Bacterial community structure and microbial activity in different soils amended with biogas residues and cattle slurry

Anaerobic digestion of organic materials generates residues of differing chemical composition compared to undigested animal manures, which may affect the soil microbial ecosystem differently when used as fertilizers. This study investigated the effects of two biogas residues (BR-A and BR-B) and cattle slurry (CS) applied at rates corresponding to 70 kg NH₄⁺-N ha⁻¹ on bacterial community structure and microbial activity in three soils of different texture (a sandy, a clay and an organic clay soil). 16S rRNA genes were targeted in PCR reactions and bacterial community profiles visualized using terminal restriction fragment length polymorphism. General microbial activity was measured as basal respiration (B-resp), substrate-induced respiration (SIR), specific growth rate (μ_SIR), metabolic quotient (qCO₂) and nitrogen mineralization capacity (NMC). Non-metric multidimensional scaling analysis visualized shifts in bacterial community structure related to microbial functions. There were significant differences in bacterial community structure after 120 days of incubation (+20 °C at 70% of WHC) between non-amended (control) and amended soils, especially in the sandy soil, where CS caused a more pronounced shift than biogas residues. Terminal-restriction fragment (TRF) 307, the predominant peak in CS-amended sandy soil, was identified as possibly Bacillus or Streptococcus. TRF 226, the dominant peak in organic soil amended with BR-B, was classified as Rhodopseudomonas. B-resp significantly increased and SIR decreased in all amendments to organic soil compared with the control, potentially indicating decreased efficiency of heterotrophic microorganisms to convert organic carbon into microbial biomass. This was also reflected in an elevated qCO₂ in the organic soil. The μ_SIR level was higher in the sandy soil amended with BR-A than with BR-B or CS, indicating a shift toward species capable of rapidly utilizing glucose. NMC was significantly elevated in the clay and organic soils amended with BR-A and BR-B and in the sandy soil amended with BR-B and CS. Thus, biogas residues and cattle slurry had different effects on the bacterial community structure and microbial activity in the three soils. However, the effects of biogas residues on microbial activities were comparable in magnitude to those of cattle slurry and the bacterial community structure was less affected. Therefore, we do not see any reason not to recommend using biogas residues as fertilizers based on the results presented.     

Effect of litter quality and soil fungi on macroaggregate dynamics and associated partitioning of litter carbon and nitrogen

We investigated the effect of plant residue decomposability and fungal biomass on the dynamics of macroaggregate (250–2000 μm) formation in a three months' incubation experiment and determined the distribution of residue-derived C and N in the microbial biomass and in aggregate size fractions (250–2000 μm, 53–250 μm and <53 μm) using ¹³C and ¹⁵N data. A silty loam soil (sieved <250 μm) was incubated with and without addition of ¹⁵N labelled maize leaves (C/N = 27.4) and roots (C/N = 86.4). Each treatment was carried out with and without fungicide application. The addition of maize residues enhanced soil respiration and microbial biomass C and N and resulted in increased macroaggregate formation with a higher and more rapid maximum macroaggregation in the soil amended with maize leaves than in that with addition of roots. Fungicide application led to a significant decline of microbial biomass C and mineralization of the added residues compared to untreated soils, which demonstrates a successful suppression of part of the active microbial biomass by the fungicide. However, this was not confirmed by a generally lower ergosterol concentration. Consequently, ergosterol was no reliable fungal biomarker in periods of rapid decline of the fungal biomass. A single addition of fungicide was insufficient for continued inhibition of the fungal biomass. Yet, a significant delay (28–42 days) in macroaggregation in fungicide treated compared to untreated samples highlighted the importance of the fungal biomass in macroaggregate formation. Macroaggregates were enriched in maize-derived ¹³C and ¹⁵N compared to microaggregates or the fraction < 53 μm. They turned over rapidly with decreasing substrate availability, which entailed a transfer of maize-derived C and N stored within macroaggregates during the first weeks of incubation to microaggregates with proceeding incubation time. Our results indicate that this transfer happened within macroaggregates, because no considerable amount of free particulate organic matter (POM) was released upon macroaggregate breakdown. We conclude that substrate decomposability and fungal activity are key factors determining extent and dynamics of macroaggregation during decomposition processes. Macroaggregate formation implied rapid incorporation and thereby short-term protection of maize-derived C and N. Moreover, macroaggregates allowed a transfer of maize-derived organic matter into microaggregates within macroaggregates, which prevented the release of significant amounts of free POM upon macroaggregate breakdown. Consequently, macroaggregates constitute to the transfer of recently added C into more stable soil organic matter fractions.     

Effects of mercury on soil microbial communities in tropical soils of French Guyana

In gold mining regions, the risk of soil pollution by mercury is a major environmental hazard, especially in tropical areas where soil microflora plays a major part in soil functioning, major bio-geochemical cycles and carbon turn-over. The impact of mercury pollution on soil microflora should thus be carefully assessed in such environments while taking into consideration the specificities of tropical soils. The aim of this study was to compare the effects of mercury (0, 1 and 20 μg of inorganic mercury per gram of soil) on the functional diversity and genetic structure of microbial communities in a tropical soil. We investigated the effects of mercury on tropical soil microflora using soil microcosms spiked with mercury and incubated at 28 °C for 1 month. Microcosm flora, its biomass and its activity, as well as its functional and genetic structure, were followed by cultural methods, measures of respiration, ECOLOG plates, and DGGE (denaturing gel gradient electrophoresis), respectively. Fate of total and bioavailable mercury was estimated by CVAFS (cold vapor atomic fluorescence spectrometry). Results obtained for the microcosms enriched with only 1 μg g^?1 mercury were indistinguishable from controls. Conversely, in the presence of high mercury contents (20 μg g⁽¹), an immediate effect was measured on soil respiration, functional diversity (ECOLOG plates) and genetic structure (DGGE), although no significant effect was observed on plate counts or microbial biomass. In addition, whereas microbial activities (respiration and functional diversity) rapidly regained control values, a lasting effect of the high mercury concentration was observed on the genetic structure of the soil microbial community. These modifications took place during the first week of incubation when total mercury concentration was declining and bioavailable mercury was at its highest.This multiple approach study is one of the first attempts at investigating the effects of mercury on soil microbial communities in tropical soils. Our results demonstrate that in the tropical soil under study, mercury affects the soil microbial communities in a different manner than was previously reported in temperate soils. Furthermore, mercury toxicity on soil microbes may be modulated by typical tropical soil characteristics.     

Effects of ecological restoration on microbial activity,microbial functional diversity,and soil organic matter in mixed-oak forests of southern Ohio,USA

As a result of many decades of fire suppression and atmospheric deposition the deciduous forests of eastern North America have changed significantly in stem density, basal area, tree size-frequency distribution, and community structure. Consequently, soil organic matter quality and quantity, nutrient availability, and microbial activity have likely been altered. This study evaluated the effects of four alternative forest ecosystem restoration strategies on soil microbial activity, microbial functional diversity, soil organic C, and soil N status in two mixed-oak (Quercus spp.) forests in southern Ohio, USA. The soils of these forests were sampled during the fourth growing season after application of (1) prescribed fire, (2) thinning of the understory and midstory to pre-settlement characteristics, (3) the combination of fire and thinning, and (4) an untreated control. Prescribed fire, with or without thinning, resulted in increased bacterial but not fungal activity when assessed using Biolog^®. In contrast, assays of acid phosphatase and phenol oxidase activity indicated greater microbial activity in the thinning treatment than in the other three treatments. Functional diversity of both bacteria and fungi was affected by restoration treatment, with the bacterial and fungal assemblages present in the thin + burn sites and the fungal assemblage present in the thinned sites differing significantly from those of the control and burned sites. Treatments did not result in significant differences in soil organic C content among experimental sites; however, the soil C:N ratio was significantly greater in thinned sites than in sites given the other three treatments. Similarly, there were no significant differences in dissolve inorganic N, dissolved organic N, or microbial biomass N among treatments. Bacterial and fungal functional diversity was altered significantly. Based on Biolog^® utilization treatments the bacterial assemblage in the thin-only treatment appeared to be relatively N-limited and the fungal assemblage relatively C-limited, whereas in the thin + burn treatment this was reversed. Although effects of restoration treatments on soil organic matter and overall microbial activity may not persist through the fourth post-treatment year, effects on microbial functional diversity are persistent.     

Recovery of soil organic matter,organic matter turnover and nitrogen cycling in a post-mining forest rehabilitation chronosequence

Recovery of soil organic matter, organic matter turnover and mineral nutrient cycling is critical to the success of rehabilitation schemes following major ecosystem disturbance. We investigated successional changes in soil nutrient contents, microbial biomass and activity, C utilisation efficiency and N cycling dynamics in a chronosequence of seven ages (between 0 and 26 years old) of jarrah (Eucalyptus marginata) forest rehabilitation that had been previously mined for bauxite. Recovery was assessed by comparison of rehabilitation soils to non-mined jarrah forest references sites. Mining operations resulted in significant losses of soil total C and N, microbial biomass C and microbial quotients. Organic matter quantity recovered within the rehabilitation chronosequence soils to a level comparable to that of non-mined forest soil. Recovery of soil N was faster than soil C and recovery of microbial and soluble organic C and N fractions was faster than total soil C and N. The recovery of soil organic matter and changes to soil pH displayed distinct spatial heterogeneity due to the surface micro-topography (mounds and furrows) created by contour ripping of rehabilitation sites. Decreases in the metabolic quotient with rehabilitation age conformed to conceptual models of ecosystem energetics during succession but may have been more indicative of decreasing C availability than increased metabolic efficiency. Net ammonification and nitrification rates suggested that the low organic C environment in mound soils may favour autotrophic nitrifier populations, but the production of nitrate (NO₃^?) was limited by the low gross N ammonification rates (≤1 μg N g^?1 d^?1). Gross N transformation rates in furrow soils suggested that the capacity to immobilise N was closely coupled to the capacity to mineralise N, suggesting NO₃^? accumulation in situ is unlikely. The C:N ratio of the older rehabilitation soils was significantly lower than that of the non-mined forest soils. However, variation in ammonification rates was best explained by C and N quantity rather than C:N ratios of whole soil or soluble organic matter fractions. We conclude that the rehabilitated ecosystems are developing a conservative N cycle as displayed by non-mined jarrah forests. However, further investigation into the control of nitrification dynamics, particularly in the event of further ecosystem disturbance, is warranted.     

Cultivation effects on temporal changes of organic carbon and aggregate stability in desert soils of Hexi Corridor region in China

Sustainable agricultural use of cultivated desert soils has become a concern in Hexi Corridor in Gansu Province of China, because loss of topsoil in dust storms has been recently intensified. We chose four desert sites to investigate the effects of cultivation (cropping) on (i) soil organic C and its size fractions and (ii) soil aggregate stability (as a measure of soil erodibility). These parameters are of vital importance for evaluating the sustainability of agricultural practices.Total organic C as well as organic C fractions in soil (coarse organic C, 0.1–2 mm; young organic C, 0.05–0.1 mm; stable organic C, <0.05 mm) generally increased with the duration of the cultivation period from 0 (virgin soil, non-cultivated) to more than 30 years (p < 0.05). Compared to total organic C in virgin soils (2.3–3.5 g kg⁻¹ soil), significantly greater values were found after 10 to >20 years of cultivation (6.2–7.1 g kg⁻¹ soil). The increase in organic C in desert soils following prolonged cultivation was mainly the consequence of an increase in the coarse organic C. The increase in total organic C in soil was also dependent on clay content [total organic C = 0.96 + 0.249 clay content (%) + 0.05 cultivation year, R² = 0.48, n = 27, p < 0.001]. This indicates that clay protected soil organic C from mineralization, and also contributed to the increase in soil organic C as time of cultivation increased.There was a significant positive correlation between aggregate stability and total organic C across all field sites. The water stability of aggregates was low (with water-stable aggregate percentage ∼4% of dry-sieved aggregates of size 1–5 mm). There was no consistent pattern of increase in the soil aggregate stability with time of cultivation at different locations, suggesting that desert soils might remain prone to wind erosion even after 50 years of cultivation. Alternative management options, such as retaining harvested crop residues on soil surface and excluding or minimizing tillage, may permit sustainable agricultural use of desert soils.     

Earthworm populations in relation to soil organic matter dynamics and management in California tomato cropping systems

Earthworms are key regulators of soil structure and soil organic matter (SOM) dynamics in many agroecosystems. They are greatly impacted by agricultural management, yet little is known about how these factors interact to control SOM dynamics. This study sought to explore linkages between agricultural management, earthworms and aggregate associated SOM dynamics through a survey of tomato (Solanum lycopersicum L.) cropping systems in northern California. Earthworms and soil samples were collected between February and April of 2005 from 16 fields under one of three types of residue management: (1) tomato mulch – no postharvest tillage and tomato residues left on the soil surface, (2) cover crop – tomato residues tilled in and leguminous cover crop planted, and (3) bare fallow – tomato residues tilled in and soil surface left exposed throughout the winter. Earthworms were collected via hand-sorting and identified to species, while soils were wet sieved to yield four aggregate size classes: large macroaggregates (>2000 μm), small macroaggregates (250–2000 μm), microaggregates (53–250 μm) and the silt and clay fraction (<53 μm). The combined large and small macroaggregate fraction was then fractionated into coarse particulate organic matter (cPOM; 250 μm), microaggregates within macroaggregates (mM; 53–250 μm) and macroaggregate occluded silt and clay (Msc; <53 μm). The earthworms identified in this survey were composed entirely of exotic species and were dominated by Aporrectodea caliginosa. Earthworm abundance was related to residue management, with the tomato mulch systems averaging 4.5 times greater fresh earthworm biomass than bare fallow (P = 0.024). Aggregate stability and total soil C and N also appeared to be influenced by residue management, such that the tomato mulch system displayed significantly greater mean weight diameters than the bare fallow system (P = 0.049), as well as more than 50% greater total soil C and N (P = 0.049 and P = 0.036; respectively). Earthworm biomass was also found to be positively correlated with total soil C (P = 0.009, R² = 0.39) and N (P = 0.010, R² = 0.039) as well as the proportion of macroaggregate C in the cPOM fraction (P = 0.028, R² = 0.30). Our findings suggest that residue handling and the associated management practices (e.g., tillage, organic vs. conventional agriculture) are important for both earthworm populations and SOM storage. Although earthworms are known to influence SOM in many ways, other factors appear to play a more prominent role in governing aggregate associated SOM dynamics.     

有机肥对棕壤不同粒级有机碳和氮的影响

采集棕壤长期肥料定位试验站不施肥和施用不同用量有机肥的土壤,通过超声波分散—离心分离得到细黏粒(<0.2μm)、粗黏粒(0.2～2μm)、粉粒(2～53μm)、细砂粒(53～250μm)和粗砂粒(250～2000μm)5个颗粒级别后,分析全土及不同粒级中土壤有机碳和氮并进行含量与分布的比较。结果表明,有机质主要分布于黏粒级中,其含量占全土有机碳的42.8%、全氮的58.3%,碳氮比随着粒级的增加而逐渐增大,表明氮易于在小粒级中富集。长期施用有机肥后,全土及各粒级有机碳和氮含量均有显著增加;砂粒级中有机碳和氮的富集系数升高,黏粒级中富集系数降低,粉粒级和砂粒级中的碳氮比降低。增加有机肥的用量加强了全土和各粒级对有机碳和氮的积累,同时加强了粉粒级和砂粒级碳氮比降低的程度。     

Effects of addition of maize litter and earthworms on C mineralization and aggregate formation in single and mixed soils differing in soil organic carbon and clay content

C mineralization and aggregate stability directly depend upon organic matter and clay content, and both processes are influenced by the activity of microorganisms and soil fauna. However, quantitative data are scarce. To achieve a gradient in C and clay content, a topsoil was mixed with a subsoil. Single soils and the soil mixture were amended with 1.0 mg maize litter C g soil⁻¹ with and without endogeic earthworms (Aporrectodea caliginosa). The differently treated soils were incubated for 49 days at 15 °C and 40% water holding capacity. Cumulative C mineralization, microbial biomass, ergosterol content and aggregate fractions were investigated and litter derived C in bulk soil and aggregates were determined using isotope analyses. Results from the soil mixture were compared with the calculated mean values of the two single soils. Mixing of soil horizons differing in carbon and clay content stimulated C mineralization of added maize residues as well as of soil organic matter. Mixing also increased contents of macro-aggregate C and decreased contents of micro-aggregate C. Although A. caliginosa had a stimulating effect on C mineralization in all soils, decomposition of added litter by A. caliginosa was higher in the subsoil, whereas A. caliginosa decreased litter decomposition in the soil mixture and the topsoil. Litter derived C in macro-aggregates was higher with A. caliginosa than with litter only. In the C poor subsoil amended with litter, A. caliginosa stimulated the microbial community as indicated by the increase in microbial biomass. Furthermore, the decrease of ergosterol in the earthworm treated soils showed the influence of A. caliginosa on the microbial community, by reducing saprotrophic fungi. Overall, our data suggest both a decrease of saprotrophic fungi by selective grazing, burrowing and casting activity as well as a stimulation of the microbial community by A. caliginosa.     

Rapid estimation of microbial biomass in grassland soils by ultra-violet absorbance

A reliable and simple technique for estimating soil microbial biomass (SMB) is essential if the role of microbes in many soil processes is to be quantified. Conventional techniques are notoriously time-consuming and unreproducible. A technique was investigated that uses the UV absorbance at 280 nm of 0.5 M K₂SO₄ extracts of fumigated and unfumigated soils to estimate the concentrations of carbon, nitrogen and phosphorus in the SMB. The procedure is based on the fact that compounds released after chloroform fumigation from lysed microbial cells absorb in the near UV region. Using 29 UK permanent grassland soils, with a wide range of organic matter (2.9–8.0%) and clay contents (22–68%), it was demonstrated that the increase in UV absorbance at 280 nm after soil fumigation was strongly correlated with the SMB C (r=0.92), SMB N (r=0.90) and SMB P (r=0.89), as determined by conventional methods. The soils contained a wide range of SMB C (412–3412 μg g⁻¹ dry soil), N (57–346 μg g⁻¹ dry soil) and P (31–239 μg g⁻¹ dry soil) concentrations. It was thus confirmed that the UV absorbance technique described was a rapid, simple, precise and relatively inexpensive method of estimating soil microbial biomass.     

The effect of glyphosate on soil microbial activity,microbial community structure,and soil potassium

The herbicide, glyphosate [N-(phosphonomethyl) glycine] is extensively used worldwide. Long-term use of glyphosate can cause micronutrient deficiency but little is known about potassium (K) interactions with glyphosate. The repeated use of glyphosate may create a selection pressure in soil microbial communities that could affect the nutrient dynamics such as K. The objective of this study was to determine the effect of single or repeated glyphosate applications on microbial and K properties of soils. A 54 day incubation study (Exp I) had a 3 × 5 factorial design with 3 soils (silt loam: fine, illitic, mesic Aeric Epiaqualf) of similar physical and chemical characteristics, that varied in long-term glyphosate applications (no, low, and high glyphosate field treatments) and five glyphosate rates (0, 0.5×, 1×, 2×, and 3× recommended field rates applied once at time zero). A second 6 month incubation study (Exp II) had a 3 × 3 factorial design with three soils (as described above) and three rates of glyphosate (0, 1×, and 2× recommended field application rates applied monthly). For each study microbial properties [respiration; community structure measured by ester linked fatty acid methyl ester (EL-FAME) analysis and microbial biomass K] and K fractions (exchangeable and non-exchangeable) were measured periodically. For Exp I, glyphosate significantly increased microbial respiration that was closely related to glyphosate application rate, most notably in soils with a history of receiving glyphosate. For Exp II, there was no significant effect of repeated glyphosate application on soil microbial structure (EL-FAME) or biomass K. We conclude that glyphosate: (1) stimulates microbial respiration particularly on soils with a history of glyphosate application; (2) has no significant effect on functional diversity (EL-FAME) or microbial biomass K; and (3) does not reduce the exchangeable K (putatively available to plants) or affect non-exchangeable K. The respiration response in soils with a long-term glyphosate response would suggest there was a shift in the microbial community that could readily degrade glyphosate but this shift was not detected by EL-FAME.     

The contribution from hyphae, roots and organic carbon constituents to the aggregation of a sandy loam under long-term clover-based and grass pastures

Water-stable macro-aggregate size fractions (>2.0 mm, 1.0–2.0 mm, 0.5–1.0 mm and 0.25–0.5 mm) and non-aggregated soil from a sandy loam under long-term clover-based pasture and from grass pasture were analysed to determine the role of acid- and water-extractable carbohydrate C, total hyphal length, microbial biomass, organic C and total and mycorrhizal root length in stabilization of the aggregates. Aggregates were examined by scanning electron microscopy (SEM) and the particle-size distribution of the size fractions was also determined. Macro-aggregation increased under grass, relative to clover-based pasture; however, the properties of the aggregate fractions measured did not reflect this difference. Microbial-biomass C, extractable-carbohydrate C, hyphal length, total and mycorrhizal root length and organic C content of the soils were poorly correlated with macro-aggregation. Within the aggregates, the proportion of 250–1000-km sand was smaller and clay, silt and fine sand (20–250 μm) were greater relative to non-aggregated soil, suggesting that the >250-μm sand in the non-aggregated soil limited the stabilization of macro-aggregates. Under SEM, no enmeshment of aggregates by hyphae and roots was apparent. Although 50–160 m hyphae g^?1 soil was found within the aggregates, calculations showed that on average only 5 to 13 lengths of hyphae were associated with each 250-μm cube of soil within the aggregates, and suggested little potential to stabilize the aggregates by enmeshing. On average, all >2.0-mm aggregates contained less than 3.6 mm of roots and less than 50% by weight of <2.0-mm aggregates contained a single length of root. The findings cast doubt about the role of hyphae and fine roots in the stabilization of macro-aggregates through an enmeshing mechanism in sandy soils.     

Texture and sesquioxide effects on water-stable aggregates and organic matter in some tropical soils

Many tropical soils include sesquioxides, which influence the stability of soil organic matter (OM) and aggregation to an extent that is not fully characterized. The present study was carried out on a range of 18 topsoil samples (0–10 cm) from low-activity clay (LAC) soils from sub-Saharan Africa and Brazil, and aimed: (i) at characterizing the size distributions of water-stable aggregates and organic constituents, (ii) at studying how these distributions were affected by texture and sesquioxides, and (iii) how they interacted.The distributions of stable aggregates were generally dominated by macroaggregates (> 200 μm), and those of organic constituents by fine OM (< 20 μm). Aggregation was not clearly affected by soil texture, while total soil carbon (Ct) and the amount of carbon (C) as fine OM increased with soil content in clay plus fine silts (< 20 μm). Stable macroaggregation correlated with Ct and with C amount as fine OM, but each of them correlated more closely with citrate-bicarbonate-dithionite-extractable aluminium (Al), which was not expected. Stable macroaggregation also correlated with C amounts as coarse- and medium-sized OM (> 200 and 20–200 μm, respectively), but each of them correlated more closely with oxalate-extracted Al. These results suggested that for the LAC tropical soils under study OM and aggregate stability depended closely on Al-containing sesquioxides, on Al-substituted crystalline hematite and goethite especially. These sesquioxides also seemed to play a dominant role in the relations between aggregation and OM. As far as soils rich in sesquioxides are concerned, this confirmed that OM is not the main aggregating agent, and suggested that physical protection within aggregates is not necessarily the main mechanism for OM stabilization. However, as soil sesquioxide content cannot be managed easily, the effect of land use on soil OM and aggregation was determinant at the local scale: indeed, for a given location, stable macroaggregation, Ct and C amount as fine OM generally decreased with land use intensification (i.e. cultivation, tillage, reduced surface cover).     

Distribution of organic matter and adenosine triphosphate after fractionation of soils by physical procedures

A mildly leached soil and a calcareous clay soil were dispersed using ultrasound. In the mildly leached soil, organic carbon, nitrogen and ATP (which was used as a guide of the soil microbial biomass) were concentrated in the finer fractions. In the calcareous clay, organic carbon and nitrogen were concentrated in the silt fraction.When slurries of the same soils were shaken vigourously in a wrist action shaker the soils were more completely dispersed but the recovery of ATP was only 30% compared with 90% after ultrasonic dispersion. It is concluded that the vigorous shaking of a soil slurry is destructive with respect to the biomass and smears cell contents, including ATP, across the colloidal fractions.The use of ¹⁴C showed that organisms, and metabolic products after incubation of [¹⁴C]glucose, existed mainly in larger aggregates (> 250 μm dia), silt and clay sized materials. Following physical dispersion the ¹⁴C shifted to silt and clay fractions.It is concluded that while fine clay may be a source of the metabolic products of organisms, the silt fraction a source of cells, and macroorganic matter contains most of the plant debris, the association of microorganisms with inorganic colloids is such that “clean” fractionations of biological components in soils cannot be realized.     

Interrelationships between microbial and soil properties in young volcanic ash soils of Nicaragua

The activity and biomass of soil microorganisms were measured in soils from 25 different arable sites in the Pacific region of Nicaragua with the objective of elucidating their interrelationship with soil textural and soil chemical properties. All soils developed from recent volcanic deposits but differ in their particle size distribution. Short-term phosphorus fixation capacity varied widely and was, on average, 11% of added P. In contrast, long-term P fixation capacity varied within a small range of around 55%. Mean basal respiration was 8.6 μg CO₂–C d⁻¹ g⁻¹ soil, average contents of biomass C, biomass P, and ergosterol as an indicator of fungal biomass were 116, 1.95, and 0.34 μg g⁻¹ soil, respectively. They were all, except biomass P, significantly lower in the sandy than in the loamy soils. The mean biomass C-to-soil C ratio was 0.69%, the mean metabolic quotient 95 mg CO₂–C d⁻¹ g⁻¹ biomass C, the mean ergosterol-to-biomass C ratio 0.31% and the mean biomass C-to-P ratio 107. The very low ergosterol-to-biomass C ratio indicates that fungi contribute only a relatively small percentage to the microbial biomass. The biomass C-to-P ratio exceeded considerably the soil C-to-total P ratio. Metabolic quotient qCO₂ and ergosterol-to-biomass C were both negatively correlated with biomass C-to-soil C ratio and clay content, indicating positive correlations between qCO₂ and ergosterol-to-biomass C ratio and between biomass C-to-soil C ratio and clay content. Key problems of soil fertility and soil quality in Nicaragua are low availability of soil organic matter and phosphorus to soil microorganisms, which are magnified by a low percentage of fungi, probably reducing the ability of soil to provide nutrients for plant growth.     

The effects of fresh and stabilized pruning wastes on the biomass,structure and activity of the soil microbial community in a semiarid climate

The incorporation of organic amendments from pruning waste into soil may help to mitigate soil degradation and to improve soil fertility in semiarid ecosystems. However, the effects of pruning wastes on the biomass, structure and activity of the soil microbial community are not fully known. In this study, we evaluate the response of the microbial community of a semiarid soil to fresh and composted vegetal wastes that were added as organic amendments at different doses (150 and 300 t ha⁻¹) five years ago. The effects on the soil microbial community were evaluated through a suite of different chemical, microbiological and biochemical indicators, including enzyme activities, community-level physiological profiles (CLPPs) and phospholipid fatty acid analysis (PLFA). Our results evidenced a long-term legacy of the added materials in terms of soil microbial biomass and enzyme activity. For instance, cellulase activity reached 633 μg and 283 μg glucose g⁻¹ h⁻¹ in the soils amended with fresh and composted waste, respectively. Similarly, bacterial biomass reached 116 nmol g⁻¹ in the soil treated with a high dose of fresh waste, while it reached just 66 nmol g⁻¹ in the soil amended with a high dose of composted waste. Organic amendments produced a long-term increase in microbiological activity and a change in the structure of the microbial community, which was largely dependent on the stabilization level of the pruning waste but not on the applied dose. Ultimately, the addition of fresh pruning waste was more effective than the application of composted waste for improving the microbiological soil quality in semiarid soils.     

Response of the bacterial diversity and soil enzyme activity in particle-size fractions of Mollisol after different fertilization in a long-term experiment

Particle-size soils were fractionated for evaluating changes in the composition of bacterial community and enzyme activity in response to 13 years of fertilization. This study focused on Mollisol and its particle-size fractions of 200–2,000 μm (coarse sand sized), 63 to 200 μm (fine sand sized), 2 to 63 μm (silt sized), and 0.1 to 2 to μm (clay-sized). Long-term chemical fertilization lowered the pH of all particle fractions, whereas organic fertilizer application mitigated soil acidification. Nutrient concentrations depended on both fertilizer treatment and particle fractions and enzymes were unevenly active throughout the soil. Generally, the highest enzyme activities were observed in the silt and clay fractions of control soil and the soil treated with chemical fertilizer (N, P, and K (NPK)) and in the sand-sized fraction of soil treated with manure and chemical fertilizer (MNPK). Except for acid phosphomonoesterase, the other tested enzyme activities in coarse-sized fractions of MNPK soil were significantly higher than those of the control and NPK soils. Fertilization and soil fraction interactively (p?<?0.05) affected the enzyme activity. Denaturing gradient gel electrophoresis analysis showed that the bacterial community structure significantly differed in different particle sizes with a higher bacterial diversity in small-sized than in coarse-sized fractions. Dominant bands were excised and sequenced. We have found the following bacterial groups: Actinobacteria, γ-proteobacteria, and Acidobacteria. In addition, enrichment of organic matter in coarser fractions was related to greater bacterial diversity than any other treatment. Principal component analysis showed a smaller variability among fractions of the organic amended treatment. Redundancy analysis showed that the tested properties significantly affected the composition of bacterial community with the exception of C/N and available P. No significant correlation between enzyme activity and bacterial community composition was detected, whereas positive correlations between other soil properties and enzyme activities were observed to various extents. Probably, enzyme activities might be affected by specific functional bacterial communities rather than by the overall bacterial community. We concluded that the long-term application of organic manures contributed to the increase of soil organic matter content of particles higher than 200 mm, with higher bacterial diversity and increases in most of the enzyme activities.     

Influence of dry–wet cycles on the interrelationship between aggregate,particulate organic matter,and microbial community dynamics

Aggregate dynamics and their relationship to the microbial community have been suggested as key factors controlling SOM dynamics. Dry–wet (DW) cycles are thought to enhance aggregate turnover and decomposition of soil organic matter (SOM), particularly in tilled soils. The objective of this study was to evaluate the effects of DW cycles on aggregate stability, SOM dynamics, and fungal and bacterial populations in a Weld silt loam soil (Aridic Paleustoll). Samples, taken from 250 μm sieved air-dried soil (i.e. free of macroaggregates > 250 μm), were incubated with ¹³C-labeled wheat residue. In one set of soil samples, fungal growth was suppressed using a fungicide (Captan) in order to discern the effect of dry–wet cycles on fungal and bacterial populations. Aggregate formation was followed during the first 14 d of incubation. After this period, one set of soil samples was subjected to four DW cycles, whereas another set, as a control, was kept at field capacity (FC). Over 74 d, total and wheat-derived respiration, size distribution of water stable aggregates and fungal and bacterial biomass were measured. We determined native and labeled C dynamics of three particulate organic matter (POM) fractions related to soil structure: the free light fraction (LF), and the coarse (250–2000 μm) and fine (53–250 μm) intra-aggregate POM fraction (iPOM). In the fungicide treated soil samples, fungal growth was significantly reduced and no large macroaggregates (> 2 mm) were formed, whereas without addition of fungicide, fungi represented the largest part of the microbial biomass (66%) and 30% of the soil dry weight was composed of large macroaggregates. During macroaggregate formation, labeled free LF-C significantly decreased whereas labeled coarse iPOM-C increased, indicating that macroggregates are formed around fresh wheat residue (free LF), which is consequently incorporated and becomes coarse iPOM. The first drying and wetting event reduced the amount of large macroaggregates from 30 to 21% of the total soil weight. However, macroaggregates became slake-resistant after two dry-wet cycles. Fine iPOM-C was significantly lower in soil after two dry–wet cycles compared to soil kept at FC. We conclude that more coarse iPOM is decomposed into fine iPOM in macroaggregates not exposed to DW cycles due to a slower macroaggregate turnover. In addition, when macroaggregates, subjected to dry–wet cycles, became slake-resistant (d 44) and consequently macroaggregate turnover decreased, fine iPOM accumulated. In conclusion, differences in fine iPOM accumulation in DW vs. control macroaggregates are attributed to differences in macroaggregate turnover.     

Influence of organic and mineral amendments on microbial soil properties and processes

Microbial diversity in soils is considered important for maintaining sustainability of agricultural production systems. However, the links between microbial diversity and ecosystem processes are not well understood. This study was designed to gain better understanding of the effects of short-term management practices on the microbial community and how changes in the microbial community affect key soil processes. The effects of different forms of nitrogen (N) on soil biology and N dynamics was determined in two soils with organic and conventional management histories that varied in soil microbial properties but had the same fertility. The soils were amended with equal amounts of N (100 kg ha⁻¹) in organic (lupin, Lupinus angustifolius L.) and mineral form (urea), respectively. Over a 91-day period, microbial biomass C and N, dehydrogenase enzyme activity, community structure of pseudomondas (sensu stricto), actinomycetes and α proteobacteria (by denaturing gradient gel electrophoresis (DGGE) following PCR amplification of 16S rDNA fragments) and N mineralisation were measured. Lupin amendment resulted in a two- to five-fold increase in microbial biomass and enzyme activity, while these parameters did not differ significantly between the urea and control treatments. The PCR–DGGE analysis showed that the addition of mineral and organic compounds had an influence on the microbial community composition in the short term (up to 10 days) but the effects were not sustained over the 91-day incubation period. Microbial community structure was strongly influenced by the presence or lack of substrate, while the type of amendment (organic or mineral) had an effect on microbial biomass size and activity. These findings show that the addition of green manures improved soil biology by increasing microbial biomass and activity irrespective of management history, that no direct relationship existed among microbial structure, enzyme activity and N mineralisation, and that microbial community structure (by PCR–DGGE) was more strongly influenced by inherent soil and environmental factors than by short-term management practices.     

Comparison of forest soil carbon dynamics at five sites along a latitudinal gradient

The aim of this study was to compare the turnover time of labile soil carbon (C), in relation to temperature and soil texture, in several forest ecosystems that are representative of large areas of North America. Carbon and nitrogen (N) stocks, and C:N ratios, were measured in the forest floor, mineral soil, and two mineral soil fractions (particulate and mineral-associated organic matter, POM and MOM, respectively) at five AmeriFlux sites along a latitudinal gradient in the eastern United States. Sampling at four sites was replicated over two consecutive years. With one exception, forest floor and mineral soil C stocks increased from warm, southern sites (with fine-textured soils) to cool, northern sites (with more coarse-textured soils). The exception was a northern site, with less than 10% silt-clay content, that had a soil organic C stock similar to the southern sites. A two-compartment model was used to calculate the turnover time of labile soil organic C (MRT_U) and the annual transfer of labile C to stable C (k₂) at each site. Moving from south to north, MRT_U increased from approximately 5 to 14 years. Carbon-13 enrichment factors (ε), that described the rate of change in δ¹³C through the soil profile, were associated with soil C turnover times. Consistent with its role in stabilization of soil organic C, silt-clay content was positively correlated (r = 0.91; P ≤ 0.001) with parameter k₂. Latitudinal differences in the storage and turnover of soil C were related to mean annual temperature (MAT, °C), but soil texture superseded temperature when there was too little silt and clay to stabilize labile soil C and protect it from decomposition. Each site had a relatively high proportion of labile soil C (nearly 50% to a depth of 20 cm). Depending on unknown temperature sensitivities, large labile pools of forest soil C are at risk of decomposition in a warming climate, and losses could be disproportionately higher from coarse textured forest soils.