Substrate-induced Respiration Rates Research Articles

Biogeographic and co-occurrence network differentiation of fungal communities in warm-temperate montane soils

Studying the biogeographic patterns of fungal communities across altitudinal and soil depth gradients is essential for understanding how environmental variations shape the diversity and functionality of these complex ecological assemblages. Here, we evaluated the response and assembly patterns of fungal communities to altitude and soil depth, and the co-occurrence patterns influencing soil fungal metabolic preferences on Dongling Mountain. We observed significant variations in fungal β-diversity, driven by elevation and soil depth, with climatic parameters (MAT and MAP) and nutrient concentrations (TOC, TP, and TN) serving as prominent influencers. Additionally, we found that the multiple substrate-induced respiration rate of fungi degrading various carbon substrates was diminished in high-altitude and subsurface soils compared to low-altitude and surface soils. Stochastic processes play a more important role in controlling fungal community assembly than deterministic processes, with dispersal limitation emerging as the main driver of community assembly. While greater network complexity was evident in the topsoil compared to the subsoil, both layers harbored altitude-sensitive OTUs (asOTUs) that belonging to distinct modules. Moreover, fungal groups sensitive to the same altitude exhibited similar metabolic preferences. The asOTUs designated for lower altitude areas favored unstable carbon substrates (glucose and sucrose), while those designated as higher altitude areas exhibited a preference for recalcitrant carbon (xylan and lignin). This evidence suggests that soil fungal communities respond to environmental changes by trading off their life strategies and metabolic characteristics.

Effect of tire wear particle accumulation on nitrogen removal and greenhouse gases abatement in bioretention systems: Soil characteristics, microbial community, and functional genes

Tire wear particles (TWPs), as predominant microplastics (MPs) in road runoff, can be captured and retained by bioretention systems (BRS). This study aimed to investigate the effect of TWPs accumulation on nitrogen processes, focusing on soil characteristics, microbial community, and functional genes. Two groups of lab-scale bioretention columns containing TWPs (0 and 100 mg g−1) were established. The removal efficiencies of NH4+-N and TN in BRS significantly decreased by 7.60%–24.79% and 1.98%–11.09%, respectively, during the 101 days of TWPs exposure. Interestingly, the emission fluxes of N2O and CO2 were significantly decreased, while the emission flux of CH4 was substantially increased. Furthermore, prolonged TWPs exposure significantly influenced the contents of soil organic matter (increased by 27.07%) and NH4+-N (decreased by 42.15%) in the planting layer. TWPs exposure also significantly increased dehydrogenase activity and substrate-induced respiration rate, thereby promoting microbial metabolism. Microbial sequencing results revealed that TWPs decreased the relative abundance of nitrifying bacteria (Nitrospira and Nitrosomonas) and denitrifying bacteria (Dechloromonas and Thauera), reducing the nitrification rate by 42.24%. PICRUSt2 analysis further indicated that TWPs changed the relative abundance of functional genes related to nitrogen and enzyme-coding genes.

Direct and indirect effects of Basta®, a glufosinate-based herbicide, on banana plantation soil microbial diversity and function

Herbicide applications have doubled over the past 30 years to control weeds, but their use may influence soil microbial communities, which mediate important ecosystem services. Here, we characterised the direct effects of a single application of Basta® (glufosinate), at 1× and 2× the recommended rate (5 and 10 kg product ha−1), as well as the indirect effects of vegetation loss on the diversity and function of soil microbial communities within a banana plantation. A 10-month pre-experimental period using Basta® to remove additional vegetation from half of the experimental area created conditions for assessing the indirect herbicide effects. Direct assessments on soil microbial communities began when the Basta® herbicide treatments were applied to the areas with and without vegetation and continued over multiple time-points, for 56 days. Herbicide treatment had no significant direct impacts on basal, and substrate induced respiration rates, or the potential activities of microbial enzymes as inferred from fluorescein diacetate hydrolysis (FDA) and β-glucosidase assays. Similarly, phylogenetic marker gene sequencing indicated that Basta® application did not significantly influence the diversity of soil bacterial or fungal communities. Indirectly, Basta® had a greater influence on the soil microbial activity and functions by removing understory vegetation cover around banana plants. This suggested that continual use of herbicides to reduce soil vegetation cover under bananas had a greater impact on soil microbial communities than a single application of the herbicide. Furthermore, the presence or absence of vegetation cover, significantly altered the abundance of Fusarium oxysporum, plus an additional eight bacterial and ten fungal taxa. Our results indicated that a single application of glufosinate as Basta® at the recommended or double the recommended rate, did not adversely affect soil microbial communities or their activities in banana plantations directly. However, application of herbicides, such as Basta® in crops like banana, indirectly alters soil microbial communities and their activities through loss of vegetation cover and should only be used as a component of an integrated weed management system.

Long-term successive rotation affects soil microbial resource limitation and carbon use efficiency in Chinese fir (Cunninghamia lanceolata) monoculture plantations

Long-term successive rotation has resulted in negative effects on stand productivity, soil nutrient pool and microbial diversity and function in monoculture tree plantations. However, how successive rotation influences soil microbial nutrient limitation and carbon use efficiency (CUE) and their linkage with resource carbon (C): nitrogen (N): phosphorus (P) stoichiometry remain largely unknown. To solve this puzzle, we compared the C:N:P stoichiometries of leaf litter, fine root and soil, as well as microbial biomass and enzyme activities among three Chinese fir (Cunninghamia lanceolata) plantations with first (FRP), second (SRP) and third (TRP) generations and a natural broad-leaved forest (BL). We found that long-term successive rotation of Chinese fir decreased litter biomass by 64.7% ∼ 80.9% and enhanced litter C:N ratio by 2.7% ∼ 36.0% compared to the BL. Successive rotation decreased the contents of dissolved organic C, total N, and soil C:P and N:P ratios, and resulted in an increased C:N imbalance between soil microorganisms and nutrients in the TRP generation. Long-term successive rotation increased microbial C limitation by 1.5% ∼ 11.1% but decreased N and P limitations by 127.3% ∼ 160.9% and 15.3% ∼ 37.5%, compared with the BL, and resulted in significant increases in microbial CUE and substrate-induced respiration rate of C to N sources in the TRP generation. Structural equation modeling suggested that successive rotation indirectly affected microbial CUE and SIR by changing litter C:N, enzyme C:N and soil C:N imbalance. Collectively, these findings indicated that long-term successive rotation aggravated soil microbial C (energy) limitation and affected microbial CUE and capacity due to the increased stoichiometric imbalance between their resources. Future management practices that could increase litter and soil quality could be helpful to decrease microbial C limitation and maintain microbial functionality for sustainable monoculture plantations.

Ant nests as a microbial hot spots in a long-term heavy metal-contaminated soils

Interactions between soil fauna and soil microorganisms are not fully recognized, especially in extreme environments, such as long-term metal-polluted soils. The purpose of the study was to assess how the presence of Lasius niger ants affected soil microbial characteristics in a long-term metal-polluted area (Upper Silesia in Poland). Paired soil samples were taken from bulk soil and from ant nests and analysed for a range of soil physicochemical properties, including metal content (zinc, cadmium, and lead). Microbial analysis included soil microbial activity (soil respiration rate), microbial biomass (substrate-induced respiration rate), and bacteria catabolic properties (Biolog® ECO plates). Soil collected from ant nests was drier and was characterized by a lower content of organic matter, carbon and nitrogen contents, and also lower metal content than bulk soil. Soil microbial respiration rate was positively related to soil pH (p = 0.01) and negatively to water-soluble metal content, integrated into TIws index (p = 0.01). Soil microbial biomass was negatively related to TIws index (p = 0.04). Neither soil microbial activity and biomass nor bacteria catabolic activity and diversity indices differed between bulk soil and ant nests. Taken together, ant activity reduced soil contamination by metals in a microscale which support microbial community activity and biomass but did not affect Biolog® culturable bacteria.

Side effects of traditional pesticides on soil microbial respiration in orchards on the Russian Black Sea coast

Agricultural use of pesticides has greatly increased worldwide over the last several decades, affecting soil microorganisms. Microbial basal respiration and substrate-induced respiration rates are commonly used to assess the detrimental effects of pesticides on soil quality. The goal of the present study was (1) to compare the impact of different pesticides on soil microbial respiration under field conditions, and (2) to characterize the recovery time of soil microbial respiration after pesticide application. The following pesticides were used in the present study: chlorpyrifos, phosalone, dimethoate (organophosphorus insecticides), λ-cyhalothrin (pyrethroid insecticide), and kresoxim-methyl (fungicide). The application of all the pesticides at commercial doses led to a decrease in soil microbial respiration. The inhibition of basal respiration and substrate-induced respiration rate decreased in the following order: chlorpyrifos > phosalone > dimethoate > λ-cyhalothrin ≈ kresoxim-methyl. Among all the pesticides assessed, chlorpyrifos showed the highest toxicity as well as the highest persistence. Several of the observed results differed greatly from previous studies; thus, local assessments are highly advisable. Given that environmental concerns can be a key decision factor for pesticide selection, assessment of different pesticides—such as undertaken in this study—could help farmers to choose the most appropriate pesticide.

No apparent effect of invasive alien goldenrod on soil microbial communities or soil fauna feeding activity

Invasive alien species spreading in abandoned agricultural landscape may negatively affect native organisms, including plants and soil biota. This study assessed the effects of invasion by Solidago sp. (goldenrod) in southern Poland on soil fauna feeding activity and on soil microorganism activity, biomass, and functional and taxonomic diversity, in a comparisons of paired plots: goldenrod-invaded plots and nearby non-invaded plots of semi-natural grassland. Goldenrod-invaded plots had fewer vascular plant species (paired t-test) than non-invaded ones, and showed a distinct plant community composition (ANOSIM). Non-invaded and invaded plots did not differ in a range of measured soil physicochemical parameters. No differences were observed between non-invaded and invaded plots in soil fauna feeding activity (measured in the field using bait-lamina test), nor in soil microbial activity (basal respiration rate) and biomass (substrate-induced respiration rate). Goldenrod invasion also did not affect soil bacterial activity and functional diversity as assessed using Biolog® ECO plates, nor bacterial and eukaryotic taxonomic diversity as assessed using Illumina 16/18S rDNA gene fragment sequencing. Bacterial community functional structure (CLPP pattern) and the taxonomic structure of bacteria and eukaryotes (OTUbact and OTUeuk patterns) were not observed to differ between non-invaded and invaded plots. None of the measured soil microbial indices or soil fauna feeding activity were related to the number of vascular plant species (alpha diversity) as tested by simple regressions. The altered vegetation diversity and composition (beta diversity) was not reflected in the CLPP, OTUbact and OTUeuk patterns (Mantel tests). The reduced alpha and beta plant diversity resulting from goldenrod invasion was not reflected in soil microbial community parameters. Results of the effects of goldenrod invasion on soil organisms should be interpreted with caution, as the effects may not be so pronounced as the effects on aboveground organisms.

Rapid effects of windfall on soil microbial activity and substrate utilization patterns in the forest belt in the Tatra Mountains

The aim of the study was to compare the activity, functional diversity, and community-level physiological profiles of soil microorganisms in light of soil physical and chemical properties in areas where a forest was damaged by hurricane-force winds and in untouched spruce forests of the lower montane belt of the Tatra Mountains (the Carpathians). Foehn winds caused a huge windfall in December 2013. The studied valley was strongly affected by windthrow, but in some places, patches of mature forest did survive. In the studied windthrow area, the first stage of secondary succession can now be observed. Sampling sites were selected in places where the soil was not mechanically disturbed. Soil samples were taken from the organic O and humus A soil horizons and basic soil properties were measured, as were the microbial parameters. Overall microbial activity was determined via the soil respiration rate (R), whereas the microbial biomass was determined via the substrate-induced respiration rate (SIR). Bacterial and fungal catabolic activity, functional diversity (H′), and community-level physiological profiles (CLPP) were determined using Biolog® ECO and FF plates, respectively. Research has shown that 21 months following the studied windthrow, in Hypereutric Skeletic Cambisols developed on calcareous parent material, changes have occurred in some soil properties: soil field moisture in O and A horizons has increased, DOC concentration in O horizons has decreased, and the C/N ratio in A horizons has decreased. The effect of the windthrow episode on overall biological activity was observed in soil A horizons, where overall microbial respiration and SIR biomass decreased. In both O and A horizons, the ratio of bacterial and fungal functional activity (AUCbact/fungi) increased as a result of a fungal AUC decrease. Significant differences in substrate utilization by bacteria occurred between forest-covered soils and windthrow soils in O horizons, where the share of polymer-utilized bacteria activity increased. Rapid effects of windfall on soil microbial parameters expressed mostly in decrease overall microbial activity caused by breakdown in fungal activity. However, those differences are more pronounced in A than in O horizons. In spite of changes in those differences, windthrow did not produce a significant effect on the functional diversity index of microorganisms found in the studied soils.

Abiotic and plant gender effects on the structure and function of soil microbial communities associated with Acanthosicyos horridus (Nara) in the Namibian sand-dune desert ecosystem

In a xeric environment, plant ecophysiological adaptation helps determine soil microbial-community structure beneath plant canopies. We compared the plant-associated microbiota of the dioecious perennial plant Acanthosicyos horridus (Nara) in the Namib Desert in relation to soil parameters, climate, and plant gender. Abiotic soil attributes (soil moisture, total organic matter, salinity) and plant gender were among the main factors correlating with soil microbial-community biomass, basal respiration, and substrate-induced respiration rates. These varied between an extremely arid Far East (FE) site and a less arid site in the sandy, saline delta ecosystem. A. horridus gender was correlated with soil microbiome composition and activity, and varied between the relatively humid and more xeric environments. This study highlighted the apparent role of plant dimorphism in determining soil biotic composition and diversity in a desert ecosystem; however, the cause of the relationship between plant gender and microbial community remains uncertain. Possible explanations include gender-related variation in the plant itself, a link to certain abiotic soil conditions that incidentally influence plant gender, or a combination of both. This is the first example of gender-related differences in microbiota reported in a plant from an arid environment, and only the second example from the plant world in general.

Similar spatial patterns of soil quality indicators in three poplar-based silvo-arable alley cropping systems in Germany

Alley cropping systems (ACS) are regarded as a sustainable land-use alternative that provides ecosystem services, assuming that beneficial tree effects extend towards crop alleys. However, the spatial range of these effects has rarely been considered. The objective of this study was to investigate soil quality indicators at different distances from trees in three German silvo-arable ACS. We analysed soil microbial biomass C and N, ergosterol, microbial activity (enzyme activities, substrate-induced respiration rates) and their functional diversity (MicroResp™ method) in topsoils. Furthermore, fungal abundance and fungal and bacterial contribution to microbial residues (amino sugars) were determined. Tree effects on soil quality indicators were estimated for each depth, for the first time considering both, spatial dependence and abiotic factors (pH, clay content) using mixed effects models with repeated measures. Additionally, differences between soil depths were tested. Analysis combining the three ACS revealed a generalisation of effect sizes and spatial range of tree effects on soil quality indicators. Tree implementation in arable systems increased SOC, microbial biomass and activity in upper topsoils and shifted the composition of main microbial groups towards a higher fungal abundance and functional diversity. Soil quality indices decreased with increasing depth. However, in alleys, no differences between distances from trees were observed. Results demonstrate that ACS are capable to enhance soil quality mediated by microorganisms under trees within 5–8 years. Long-term studies are required to estimate whether beneficial tree effects extend towards crop alleys and deeper soil layers when systems are mature.

The Effects of Heavy Metals and Total Petroleum Hydrocarbons on Soil Bacterial Activity and Functional Diversity in the Upper Silesia Industrial Region (Poland).

Various inorganic and organic pollutants in industrial soils may adversely affect soil microorganisms and terrestrial ecosystem functioning. The aim of the study was to explore the relationship between the microbial activity, microbial biomass, and functional diversity of soil bacteria and the metals and total petroleum hydrocarbons (TPHs) in the Upper Silesian Industrial Region (Poland). We collected soil samples in pine-dominated forest stands and analyzed them according to a range of soil physicochemical properties, including metal content (cadmium, lead, and zinc) and TPH content. Metal concentrations were normalized to their toxicity to soil microorganisms and integrated in a toxicity index (TI). Soil microbial activity measured as soil respiration rate, microbial biomass measured as substrate-induced respiration rate, and the bacterial catabolic activity (area under the curve, AUC) assessed using Biolog® ECO plates were negatively related to TPH pollution as shown in multiple regressions. The canonical correspondence analysis (CCA) showed that both TPH and TI affected the community-level physiological profiles (CLPPs) of soil bacteria and the pollutants’ effects were much stronger than the effects of other soil properties, including nutrient content.Electronic supplementary materialThe online version of this article (doi:10.1007/s11270-016-2966-0) contains supplementary material, which is available to authorized users.

Functional diversity of soil microbial communities in boreal and temperate Scots pine forests

Scots pine (Pinus sylvestris L.) is one of the most widespread conifer species in Europe, able to tolerate a wide variety of climatic conditions. The aim of the study was to compare the activity, functional diversity and community-level physiological profiles (CLPPs) of soil microorganisms in Scots pine forests of the boreal and temperate climatic zones. The soil samples were taken from the O and A soil horizons in northern Finland (boreal pine forest, BP) and Poland (dry and mesic temperate pine forest, TDP and TMP, respectively) and measured for water-holding capacity, pH, organic C, dissolved organic C (DOC) and the total contents of N, P, Ca, Mg, K, Na and Mn. The microbial activity (multiple substrate-induced respiration rate) and functional diversification (community-level physiological profiles, CLPPs) were assessed using the MicroResp™ system with 22 different C substrates. The BP soils were finer textured and contained more Ca, K, Mg, Mn and Na but less N and P than the soils under the temperate forests. The pH values did not differ between the studied forests. The studied pine forests did not differ in the measured microbial properties in the O horizon. However, in the A horizon, the microorganisms from the BP soil were less active and less functionally diverse than those from the temperate forest soils. The CLPPs of the BP soils differed from those of the temperate forest soils, wherein the largest difference was from the use of carboxylic acids and amino acids. The microorganisms from the BP soils used carboxylic acids more efficiently but were much less efficient in decomposing amino acids than those from the temperate forest soils. These differences were related to the contents of DOC, N and P which are influenced by climate and bedrock properties. Our results indicate that soil microbial properties in the O horizon depend mainly on the vegetation, whereas in deeper layers, they depend to a larger extent on bedrock properties and climatic conditions.

Microbial Communities, Biomass, and Carbon Mineralization in Acidic, Nutrient-Poor Peatlands Impacted by Metal and Acid Deposition

Peatlands serve as important stores of organic matter and regulators of nutrient and metal export to surface waters, yet relatively little is known regarding the impact of more than a century of metal, sulfur, and acid deposition on microbial activity in acidic, nutrient-poor peatlands that are common features around Sudbury, Ontario. In this study, eight peatlands were selected at varying distances from the Copper Cliff Smelter that was once the largest point source of sulfur dioxide and sampled for analysis of nutrient and metal content. Basal microbial respiration, relative response to substrate addition (four synthetic and four natural substrates) assessed as CO2 production rates and microbial biomass were assessed in surface (0–10 cm) peat samples. Bacterial and fungal communities within the peat samples were profiled using terminal restriction fragment length polymorphism analysis. Basal respiration (i.e., carbon mineralization in absence of substrate addition) was lowest and Cu and Ni concentrations and the degree of humification (assessed by the von Post scale) in surface peat samples were highest close to the smelter. Each peatland had a unique bacterial community when assessed using non-metric multidimensional scaling, whereas the fungal community was variable with no consistent patterns across the sites. Despite differences in microbial communities, substrate-induced respiration rates did not differ among peatlands as sites generally responded similarly to carbon substrate additions. Basal respiration rates were related to the humification status of the peat, which was potentially related to environmental degradation in the peatlands or surrounding terrestrial systems closer to the Sudbury smelters.

Effect of long-term nutrient managements on biological and biochemical properties of semi-arid tropical Alfisol during maize crop development stages

Understanding the influence of organic or inorganic nutrient management on soil biology and biochemistry during crop growth may help to develop more sustainable fertilization strategies. Hence, the biological variables including soil organic carbon (SOC), microbial biomass carbon (MBC), six cultivable microbial communities, five hydrolytic enzymes activity and soil respiratory indices from a long-term fertility experiment field (>100 years) were assessed at different growth stages of maize. The samples were taken from four long-term treatments viz., control (no fertilization), balanced inorganic fertilizers (IC), organic amendments (OM) and integrated nutrient management (INM, organic manure plus chemical fertilizers) at five different stages of maize cropping (S1, pre-cropping; S2, five days after sowing; S3, vegetative; S4, flowering; S5, after harvesting). Responses of most of the assessed parameters to organic fertilization (OM and INM) were significantly higher than those from inorganically managed and control soils. There was significant difference in SOC due to long-term nutrient managements (OM>INM>IC>control) but not due to growth stages of maize. MBC was also higher in OM and INM compared to IC and control and found significantly different at growth stages of maize. Values of microbial counts and assessed enzyme activities were highest at vegetative stage of maize following a declined trend at later stages. The respiration studies indicate a difference between the responses of substrate induced respiration rate (SIR) and metabolic quotient (qCO2). SIR was more significantly influenced by long-term nutrient managements than crop stages, while qCO2 was by early stage of maize growth (S2) alone. The principal component analysis (PCA) identifies MBC, qCO2, SIR, dehydrogenase, phosphatase and aryl sulphatase and counts of Actinobacteria and diazotrophs as major drivers for the variability among the samples. PCA discriminated OM and INM samples from IC and control and vegetative stage of maize from other stages. The interaction effects of long-term nutrient managements and maize growth stages were found significant to MBC, counts of Actinobacteria and diazotrophs and activities of dehydrogenase, acid phosphatase and aryl sulphatase. However, the resilience of semi-arid tropical soil, independent of long-term nutrient management adoptions, was not affected due to maize growth. The present study thus provides some reliable biological indicators to monitor the semi-arid tropical soils, those influenced by nutrient managements.

Long term effects of nutrient management regimes on abundance of bacterial genes and soil biochemical processes for fertility sustainability in a semi-arid tropical Alfisol

Semi-arid tropical soils have low soil organic carbon and microbial biomass carbon with limited available macro- and micronutrients for crop plants. These soils may have future yield sustainability problems due to intensive cropping, erosion and limited adoption of nutrient management strategies. Therefore monitoring the abundance, community shift and physiological status of the soil microbiome in response to agricultural practices is vital to understand soil fertility sustainability. We measured the long term effects of organic and inorganic nutrient management practices on bacterial communities and soil biochemical processes. Samples were from a long term nutrient experiment field trial on an Alfisol established in 1909. The abundance of bacterial 16S rRNA, nifH and amoA genes was measured in soil samples for two consecutive years, 2009 and 2010 using quantitative real-time polymerase chain reaction (qPCR). The 16S rRNA and nifH genes were abundant in organically managed soil while the inorganic nutrient amendments increased the abundance of amoA gene. Respiration studies indicated that organic management encouraged higher substrate induced respiration rates compared to inorganically fertilized and control soils. However, the metabolic quotient of the soil remained unaffected by long term nutrient management regimes. The inorganic fertilizer amended soil showed higher nitrification potential compared to organically managed and control soils. Multivariate regression analysis revealed that soil organic carbon, microbial biomass carbon and substrate induced respiration rate significantly drive the abundance of 16S rRNA and nifH gene; while for amoA, the drivers were available nitrogen, substrate induced respiration rate and nitrification potential. Our results show that long term organic and inorganic nutrient managements had strong influences on the abundance of key bacterial genes and related biochemical processes in a semi-arid tropical Alfisol. This study further underlines the importance of fertility management options for improving or sustaining the biological properties of tropical soils.

Soil biological attributes in arsenic-contaminated gold mining sites after revegetation

Recovery of arsenic contaminated areas is a challenge society faces throughout the world. Revegetation associated with microbial activity can play an essential role in this process. This work investigated biological attributes in a gold mining area with different arsenic contents at different sites under two types of extant revegetation associated with cover layers of the soil: BS, Brachiaria sp. and Stizolobium sp., and LEGS, Acacia crassicarpa, A. holosericea, A. mangium, Sesbania virgata, Albizia lebbeck and Pseudosamanea guachapele. References were also evaluated, comprising the following three sites: B1, weathered sulfide substrate without revegetation; BM, barren material after gold extraction and PRNH (private reserve of natural heritage), an uncontaminated forest site near the mining area. The organic and microbial biomass carbon contents and substrate-induced respiration rates for these sites from highest to lowest were: PRNH > LEGS > BS > B1 and BM. These attributes were negatively correlated with soluble and total arsenic concentration in the soil. The sites that have undergone revegetation (LEGS and BS) had higher densities of bacteria, fungi, phosphate solubilizers and ammonium oxidizers than the sites without vegetation. Principal component analysis showed that the LEGS site grouped with PRNH, indicating that the use of leguminous species associated with an uncontaminated soil cover layer contributed to the improvement of the biological attributes. With the exception of acid phosphatase, all the biological attributes were indicators of soil recovery, particularly the following: microbial carbon, substrate-induced respiration, density of culturable bacteria, fungi and actinobacteria, phosphate solubilizers and metabolic quotient.

Response of Selected Soil Microbial Populations and Activities to Land Conversion

A native shrub–steppe ecosystem converted to a series of irrigated agricultural fields was evaluated for biological indicators that may signal changes in soil processes during the initial stages of conversion and disturbance. Nine sites including undisturbed native shrub–steppe and center-pivot-irrigated fields with 1, 2, and 3 years of cultivation following conversion were evaluated. Cultivated fields had greater populations of culturable aerobic and pseudomonad bacteria, greater populations of nitrifying bacteria, increased nitrification potential, greater values of microbial biomass nitrogen (MBN), and different rates of substrate-induced respiration compared to native sites. Disturbance and soil mixing from field development, tillage, irrigation, compost amendments, and residue incorporation contributed to shifts in soil microbial populations and activities following conversion. Differences observed in microbial characteristics were influenced more by conversion of the native ecosystem to an irrigated agroecosystem and the addition of compost than by the length of time of cultivation.

Distinct Microbial Limitations in Litter and Underlying Soil Revealed by Carbon and Nutrient Fertilization in a Tropical Rainforest

Human-caused alterations of the carbon and nutrient cycles are expected to impact tropical ecosystems in the near future. Here we evaluated how a combined change in carbon (C), nitrogen (N) and phosphorus (P) availability affects soil and litter microbial respiration and litter decomposition in an undisturbed Amazonian rainforest in French Guiana. In a fully factorial C (as cellulose), N (as urea), and P (as phosphate) fertilization experiment we analyzed a total of 540 litterbag-soil pairs after a 158-day exposure in the field. Rates of substrate-induced respiration (SIR) measured in litter and litter mass loss were similarly affected by fertilization showing the strongest stimulation when N and P were added simultaneously. The stimulating NP effect on litter SIR increased considerably with increasing initial dissolved organic carbon (DOC) concentrations in litter, suggesting that the combined availability of N, P, and a labile C source has a particularly strong effect on microbial activity. Cellulose fertilization, however, did not further stimulate the NP effect. In contrast to litter SIR and litter mass loss, soil SIR was reduced with N fertilization and showed only a positive effect in response to P fertilization that was further enhanced with additional C fertilization. Our data suggest that increased nutrient enrichment in the studied Amazonian rainforest can considerably change microbial activity and litter decomposition, and that these effects differ between the litter layer and the underlying soil. Any resulting change in relative C and nutrient fluxes between the litter layer and the soil can have important consequences for biogeochemical cycles in tropical forest ecosystems.

Air-Drying, Cooling and Freezing for Soil Sample Storage Affects the Activity and the Microbial Communities from Two Mediterranean Soils

The selection of soil storage conditions must take into account the diversity of soils and their environmental characteristics, because different soil types may vary in their physical and chemical characteristics and microbial populations. As a result, identical storage conditions can produce different effects on different soil samples, and understanding the influence of soil storage in respect to the microbial community is essential for further microbial research. In this study, two different characteristics were used to assess the influence of soil processing and storage on two Mediterranean soils: respiratory activity and bacterial community composition in relation to three common storage conditions: air-drying, cooling and freezing. Samples from both soils (a Calcaric Regosol and a Haplic Arenosol) were air-dried or stored at either 4°C or −20°C for 12 months, and a PCR-DGGE analysis was performed to reveal changes in the whole bacterial community, and more specifically in the Firmicutes group, throughout the storage period. After storage, aliquots of the soil samples were incubated for 28 days at 25°C to assess changes in microbial activity, using respirometry, and molecular methods were used to determine the differences in the microbial community composition during the respirometric incubation. Results clearly show that any storage condition affects the microbial community and its activity, and this effect increases with the vulnerability of the soil. The study also reveals the need of incubating the soil samples to allow active bacteria to reach sufficiently high population sizes to be detected, as the non-incubated samples have not shown any change. The soil microbial community has been found to be adapted to its particular environmental conditions. In that sense, results suggest that Firmicutes may have a more common occurrence in the soil that is usually dried, since these bacteria can be more resistant to drying due to their spore-forming strategy. The stored samples undergo significant increases (45 to 70%, generally speaking) in the Cumulative Respiration, mainly in the most aggressive treatments (drying and freezing) whereas Basal and Substrate Induced Respiration rates tend to decrease (30 to 45%, depending on the soil and treatment), and the Respiratory Activation Quotient remains lower or unaltered, indicating low stress levels. The different physical, chemical and biological properties of the two soils lead to different suitable storage requirements, although all of them produce alterations in the studied parameters. Considering the results from microbial communities and activity, for the Calcaric Regosol, freezing could be the most suitable method, while for the Haplic Arenosol, it would be more appropriate to use air-drying.

Effects of Zeolite-Containing Material and Ammonium Nitrate on Biodegradation of n-Tridecane in Heavy Clay-Loam Leached Chernozem with High Organic Matter Content

Biostimulation based on usage of soil amendments is growing due to their efficiency in removing different petroleum hydrocarbons (PHC) from contaminated sand or loam-sand soils. However, the research on clay-rich soils with higher organic carbon content, in which PHC biodegradation may proceed differently and which are more difficult to clean up, has been less extensive. In a pot experiment, we studied and compared the effects of two soil amendments, natural zeolite-containing material (ZCM, 50 g kg−1) as a bulking agent and ammonium nitrate (0.3 g N kg−1) as a nitrogen fertilizer, on biodegradation of n-tridecane (1 wt.%) in a weakly acidic heavy clay loam leached chernozem with fairly high organic carbon content (3.71%). After 48 days, the nitrogen-amended contaminated soil showed enhancement of both respiratory activity (basal and substrate-induced respiration rates) and the number of n-tridecane- degraders. As a consequence, the extent of n-tridecane biodegradation (86.5%) was essentially higher in the presence of added nitrogen than that in the non-amended soil (73.7%). In contrast, due to the partial retention of n-tridecane molecules in its pores, ZCM retarded biodegradation to 56.0%, showed no significant effect on the number of n-tridecane-degraders and, moreover, enhanced the decomposition of the soil intrinsic organic matter. The obtained data indicate that more precautions should be considered when using porous sorbents such as ZCM for remedial arrangements in PHC-contaminated soils.