were present in old fallows. The multiplication of the latter appeared closely related to the presence of woody fine roots, whereas, that of the former seemed to be favoured by the presence of the coarsest root of trees. #Xiphinema$ had a higher density in soils with higher bulk density. Microbial biomass was not affected by fallow duration and was not correlated with the abundance of non-parasitic nematodes... (D'après résumé d'auteur)
 
Article
Interactions between plants, soils and microbes regulate terrestrial ecosystem functioning. Biotic and abiotic interactions can strongly affect the community structure which in turn will impact on ecological processes. Plant species with different ecophysiological traits can exert strong effects on soil biological properties. Our objective was to investigate and identify the effects of different biotic and abiotic variables on soil microbial community structure and functions and to examine if plant species with different physiological traits support different microbial communities in soils. Here, we show that 3 years of the presence of plants had direct impacts on soil function in terms of total heterotrophic respiration and on microbial biomass and microbial community structure. However, the plant species-specific impact on bacterial community structure was weak, and differences were mainly driven by sample field location. The fungal community analysis gave similar results, with soil location being the most important factor driving fungal community structure. The effect of plant species on fungal community structure was weak but statistically significant. There was a strong concordance between bacterial and fungal communities (P < 0.001) which suggested that the bacteria and fungi have an influence on shaping the structure of each other's community. Among the abiotic factors, moisture had a comparatively higher impact on bacterial communities compared to soil N and C. However, the fungal community was not affected by the soil moisture but soil N and C had a stronger impact than on the bacterial community. These results indicate that the microbial community structure in the natural environment is influenced by interactions between both biotic and abiotic factors.
 
2 3 hal-00497151, version 1 -2 Jul 2010  
pH values of the topsoil from the acid beech forest and the three polluted plots
Article
A short-term microcosm experiment was carried out to determine whether acid-tolerant collembolans are able to colonise metal-polluted soil. Polystyrene boxes were divided into two compartments by a perforated wall allowing free passage of soil fauna and preventing physical contact between soil substrates. All compartments were filled either with an acid dysmoder (pH 4.4) collected in a beech forest from Belgian Ardennes (Willerzie, Belgium) or with one of three neutral polluted soils (P1–P3) collected in the Bois des Asturies, along a metal-pollution gradient downwind of a zinc smelter (Auby, France). Different combinations were established, with five replicates each, and were incubated for 3 weeks at 15 °C, in darkness. Afterwards, Collembola were extracted and determined to the species level. It appeared that populations from the acid soil colonised the neutral soil polluted by heavy metals. Within 3 weeks, the number of species increased in compartments filled with the most heavily polluted soils (P2, P3) when they were in contact with the acid soil. However, colonisation was effected by only a few individuals. At the species level, the onychiurid Protaphorura eichhorni and the isotomid Folsomia quadrioculata colonised the polluted soil. For Protaphorura eichhorni the migration rate was highest when the soil was the least polluted (P1), while Folsomia quadrioculata showed a higher rate of dispersion to heavily polluted soil (P2) compared with the least polluted soil (P1). This behaviour could be explained by the humus form which was a mull in P1, more compact than the mor observed in P2 and P3, the physical structure of which approaches that of the dysmoder. Our observations indicate that both species are more affected by soil structure than by pollution.
 
Layout of sampling design of short-term trampling. One block consists of 4 lanes, each with two subplots. 
Short-term effects of experimental human trampling on (a) plant cover, (b) plant height and (c) plant species density in the forests Allschwil and Sichtern in the vicinity of Basel, Switzerland. All values are means of relative values AE SE, in each case N = 6. 
Short-term effects of experimental human trampling on (a) soil microbial biomass C (C mic ), (b) soil microbial biomass N (N mic ), (c) dehydrogenase activity, (d) b 
Long-term effects of human trampling on (a) soil microbial biomass C (C mic ), (b) soil microbial biomass N (N mic ), (c) dehydrogenase activity, (d) b-glucosidase activity and (e) phosphomonoesterase activity along 20 m transect lines at three fire places in each of the two forests Allschwil and Sichtern in the vicinity of Basel, Switzerland. Means (AESE) of nine transect lines are shown. 
Article
Understanding the effects of disturbance by human trampling on ecosystem processes is essential for the management of recreational areas. Discussions on recreational impacts are based either on data from trampling experiments or on field survey data from sites subjected to long-term recreational use, but rarely on a combination of both. We examined whether results from a short-term trampling experiment reflect the impact of long-term trampling around frequently used fire places. We compared short- and long-term effects of human trampling on above-ground forest vegetation and soil physical, chemical and microbial characteristics. We found both similarities and differences in short- and long-term trampling effects. Both short- and long-term trampling reduced plant cover, plant height and species density, though long-term effects were more pronounced than short-term effects. In both approaches, leaf litter biomass decreased, whereas soil density increased with trampling intensity. Other soil characteristics including soil moisture, total soil organic matter content and total organic nitrogen content were not or only marginally affected by short- and long-term trampling. Furthermore, soil microbial biomass and the activity of dehydrogenase did not change in both approaches. In contrast, the activity of β-glucosidase was only reduced by short-term trampling, whereas activity of phosphomonoesterase was reduced only by long-term trampling. Soil compaction was one factor reducing microbial activities at low and medium trampling intensities in our experiment and in the highly compacted area around the fire rings. We conclude that it could be problematic to use the results of short-term trampling experiments to predict general long-term trampling effects. Our results imply also that the restoration of degraded sites might be hampered by the low nutrient turnover resulting from the reduced litter layer and changes in enzyme activities, mitigating a successful re-establishment and growth of plants.
 
Article
Earthworms affect plant performance and can influence plant–herbivore interactions. Both primary and secondary metabolites and the expression of stress-responsive genes of plants can be affected by earthworms. Plant-mediated effects of earthworms on aboveground herbivore performance range between positive and negative. These indirect, plant-mediated effects likely depend on the altered resource uptake of plants or changes in the soil microbial community composition in presence of earthworms. Studies on belowground interactions between earthworms and root herbivores focussed almost exclusively on root-feeding nematodes. These interactions can be either direct (e.g. ingesting of nematodes) or indirect, mediated by changes in host plant performance or biotic and abiotic soil characteristics. Earthworms were documented to counteract the negative effects of root-feeding nematodes on plants. Consistently, earthworm-worked soils (vermicompost) have been reported to reduce numbers of root-feeding nematodes and plant damage by aboveground herbivores. The results suggest context dependent impacts of earthworms on herbivore performance and an alleviation of herbivore damage of plants by earthworms, besides their well-known effects on plant growth. This knowledge is crucial for understanding the impact of earthworms on plants in natural environments, and may be applied as alternative plant protection in sustainable agriculture.
 
Article
Goals of ecosystem restoration in California grasslands include the reestablishment of plant communities with a high proportion of native species, and simultaneously improve soil nutrient cycling. Addition of annual lupines and a litter mulch layer were hypothesized to be factors that would promote the growth of the native perennial bunchgrass, Nassella pulchra, in a restored California grassland. To test this hypothesis, field mesocosms were installed, each encircling a Nassella plant, at a perennial grassland restoration site in Carmel Valley, California. Two sets of treatments were imposed: (1) seeding of the annual N-fixing legume, Lupinus bicolor; and (2) exchanging the grassland litter for a thicker mulch layer of C4 grass litter (C/N = 99). Stable isotope analysis allowed the tracking of fates of N fixed by the legume and the C4-litter derived C. Treatments continued for 28 months, from December 2002 to April 2005, when most of the destructive measurements were taken. In 2005, neither treatment had significantly increased the biomass of the annuals or the perennial bunchgrass, and there was little effect on total soil C and N. Lupinus decreased the δ15N content, but did not affect the biomass, N and P content of the litter, which was largely composed of annual plants from the previous year. Lupinus resulted in higher soil microbial biomass carbon (SMB-C), and distinct effects on soil microbial communities, especially soil fungi, as measured by phospholipid fatty acid analysis (PLFA) and ergosterol. The high C/N litter mulch tended to increase biomass of Nassella, despite its lower P concentration, and it reduced SMB-C, presumably due to lower decomposition rates compared to the ambient litter. Using a high C/N litter mulch thus is ambiguous for grassland restoration. Repeated increases of legumes over a longer time frame may potentially increase soil fertility and soil C pools in California grasslands, but this study suggests that native perennial grasses may be slow to benefit.
 
Diagram illustrating the various mechanisms by which aboveground and belowground invaders influence ecosystem structure and function. Please see text for discussion. 
Article
The 9th biennial meeting of the Soil Ecology Society held in Palm Springs, CA in May 2003, addressed the theme of “Invasive species and soil ecology”. This meeting prompted interest in pursuing this special issue of Applied Soil Ecology, which includes papers presented at the meeting and other papers contributed after the meeting. This paper highlights some of the major issues addressed at the meeting and in the subsequent papers published in this special issue, and also provides a conceptual framework for examining interactions between aboveground and belowground invasions.
 
Article
Arctic ecosystems are sensitive to disturbance yet there is little information on the fate and recovery of soil microbial communities after disturbance and persistence in the absence of plants. Neighbouring plants may facilitate seedling establishment through amelioration of the physical environment and maintenance of arbuscular fungal community in soil. The inoculum of arbuscular mycorrhizal symbionts is critical for the establishment of low-latitude arctic herbs that are obligately mycorrhizal. In the present work, we investigated plant-soil and plant-plant interactions in low arctic meadow habitat. Plant cover was experimentally removed and field plots were left without plant cover, or a monoculture of the common local herb, Solidago virgaurea, was planted on the plots or the plant cover was left intact. After two years, three herb species were sown on the plots and their growth, mycorrhizal colonization and soil microbial communities were measured. Relative fungal abundance decreased in the soil community in the treatments where the soil had been disturbed. Soil microbial community structure by functional group was maintained in the soil two years after no plant cover and microbial biomass per organic matter was not reduced. Mycorrhizal colonization potential was not impaired after two years of absence of host plants and thus it is concluded that symbiotic propagules are able to persist for two years in the absence of host plants. The Solidago monoculture did not facilitate seedling establishment nor change soil microbial community markedly in short-term. Overall, the low arctic soil microbial community was markedly resistant to disturbance.
 
Trenches were dug perpendicular to the Sorghum planting ridges to expose the rootzones. Roots were counted using a grid with 25 cm 2 grid cells hung on the 
Macrofauna abundance and biomass of Saria I, Burkina Faso. Classification of means based on the least significance difference given by the ANOVA.
Effect of manure, straw and nitrogen applications on termite and earthworm abun- dance and biomass in Saria II, Burkina Faso.
Article
Unsustainable crop and soil management practices are major causes of soil degradation and declining soil biodiversity in West Africa. Identifying soil management practices that favor macrofauna abundance is highly desirable for long-term soil health. This study investigates the effects of long-term conservation soil management on termite and earthworm abundance and taxonomic richness in the central plateau of Burkina Faso. Trials included rotations with 5 Mg ha−1 yr−2 of organic matter added (established in 1960), application of 10 Mg ha−1 yr−1applied with additional organic (manure or straw) and mineral inputs (established in 1980) and different tillage systems (established in 1990) where 10 Mg ha−1 yr−1 of organic matter was also applied. Soil macrofauna was surveyed at the soil surface and in the upper 30 cm using transect and monolith sampling methods, eight weeks after sorghum crop planting. A total of five termite taxa: Trinervitermes sp., Microtermes sp., Odontotermes magdalenae, Macrotermes sp. and Amitermes stephensoni; belonging to the family of Termitidae, and two earthworm taxa: Dichogaster affinis, Millsonia inermis; from the family of Acanthodrilidae were found. Termite taxonomic richness per treatment ranged between 1 and 4, while earthworm taxa ranged from 0 to 2. Under rotation, one termite taxa and no earthworm taxa were identified. In the organic amendment plots, three termite and two earthworm taxa were found. And light tillage (animal or hand) resulted in four termite taxa and one earthworm taxa. The two types of fauna clearly responded differently to the different conservation soil management practices. Under rotation lower recorded macrofauna population was attributed to the lower rate of applied organic matter compared to levels applied in the organic amendment and tillage trials and where more macrofauna were found. Location of food stock (rooting depth of different crops in the rotation) also had a significant effect on termite presence. Effect of rooting depth on earthworms was not observable due to the absence of earthworms in the rotation trials (possibly due to insecticide application. Manure treatments favored earthworms, while sorghum straw treatments favored termites likely due to respective preference for easy versus difficult to digest organic sources. Animal plowing and hand hoeing had similar and significantly positive effects and both termite and earthworm biological components compared to tractor tillage. We conclude that termite and earthworm abundance and taxonomic richness are most significantly affected by the type and amount of organic matter applied and tillage regimes, with rooting depth of rotations crops also playing a significant role. To promote macrofauna abundance and taxonomic richness in soils, integrated conservation soil management practices with attention to the particular needs and preferences of termites and earthworms is needed.Highlights► Biodiversity declining is due to unsustainable land management. ► That affects earthworms and termites abundance, biomass and taxonomic richness. ► Manure favored earthworms, while sorghum straw treatments favored termites. ► Light tillage improve both macrofauna biological component compared to tractor plow. ► Integrated conservation soil management is recommended.
 
Article
An experimental platform of free-air CO2 enrichment (FACE) was established in mid June of 2004 over a rice–wheat rotation ecosystem located at a suburb of Jiangdu, China. We compared the abundance and diversity of soil nematodes from a wheat field with high (225.0 kg N ha−1) and low (112.5 kg N ha−1) levels of N fertilisation exposed to the elevated and ambient CO2 during the wheat growing season in 2005. The results showed that elevated CO2 and N fertilisation had significant effects on the abundance and diversity of soil nematodes. Elevated CO2 increased the abundance of omnivores-predators, the values of maturity index (MI) and structural index (SI) of nematode assemblage at the jointing stage of wheat. Two levels of N fertilisation had significant effects on the abundance of fungivores at the wheat jointing stage, while nematode channel ratio (NCR) showed responses to different N fertilisation and the interaction effects of elevated CO2 and N fertilisation at the wheat ripening stage.
 
Article
Earthworms play an important role in soil ecology and can serve as practical indicators in land quality evaluation. The abundance and distribution of earthworms were determined in 84 cropping and pasture soils in north-east Victoria and southern New South Wales (NSW), Australia. Overall, an average density of 89 earthworms m−2 was found, with an average species richness of 1–2 per site, indicating relatively low abundance and species poverty. Introduced lumbricid earthworms, Aporrectodea trapezoides and A. caliginosa were the most widely distributed (88% and 61% of all sites, respectively) and numerically dominant (respective population densities of 35.8 and 32.1 m−2). Soils under pasture supported on average 3.2 times more earthworms than those under cropping. The age structure of populations varied with species, introduced lumbricids and acanthodrilids displayed an adult-dominant structure and the native megascolecids displayed a juvenile-dominant population. Indigenous earthworms belonged to a single genus, Spenceriella. Whilst not occurring in high densities these indigenous earthworms were widespread in their distribution and their numbers were negatively correlated with soil P, K, and Mg suggesting an adaptation to low levels of soil fertility. Although the relationship between earthworm densities and mean annual total precipitation (MATP) was not close (r2 = 0.35), of the 33 sites containing >100 earthworms m−2, 25 received MATP in excess of 600 mm. Correlations between earthworm densities and a range of physical and chemical parameters were generally poor. This may highlight the short-comings of these parameters in describing distribution patterns.
 
Article
Earthworm populations were sampled in 19 coniferous or mixed forests in Bavaria. The stands are dominated by Scots pine (Pinus sylvestris L.), or had been pure Scots pine stands before conversion to mixed stands with the broad-leaved tree species European beech (Fagus sylvatica L.), and/or pedunculate oak (Quercus robur L.) and sessile oak (Quercus petraea (Matt.) Liebl.) was started 14–66 years ago. Based on this survey, we tested whether the introduction of beech and oak into pure pine stands resulted in an altered earthworm community. In addition, we tried to explain the high observed variance in earthworm abundance and biomass by regressing them against the factors extracted by principal component analysis (PCA). The variables included in the PCA comprised soil nutrient concentrations in the Of-layer, stand parameters, annual mean precipitation and temperature, the number of diplopods as potential competitors for food and habitat, the number of invertebrate predators, and the distance to agricultural land and roadside as potential sources of earthworm immigration, respectively.
 
Article
We studied the effects of long-term organic and mineral fertilization on soil microarthropods and soil chemical parameters in a field experiment under semi-arid conditions in Central Spain. Two different regimes of organic manuring, i.e. farmyard manure applied once in 3 years versus annual manuring with crop residues were compared. Soil carbon and nitrogen contents were increased markedly by farmyard manure, whereas straw and green manure had no significant effect. In contrast, the abundance of soil microarthropods was increased by annual application of straw and green manure, but not by farmyard manure last applied 2.5 years before sampling. We conclude that in the field experiment under study the abundance of soil microarthropods was influenced by the immediate food supply rather than by soil chemical parameters, such as carbon and nitrogen content or the pH. Biodiversity of soil microarthropods, as estimated by the Shannon index, was not affected significantly by straw and green manure. Obviously, other management practices, especially tillage, are limiting the species composition of soil microarthropods and thereby overshadow possible effects of fertilization on diversity.
 
Article
Endogeic and juvenile anecic earthworm abundance was measured in soil samples and anecic populations were studied by counting midden numbers at the sites of two long-term cropping systems trials in South-central Wisconsin. The three grain and three forage systems at each site were designed to reflect a range of Midwestern USA production strategies. The primary objectives of this work were to determine if the abundance of endogeic or anecic earthworms varied among cropping systems or crop phases within a cropping system and were there specific management practices that impacted endogeic or anecic earthworm numbers. The earthworms present in the surface soil were: Aporrectodea tuberculata (Eisen), A. caliginosa (Savigny), A. trapezoides (Dugés); and juvenile Lumbricus terrestris (L.). True endogeic abundance was greatest in rotationally grazed pasture [188 m−2 at Arlington (ARL) and 299 m−2 at Elkhorn (ELK)], and smallest in conventional continuous corn (27 m−2 at ARL and 32 m−2 at ELK). The only type of anecic earthworm found was L. terrestris L. There was an average of 1.2 middens per adult anecic earthworm and the population of anecics was greatest in the no-till cash grain system (28 middens m−2 at ARL, 18 m−2 at ELK) and smallest in the conventional continuous corn system (3 middens m−2 at ARL, 1 m−2 at ELK). Earthworm numbers in individual crop phases within a cropping system were too variable from year-to-year to recommend using a single phase to characterize a whole cropping system. Indices for five management factors (tillage, manure inputs, solid stand, pesticide use, and crop diversity) were examined, and manure use and tillage were the most important impacting earthworm numbers across the range of cropping systems. Manure use was the most important management factor affecting endogeic earthworm numbers; but no-tillage was the most important for the juvenile and adult anecic groups and had a significantly positive influence on endogeic earthworm counts as well. The pesticides used, which were among the most commonly applied pesticides in the Midwestern USA, and increasing crop diversity did not have a significant effect on either the endogeic or anecic earthworm groups in this study. Consequently, designing cropping systems that reduce tillage and include manure with less regard to omitting pesticides or increasing crop diversity should enhance earthworm populations and probably improve sustainability.
 
Article
The annual feeding activity on paper baits of subterranean termites in desertified (degraded-shrub dominated ecosystems) and relatively undegraded black-grama (Bouteloua eriopoda) grasslands was measured over six years on 12 sites. There were no significant differences in mass losses from termite baits among the desertified and undesertified sites. Mass of paper consumed by termites on two sites dominated by creosotebush, Larea tridentata, was higher than on the other 10 sites. These sites were characterized by shallow, coarse soils and shrubs that did not retain a below-canopy litter layer. The spatial locations of the highest termite bait removal remained relatively constant over the duration of the study. Interannual variations in mass losses from termite baits were highly correlated with winter–spring rainfall (r2 between 0.60 and 0.95) except at one site on shallow soils. The relationship between annual rainfall and termite activity was less significant (r2 between 0.48 and 0.83). Frequency of attack as measured by percent of bait rolls “hit” were not different among sites indicating no differences in densities of subterranean termites. Degradation of Chihuahuan desert grasslands and associated vegetation change has had minimal effect on the activity of subterranean termites. Subterranean termites continue to affect soil properties and processes in both degraded (desertified) and undesertified ecosystems.
 
Top-cited authors
Patrick Lavelle
  • Sorbonne Université
Howard Ferris
  • University of California, Davis
Goede De R. G. M.
  • Wageningen University & Research
Antonio Roldán
  • Spanish National Research Council
B. S. Griffiths
  • Scotland's Rural College