It takes an individual plant to raise a community: TRFLP analysis of the rhizosphere microbial community of two pairs of high- and low-metal-accumulating plants

We used terminal restriction fragment length polymorphism (TRFLP) analysis to look at the microbial community profiles of the rhizosphere surrounding two pairs of high- and low-metal (Cd)-accumulating plants (Brassica and Triticum). Unexpectedly, the microbial community did not vary with soil type, time, plant type, or metal-accumulating ability of the plant. Instead, when a plant's metal-accumulating ability was well matched to the level of metal contamination in the soil, the microbial populations in the rhizosphere were different than those of the seed endophytes and bulk soil. Unmatched plants had the same microbial community as bulk soil. The plant interaction with the soil, therefore, is essential to forming the bacterial community in the rhizosphere.     

Metal removal from and microbial property improvement of a multiple heavy metals contaminated soil by phytoextraction with a cadmium hyperaccumulator Sedum alfredii H.

Purpose

Effects of phytoextraction by Sedum alfredii H., a native cadmium hyperaccumulator, on metal removal from and microbial property improvement of a multiple heavy metals contaminated soil were studied under greenhouse conditions.

Materials and methods

A rhizobox experiment with an ancient silver-mining ecotype of S. alfredii natively growing in Zhejiang Province, China, was conducted for remediation of a multiple heavy metals contaminated soil. The rhizobox was designed combining the root-shaking method for the separation of rhizospheric vs near-rhizospheric soils and prestratifying method for separation of sublayers rhizospheric soils (0–10 mm from the root) and bulk soil (>10 mm from the root). Soil and plant samplings were carried out after 3 and 6 months of plant growth.

Results and discussion

Cadmium (Cd), zinc (Zn), and lead (Pb) concentrations in shoots were 440.6, 11,893, and 91.2 mg kg^?1 after 6 months growth, and Cd, Zn, and Pb removed in the shoots were 0.862, 25.20, and 0.117 mg/plant. Microbial biomass C, basal respiration, urease, acid phosphatase, and invertase activities of the rhizospheric soils were significantly higher than that of unplanted soils after 6 months growth. Microbial biomass carbon (MBC) of 0–2 mm and basal respiration (BR) rate of 0–8 mm sublayer rhizospheric soils were significantly higher than that of bulk soil after 6 months growth. So were the three enzyme activities of 0–4 mm sublayer rhizospheric soils. BR rate and urease were significantly negatively correlated with soluble Cd, so were MBC, acid phosphatase, and intervase activities with soluble Zn, MBC, BR rate, and three enzyme activities with soluble Pb.

Conclusions

Harvesting shoots of S. alfredii could remove remarkable amounts of Cd, Zn, Pb, and lower water-soluble Cd, Zn, and Pb concentrations in the rhizospheric soils. MBC, BR rate, and enzyme activities of the metal polluted soil, especially the rhizospheric soils increased with phytoextraction process, which is attributed to the stimulation of soil microbes by planting as well as the decrease in soil-soluble metal concentration.     

菌肥对青稞根际土壤理化性质以及微生物群落的影响

应用化学分析、聚合酶链反应-变性梯度凝胶电泳(PCR-DGGE)技术和DNA测序技术,研究了西藏棕色砂壤土中微生物肥料不同施用量和施用期对青稞根际土壤理化性质和细菌群落多样性的影响。结果表明,施用谷特菌肥能显著提高土壤全氮、全磷、全钾、有机质、碱解氮、有效磷和速效钾的水平,如播前施用菌肥浓度750 ml hm-2的处理较不施用菌肥的处理上述指标分别提高13.32%、28.42%、16.20%、9.81%、21.36%、39.35%和30.48%,拔节期施用菌肥浓度2 250 ml hm-2的处理较不施用菌肥的处理分别提高7.25%、29.35%、18.04%、12.86%、15.90%、43.27%和53.99%。DGGE分析表明,相同施用方式中不同施用量土样中微生物的DGGE图谱相似。非加权组平均法(UPGMA)聚类分析将DGGE图谱分为2大类群。Shannon-Wiener指数表明,施用菌肥的土壤细菌多样性先增加后逐渐降低,播前以喷施谷特菌浓度750 ml hm-2时的细菌多样性最高;拔节期则以喷施谷特菌浓度2 250 ml hm-2处理的细菌多样性最高,且两种施用方式土壤养分的释放与Shannon指数的变化规律均为播前﹥拔节期。测序结果表明,不同施肥浓度土样微生物种群分布较为广泛,其中Actinobacteria纲细菌种类略多,少数菌种为未经培养菌种(Uncultured bacterium)。典型对应分析(CCA)表明,DGGE图谱条带分布与土壤理化性质密切相关,碱解氮、全磷和全氮是影响微生物群落的主要环境因子。研究结果表明,施用谷特菌肥可明显改善青稞根际土壤理化性状,提高土壤细菌多样性。     

Estimating microbial biomass N in soils with and without living roots: Limitations of a pre-extraction step

Special net-closed soil containers were used in a pot experiment with low and high plant densities to give soil samples with and without roots. Soils from the containers were analysed either by the fumigation-extraction method or by a modified procedure starting with a pre-extraction and sieving step to remove plant roots from the samples. In the extracts NO ₃ ^- -N, NH ₄ ⁺ -N, organic N, and total N were measured. Microbial biomass N was calculated from the differences in total N in fumigated and unfumigated soils. Different plant densities had almost no influence on the values of the N compounds using either method. In soils with roots, significantly more organic N (and total N) was found by the fumigation-extraction method compared to soils without roots while no differences were obtained using pre-extractions and sieving. Though the organic N content in pre-extracts from soils with roots was significantly higher than from soils without roots, the NO ₃ ^- -N and NH ₄ ⁺ -N content was lower. Significant differences in biomass N in soils with and without roots were found only with the fumigation-extraction method. Biomass N levels calculated using the results after pre-extraction and sieving were about 50% lower than levels detected using fumigation-extraction alone. With the use of special net-closed soil containers, not only were soil samples produced with and without roots, but it was also possible to induce a rhizophere in the soils. A comparison of the two methods using these soils clearly demonstrated that the method used has profound influence on the final biomass N results. While higher biomass levels were found by fumigation-extraction in soils with roots, because root N becomes extractable after fumigation, the use of a pre-extraction and a sieving step may underestimate the total biomass N content due to the pre-extraction of microbial N (especially from rhizosphere microorganisms) from the sample. Nevertheless, pre-extraction and sieving followed by fumigation-extraction does seem to be the preferable method for biomass N measurement in comparative studies, because in most cases only minor errors will occur.     

Growth,P uptake and rhizosphere properties of wheat and canola genotypes in an alkaline soil with low P availability

The aim of the present study was to assess the role of soil type on growth, P uptake and rhizosphere properties of wheat and canola genotypes in an alkaline soil with low P availability. Two wheat (Goldmark and Janz) and two canola genotypes (Drum and Outback) were grown in a calcareous soil (pH 8.5) at two P levels [no P addition (0P) or addition of 200 mg kg⁻¹ P as Ca₃(PO₄)₂ (200P)] and harvested at flowering or maturity. Shoot and root dry weight, root length and shoot P content were greater in the two canola genotypes than in wheat. There were no consistent differences in available P, microbial P and phosphatase activity in the rhizosphere of the different genotypes. Shoot P content was significantly positively correlated with root length, pH and phosphatase activity in the rhizosphere. The microbial community composition, assessed by fatty acid methylester analysis, of the canola genotypes differed strongly from that of the wheat genotypes. The weight percentage bacterial fatty acids, the bacteria/fungi (b/f) ratio and the diversity of fatty acids were greater in the rhizosphere of the canolas than in the rhizosphere of the wheat genotypes. In contrast to the earlier studies in an acidic soil, only small differences in growth and P uptake between the genotypes of one crop were detected in the alkaline soil used here. The results confirmed the importance of root length for P uptake in soils with low P availability and suggest that the rhizosphere microbial community composition may play a role in the better growth of the canola compared to the wheat genotypes.     

Growth, P uptake and rhizosphere properties of intercropped wheat and chickpea in soil amended with iron phosphate or phytate

Intercropping has been shown to increase total yield and nutrient uptake compared to monocropping. However, depending on crop combinations, one crop may dominate and decrease the growth of the other. Interactions in the soil, especially in the rhizosphere, may be important in the interactions between intercropped plant genotypes. To assess the role of the rhizosphere interactions, we intercropped a P-inefficient wheat genotype (Janz) with either the P-efficient wheat genotype (Goldmark) or chickpea in a soil with low P availability amended with 100 mg P kg⁻¹ as FePO₄ (FeP) or phytate. The plants were grown for 10 weeks in pots where the roots of the genotypes could intermingle (no barrier, NB), were separated by a 30 μm mesh (mesh barrier, MB), preventing direct root contact but allowing exchange of diffusible compounds and microorganisms, or were completely separated by a solid barrier (SB). When supplied with FeP, Janz intercropped with chickpea had higher shoot and grain dry weight (dw) and greater plant P uptake in NB and MB than in SB. Contact with roots of Janz increased shoot, grain and root dw, root length, shoot P concentration and shoot P uptake of chickpea compared to SB. Root contact between the two wheat genotypes, Janz and Goldmark, had no effect on growth and P uptake of Janz. Shoot and total P uptake by Goldmark were significantly increased in NB compared to MB or SB. In both crop combinations, root contact significantly increased total plant dw and P uptake per pot. Plant growth and P uptake were lower with phytate and not significantly affected by barrier treatment. Differences in microbial P, available P and phosphatase activity in the rhizosphere among genotypes and barrier treatments were generally small. Root contact changed microbial community structure (assessed by fatty acid methyl ester (FAME) analysis) and all crops had similar rhizosphere microbial community structure when their roots intermingled.     

铅胁迫下接种AM真菌对龙葵根际土壤微生物群落代谢特征的影响

为从微生态角度探索接种AM真菌对铅污染根际土壤微生物群落代谢特征的影响,以摩西管柄囊霉（Funneliformis mosseae）和幼套近明囊霉（Claroideoglomus etunicatum）为接种菌剂,在温室盆栽条件下以Pb⁴⁺含量为0 mg·kg^-1、200 mg·kg^-1、400 mg·kg^-1和800 mg·kg^-1土壤种植龙葵（Solanum nigrum）10周后采集根际土壤,采用Biolog微平板法测定龙葵根际土壤微生物群落的代谢变化。结果表明：1）微生物平均代谢活性（AWCD）随铅浓度增加呈降—升—降趋势;接种AM真菌显著提高了铅胁迫下根际土壤微生物的AWCD值,仅中浓度（400 mg·kg^-1）下未达显著差异。2）中浓度铅处理能显著提高根际土壤微生物对糖类及其衍生物、氨基酸类、脂肪酸和脂类及代谢产物类四大类碳源底物利用能力;接种AM真菌,高浓度（800 mg·kg^-1）铅处理显著提高了根际土壤微生物对氨基酸类底物的利用能力。3）铅胁迫下接种AM真菌提高了根际土壤微生物多样性指数,在中浓度下丰富度指数、Shannon-Wiener多样性指数、Simpson优势度指数均达显著水平。4）主成分分析显示,代谢产物类在PC1和PC2中种类最多,分别为6种和4种;糖类及其衍生物在PC3中种类最多（5种）。5）在铅胁迫和接种AM真菌共同作用下,微生物碳源利用主要受铅浓度调节,并且二者对微生物碳源利用具有显著交互效应。综上可知,接种AM真菌能够提高铅胁迫下龙葵根际土壤微生物多样性指数,增强根际土壤微生物对碳源底物的利用能力。该研究为进一步探究AM真菌强化植物联合修复技术提供了依据。     

Changes in microbial biomass and microbial activity of pig slurry after the transit through the gut of the earthworm Eudrilus eugeniae (Kinberg, 1867)

Here we studied the effects of gut transit through the earthworm Eudrilus eugeniae, on the physicochemical, biochemical, and microbial characteristics of pig slurry, by analyzing fresh casts. The reduction in the dissolved organic C contents in casts we recorded suggests that during digestion, earthworms assimilated labile organic C preferentially, which is a limiting growth factor for them. Furthermore, both microbial biomass and activity in pig slurry were significantly decreased by earthworm gut transit. It appears that E. eugeniae is able to digest microorganisms, although the addition of glucose to the food increased respiration, indicating that growth of microorganisms in casts could be limited by depletion of labile C. Despite reduced microbial biomass and activity, the metabolic diversity of microbial communities was greater in casts than in original pig slurry. Community level physiological profiles obtained from Biolog Ecoplate data revealed that, after earthworm gut transit, the microbial communities in casts and pig slurry were clearly differentiated by their physiological profiles. The results indicate that first stage in vermicomposting of pig slurry by E. eugeniae, i.e., casting, produced changes that will influence the dynamics of the organic matter degradation by reducing forms of N and C available to microorganisms, hence restricting their growth and multiplication. Nevertheless, the reduced microflora of casts was characterized by an increased catabolic potential that might lead to thorough degradation of pig slurry.     

Changes in the microbial activity of an arid soil amended with urban organic wastes

Changes produced in the biological characteristics of an arid soil by the addition of various urban wastes (municipal solid waste, sewage sludge and compost) at different doses, were evaluated during a 360-day incubation experiment. The addition of organic materials to the soil increased the values of biomass carbon, basal respiration, biomass C/total organic C ratio and metabolic quotient (qCO₂), indicating the activation of soil microorganisms. These biological parameters showed a decreasing tendency with time. Nevertheless, their values in amended soils were higher than in control soil, which clearly indicates the improvement of soil biological quality brought about by the organic amendment. This favorable effect on soil biological activity was more noticeable with the addition of fresh wastes (municipal solid waste or sewage sludge) than with compost. In turn, this effect was more permanent when the soil was amended with municipal solid waste than when it was amended with sewage sludge. Received: 28 May 1996     

Spatio-temporal variability of microbial abundance and community structure in the puddled layer of a paddy soil cultivated with wetland rice (Oryza sativa L.)

The puddled layer of paddy soils represents a highly dynamic environment regarding the spatio-temporal variability of biogeochemical conditions. To study these effects on the abundance and community structure of microbial populations, a rhizotron experiment was conducted throughout an entire growing season of wetland rice. Soil samples were taken from selected areas of the puddled layer (bulk soil, oxidized layer, rhizosphere) at main plant developmental stages such as (i) the initial stage, (ii) tillering, (iii) panicle initiation, (iv) flowering, and (v) maturity. Cell numbers of archaea, bacteria, and selected phyla were assessed by catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). The structure and diversity of microbial communities was analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) along with sequencing of selected bands. Following submergence of the paddy soil, shifts of bacterial community structure were observed in the oxidized layer and the rhizosphere. Members of the β-Proteobacteria became predominant in the rhizosphere at tillering stage and were affiliated with aerobic, iron-oxidizing bacteria of the genus Sideroxydans. Seasonal effects were mainly visible in the rhizosphere, as several phylogenetic subgroups including methanotrophic bacteria showed increased cell numbers at flowering stage. Cell numbers of methanogenic archaea were also highest at flowering stage (bulk soil, rhizosphere) and members of the Methanocellales were identified as predominant archaeal populations in areas of oxic and anoxic conditions. In contrast to bacteria, the communities of archaea in the puddled layer of the studied paddy soil were less influenced by spatio-temporal variations of biogeochemical conditions.     

Changes in microbial communities and carbohydrate profiles induced by the mycorrhizal fungus (Glomus intraradices) in rhizosphere of olive trees (Olea europaea L.)

The influence of inoculation of olive trees with arbuscular mycorrhizal (AM) fungi, Glomus (G) intraradices, on microbial communities and sugar concentrations, were examined in rhizosphere of olive trees (Olea europaea L.). Analyses of phospholipid and neutral lipid fatty acids (PLFA and NLFA, respectively) were then used to detect changes in microbial community structure in response to inoculation of plantlets with G. intraradices.Microscopic observations studies revealed that the extraradical mycelium of the fungus showed formation of branched absorbing structures (BAS) in rhizosphere of olive tree. Root colonization with the AM fungi G. intraradices induced significant changes in the bacterial community structure of olive tree rhizosphere compared to non-mycorrhizal plants. The largest proportional increase was found for the fatty acid 10Me18:0, which indicated an increase in the number of actinomycetes in mycorrhizal rhizosphere soil, whereas the PLFAs i15:0, a15:0, i16:0, 16:1ω7 and cy17:0 which were used as indicators of bacteria decreased in mycorrhizal treatment compared to non-mycorrhizal control treatment. A highest concentration of glucose and trehalose and a lowest concentration of fructose, galactose, sucrose, raffinose and mannitol were detected in mycorrhizal rhizosphere soil. This mycorrhizal effect on rhizosphere communities may be a consequence of changes in characteristics in the environment close to mycorrhizal roots.     

Changes in chemical and biological soil properties as induced by anthropogenic disturbance: A case study of an agricultural soil under recurrent flooding by wastewaters

Monitoring the environmental impact of anthropogenic disturbance on soil ecosystem is of great importance for optimizing strategies for soil use, conservation and remediation. The aim of this study was to assess whether and to what extent a long-term, human-induced disturbance could have affected main chemical and biological properties in an agricultural soil. The study site was a hazel (Corylus avellana L.) orchard located in the area surrounding the volcanic apparatus of Somma-Vesuvius (Southern Italy). For the last two decades, the site has been repeatedly subjected to floodings by wastewaters containing not only alluvial sediments but also potentially hazardous compounds from illegally disposed wastes. Soil disturbance was assessed by a multitechnique approach, which combined chemical, biochemical and physiological (Biolog^®) methods together with community fingerprinting by denaturing gradient gel electrophoresis (DGGE) and amplified ribosomal DNA restriction analysis (ARDRA). A hazel site never subjected to flooding provided the control soil. Soil sampling was repeated three times over a 1-year period. The effect of flooding by wastewaters, sampling time and their interaction were statistically evaluated. Under wastewater flooding, soil pH and most organic matter-related pools, i.e. total organic C, total N, and active soil C-resources such as basal (SBR) and substrate-induced respiration (SIR) and microbial biomass C (MBC) were all increased; whereas sampling time mostly affected two active-N pools, namely K₂SO₄-extractable N (Extr-N) and potentially mineralizable N that varied unconcurrently in tested soils. Also the electrical conductivity varied across samplings. Parameters related to microbial maintenance energy (ATP and qCO₂) were higher in the flooded soil, even though they were not statistically affected by wastewater flooding or by sampling time. The Biolog^® method evidenced that under recurrent flooding, soil microbial populations became functionally more uniform when compared to the control soil. Molecular fingerprinting of PCR-amplified 16S rDNA targets revealed that, along with seasonal shifts, a marked change in the genetic structure of total bacterial community occurred in the flooded soil. Furthermore, compositional shifts in the actinomycete community were less marked and mostly influenced by seasonal effects. Yet, a decreased genetic diversity in the ammonia-oxidizing bacteria community was evidenced in the flooded soil by ARDRA. Thus both the genetic and the functional structure of native soil bacterial populations were changed under repeated flooding by wastewaters. Repeated sampling over a 1-year period allowed us to reveal soil disturbance effects beyond seasonal variations.     

Denitrification in the rhizosphere of plants with inherently different aerenchyma formation: Wheat (Triticum aestivum) and rice (Oryza sativa)

Summary Denitrification in the rhizosphere of wheat and rice was studied in relation to aerenchyma formation. Seedlings were grown in quartz silt amended with mineral nutrients at given bulk densities and water tensions. In adventitious wheat roots the formation of cortical lacunae was strongly dependent on soil aeration. Growing the wheat plants in dry (–20 kPa) and moist substrate (–2 kPa) established aerenchyma contents of 3% and 15%, respectively. Denitrification was measured after the introduction of equal moisture levels in the substrates of both treatments. The higher aerenchyma content of roots pregrown in the wetter substrate did not counteract denitrification in the rhizosphere which had doubled in this treatment. In contrast to the unspecific lysis of cortical cell walls, the well organized formation of aerenchyma in rice roots was independent of soil aeration. Root porosity averaged 14%. As in wheat, it was not related to denitrification. However, the level of denitrification per mg of root dry matter was about four times lower than that of wheat. The addition of decomposable organic matter (cellulose) to the substrate stimulated aerenchyma formation in rice and considerably increased denitrification. The results suggest that denitrification in the rhizosphere is independent of aerenchyma formation.     

Comments on the paper by Kemmitt et al. (2008) ‘Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass - A new perspective’ [Soil Biology & Biochemistry 40, 61-73]: The biology of the Regulatory Gate

Kemmitt et al. (Kemmitt, S.J., Lanyon, C.V., Waite, I.S., Wen, Q., Addiscott, T.M., Bird, N.R.A., O'Donnell, A.G., Brookes, P.C., 2008. Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass - a new perspective. Soil Biology & Biochemistry 40, 61-73) recently proposed the “Regulatory Gate” hypothesis, which states that decomposition of soil organic matter (SOM) is regulated solely by abiotic factors. Without studying the mechanisms of such regulation, Kemmitt with coauthors challenged the classical Winogradsky theory of soil microbiology and questioned the concept of autochtonous and zymogenous microbial populations. In this letter, we revive the significance of microbial activity for SOM decomposition especially for the short-term (hours to weeks) processes and show that the “Regulatory Gate” is (micro)biologically driven.We explain the results of the three experiments in Kemmitt et al. (2008) from a microbiological point of view and suggest that SOM decomposition is mainly regulated by exoenzymes. We criticize the abiotic Regulatory Gate hypothesis based on bottleneck processes and pools limiting the SOM decomposition rate, comparison of constant and changing environmental conditions, as well as the connection between community structure and functions. We explain the results of Kemmitt et al. (2008) according to the properties of soil microbial community: functional redundancy and inconsistency between the excessive (but largely inactive) pool of total microbial biomass and the real mineralization activity. Finally, we suggest that to gain new perspectives on SOM decomposition and many other biochemical processes, future studies should focus on hot spots of (micro)biological activity (i.e., the rhizosphere, drillosphere, detritosphere, biopores, etc.) rather than on the bulk soil.     

Changes in recovery of native and applied phosphorus with time as affected by soil properties in some calcareous soils

In an attempt to investigate variations in availability of native and applied phosphorus (P) with time, twenty five calcareous soil samples were treated with 0, 50 and 500 mg P kg^?1 soil and incubated at 80–90% of field capacity moisture content in an open door glasshouse for a period of one year. Soil samples were taken out at certain intervals for P extraction with Olsen extractant under moist condition. Results indicated that following wetting the mean value of native Olsen-P decreased initially and then increased gradually with time of incubation. Generally, the short term (24 h) recoveries were not correlated with long term ones. The recovery of added P with time was described properly by the following new proposed model: R = 100/(1 + kt^b), where R is percent recovery at time t, and k and b are empirical parameters. The values of k constant at 50 and 500 mg P kg^?1 were in the ranges of 0.40 to 1.22 (0.84 ± 0.25, on average) and 0.04 to 0.52 (0.23 ± 0.14, on average), respectively. The corresponding respective values of b constant also ranged from 0.05 to 0.32 (0.15 ± 0.06, on average) and 0.12 to 0.92 (0.46 ± 0.23, on average).     

Microcalorimetric study of changes in the microbial activity in a humic Cambisol after reforestation with eucalyptus in Galicia (NW Spain)

The microcalorimetric technique was used to analyse the influence of successive reforestations with Eucalyptus globulus Labill, a fast growing species, on the microbial activity in soil. With this aim, samples of similar origin soils, humic-eutrophic Cambisol, were collected from two adjacent land plots. One of the plots, to be taken as the reference, was not subjected to man activities for the last 100 years. The other plot was subjected to two reforestations in the last 20 years. For collection of the two samples, 100 m² homogeneous and perfectly defined zones were chosen in each of the adjacent land plots to obtain final representative bulk samples of 400 g each.The study was carried out using the microbial population as a bioindicator of the productive potential in soil. The experiments were carried out using 1 g soil samples that were treated with 1.25 mg glucose and stored at 4 °C for 3 months. The analysis was complemented by the determination of physical, chemical, and biological properties and environmental parameters.The study was performed over 1 year and samples were seasonally collected (spring, summer, autumn and winter) in the same zone situated in Viveiro (Galicia, NW Spain) with the objective of checking the influence of environmental conditions on the microbial activity in the two soils studied.From the measured results, it can be observed that soils subjected to reforestations suffer not only important changes in physical structure, such as an increase in bulk density, from 600 to 660 kg m⁻³, a reduction in hydraulic conductivity, from 8.85×10⁻³ to 4.4×10⁻³ m s⁻¹, or a decrease in the C-to-N ratio, from 13 to 8, but also they have lower microbial activity, for example 2.84 J g⁻¹ in the reforested soil versus 6.14 J g⁻¹ in the reference soil, in spring, thus presenting a lower productive potential that suggests the use of both amendments and adequate management techniques to ensure a sustainable exploitation, thus avoiding future degradation of soil.     

Continuous defoliation of perennial ryegrass (Lolium perenne) and white clover (Trifolium repens) and associated changes in the composition and activity of the microbial population of an upland grassland soil

A microcosm study was conducted to investigate the effect of continuons plant defoliation on the composition and activity of microbial populations in the rhizosphere of perennial ryegrass (Lolium perenne) and white clover (Trifolium repens). Continuons defoliation of ryegrass and clover resulted in sigmficant (P <0.01) increases in soil microbial biomass, although whilst increases were measured from day 2 in soil sown with clover significant increases were only seen from day 21 in soil sown with ryegrass. These increases were paralleled, from day 10 onwards, by increases in the numbers of culturable bacteria. Numbers ofPsendomonas spp. also increased in the later stages of the study. No influence on culturable fungal populations was detected. Whilst shifts in the composition of the microbial populations were measured in response to defoliation there was little effect on microbial activity. No changes in either dehydrogenase activity or microbial respiration in the rhizosphere of ryegrass or clover were measured in response to defoliation, but both dehydrogenase activity and microbial respiration were greater in ryegrass than clover when values over the whole study were combined. Continuous defoliation resulted in significant (P <0.001) reductions in the root dry weight of ryegrass and clover, of the order 19% and 16%, respectively.     

Efficacy of an artificial microbial siderophore-Fe(III) with high redox potential on correcting Fe chlorosis in rice

ABSTRACT

Microbial siderophore-chelated Fe(III) is suggested to be an important source of Fe for plants, although it is hardly reduced by plant roots. Here, we investigated the efficacy of the easily reducible artificial microbial siderophore tris[2-{(N-acetyl-N-hydroxy)glycylamino}ethyl]amine (TAGE)-Fe(III) as an alternative Fe source to correct Fe deficiency in rice plants, and compared it to that of the natural siderophore deferoxamine B (DFOB)-Fe(III). We also evaluated the absorption of Fe from TAGE-Fe(III) by the Strategy I-like system of gramineous plants using nicotianamine aminotransferase 1 (naat1) mutant rice, which does not synthesize phytosiderophores. Fe(III)-siderophores were synthesized in vitro. Nipponbare rice and its naat1 mutant were reared in soil and gel cultures to determine Fe availability. Hydroponically grown naat1 mutant seedlings were used for reducibility assays to determine the ability of rice roots to reduce Fe(III) chelated by TAGE or DFOB. The expression of a Fe-deficiency inducible gene was also determined, as well as chlorophyll and Fe concentrations. Reduci bility assays on naat1 mutant seedlings revealed that the reduction level of TAGE-Fe(III) was approximately three times higher than that of DFOB-Fe(III). Application of TAGE-Fe(III) to both culture medium and alkaline soil improved Fe chlorosis, growth, and Fe concentration in both naat1 and wild type plants, whereas application of DFOB-Fe(III) only did so in wild type plants. Easily reducible Fe(III)-chelates such as TAGE-Fe(III) can be a better source of Fe for rice plants than most natural microbial siderophores-Fe(III). Our study also demonstrated that rice plants have the ability to utilize microbial siderophores-Fe(III) as the Fe source through the Strategy I-like Fe acquisition system.     

Toxicity of chemical warfare agent HD (mustard) to the soil microinvertebrate community in natural soils with contrasting properties

A microcosm technique was used to determine the ecotoxicity of the chemical warfare agent HD (mustard) to the indigenous soil microinvertebrate communities. HD was thoroughly incorporated into Sassafras sandy loam (SSL) soil (4.9% OM) and an oak-beech forest silt loam soil (FS, 16% OM) at nominal HD concentrations ranging from 6 to 1076 mg kg⁻¹. After a 7-day incubation period, microarthropods were extracted from soils using a high-gradient extractor and sorted to Acari suborders Prostigmata, Mesostigmata, and Oribatida, and the insect order Collembola. Nematodes were extracted using Baermann funnels and were sorted into bacterivore, herbivore, fungivore and omnivore/predator trophic groups. Microarthropods were more sensitive to HD in both soil types compared with nematodes. The EC₅₀ values for total numbers of microarthropods in SSL and FS were similar (65 and 71 mg kg⁻¹, respectively). The EC₅₀ values for total numbers of nematodes were 130 and 235 mg kg⁻¹, respectively. Toxicity of HD to nematodes was significantly greater in SSL soil compared to FS, based on 95% confidence intervals. Results show that community-level assessment of chemical toxicity in soil using a microcosm assay is sufficiently robust and can provide the means for validating the ecotoxicity data from standardized laboratory single-species toxicity tests.     

Evaluation of an optimal extraction method for measuring d-ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) in agricultural soils and its association with soil microbial CO2 assimilation

Assimilating atmospheric carbon (C) into terrestrial ecosystems is recognized as a primary measure to mitigate global warming. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is the dominant enzyme by which terrestrial autotrophic bacteria and plants fix CO₂. To investigate the possibility of using RubisCO activity as an indicator of microbial CO₂ fixation potential, a valid and efficient method for extracting soil proteins is needed. We examined three methods commonly used for total soil protein extraction. A simple sonication method for extracting soil protein was more efficient than bead beating or freeze–thaw methods. Total soil protein, RubisCO activity, and microbial fixation of CO₂ in different agricultural soils were quantified in an incubation experiment using ¹⁴C-CO₂ as a tracer. The soil samples showed significant differences in protein content and RubisCO activity, defined as nmol CO₂ fixed g⁻¹ soil min⁻¹. RubisCO activities ranged from 10.68 to 68.07 nmol CO₂ kg⁻¹ soil min⁻¹, which were closely related to the abundance of cbbL genes (r = 0.900, P = 0.0140) and the rates of microbial CO₂ assimilation (r = 0.949, P = 0.0038). This suggests that RubisCO activity can be used as an indicator of soil microbial assimilation of atmospheric CO₂.