Applied Soil Ecology

Published by Elsevier BV

Print ISSN: 0929-1393


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

July 2009


275 Reads


C Guerrero





J Mataix-Beneyto
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.

van Diepeningen AD, de Vos OJ, Korthals GW, van Bruggen AHC.. Effects of organic versus conventional management on chemical and biological parameters in agricultural soils. Appl Soil Ecol 31: 120-135

January 2006


581 Reads

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.

Wall D, Virginia R.. Controls on soil biodiversity: insights from extreme environments. Appl Soil Ecol 13: 137-150

October 1999


81 Reads

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.

Jordan D, Li F, Ponder F, Berry EC, Hubbard VC, Kim KY.. The effects of forest practices on earthworm populations and soil microbial biomass in a hardwood forest in Missouri. Appl Soil Ecol 13: 31-38

September 1999


28 Reads

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.

Fig. 1. 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’). 
Fig. 2. 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’). 
Fig. 3. 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. 
Fig. 4. 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). 
van Bruggen AHC, Semenov AM.. In search of biological indicators for soil health and disease suppression. Appl Soil Ecol 15: 13-24
ArticleFull-text available

August 2000


2,571 Reads

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.

Carbon fluxes from plants through soil organisms determined by field 13CO2 pulse-labelling in an upland grassland

September 2006


151 Reads

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.

Singh BK, Munro S, Potts JM, Millard P.. Influence of grass species in soil type on rhizosphere microbial community structure in grassland soils. Appl Soil Ecol 36: 147-155

March 2007


171 Reads

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.

Development of a soil ecotoxicology method: Preparation and soil degradation of 14C-labeled grass

April 1999


23 Reads

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.

Nitrogen mineralization in soil incubated with 15N-labeled Brassicaceae seed meals

September 2010


74 Reads

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.

Growth and accumulation of 15N in rice inoculated with the parent and a nitrogenase-derepressed mutant strain of Anabaena variabilis

May 1997


27 Reads

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.

The effects of different methods of preservation on the 15N concentration in Folsomia Candida (Collembola)

September 1998


12 Reads

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.

The characterization and quantification of methanotrophic bacterial populations in constructed wetland sediments using PCR targeting 16S rRNA gene fragments

March 2007


55 Reads

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.

Effects of mulching and fertilization on soil nutrients, microbial activity and rhizosphere bacterial community structure determined by analysis of TRFLPs of PCR-amplified 16S rRNA genes

July 2002


858 Reads

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.

Labile soil organic matter pools in a calciorthent after 18 years of afforestation by different plantations

June 2009


210 Reads

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.

Assessing interactions between the soil foodweb and a strain of Pseudomonas putida genetically engineered to degrade 2,4-D

December 1995


53 Reads

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.

Table 2 – Design of soil microcosms experiments 
An Integrated Approach to Evaluate the Impacts of the Herbicides Glyphosate, 2,4-D and Metsulfuron-Methyl on Soil Microbial Communities in the Pampas Region, Argentina

September 2008


810 Reads

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.

Kaneko N, McLean MA, Parkinson D.. Do mites and Collembola affect pine litter fungal biomass and microbial respiration? Appl Soil Ecol 9: 209-213

September 1998


130 Reads

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.

Response of soil microbiota to the addition of 3,3′-diaminobenzidine

June 2003


30 Reads

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.

Soil biological quality after 36 years of ley-arable cropping, permanent grassland and permanent arable cropping

November 2008


278 Reads

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.

Pinus pinea L. seedling growth and bacterial rhizosphere structure after inoculation with PGPR Bacillus (B. licheniformis CECT 5106 and B. pumilus CECT 5105)

May 2002


220 Reads

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.

Turnover of cobalt-60 by earthworms (Eisenia foetida) (Lumbricidae, Oligochaeta)

June 1995


28 Reads

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.

Gimsing AL, Borggaard OK, Jacobsen OS, Aamand J, Sorensen J Chemical and microbiological soil characteristics controlling glyphosate mineralisation in Danish surface soils. Appl Soil Ecol

November 2004


269 Reads

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.

Assessment of arbuscular mycorrhizal fungal propagules and colonization from abandoned agricultural fields and semi-arid grasslands in riparian floodplains

June 2002


55 Reads

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.

Fig. 1. 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.
Fig. 2. 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).
Changes of the functional diversity of soil microbial community during the colonization of abandoned grassland by a forest

October 2009


250 Reads

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.

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