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Natural peatlands provide ecosystem services such as carbon storage and habitat, which can be negatively affected (degraded) by the proximity of agricultural land due to lowered water table and increased nutrient deposition. We assessed peat biochemistry and microbial function in the dry, fluctuating and saturated zones of the peat deposits at Moanatuatua (degraded) and Kopuatai (intact) raised bogs in New Zealand to investigate the effects of adjacent agriculture on carbon (C) and nitrogen (N) cycling. Peat C and N density were elevated, due in part to greater bulk density, in the dry and saturated zones at Moanatuatua compared with Kopuatai. Functional capacity (multi-substrate induced respiration) at Moanatuatua was greater than at Kopuatai, and water-soluble C was at lower concentration but more degradable, indicating that microbes were C limited at Moanatuatua but N limited at Kopuatai. Greater microbial function at Moanatuatua infers C inputs may be more rapidly converted to gaseous or waterborne exports, and agriculturally affected peatlands may be more susceptible to losses of labile C. We conclude that proximity to agriculture is likely to have caused changes in chemical properties and altered microbial functioning of restiad bog and has important implications for C and N turnover within these peatland systems.

We described the bacterial diversity of walnut grove soils under organic and conventional farming. The bacterial communities of rhizospheric and nonrhizospheric soils of pecan tree (Carya illinoensis K. Koch) were compared considering two phenological stages (sprouting and ripening). Sixteen operational taxonomic units (OTUs) were identified significantly more abundant according to the plant development, only one according to the farming condition, and none according to the soil origin. The OTUs specificaly abundant according to plant development included Actinobateria (2) and Betaproteobacteria (1) related OTUs more abundant at the sprouting stage, while at the fruit ripening (FR) stage the more abundant OTUs were related to Actinobacteria (6), Alphaproteobacteria (6), and unclassified Bacteria (1). The Gaiellaceae OTU18 (Actinobacteria) was more abundant under conventional farming. Thus, our study revealed that the plant development stage was the main factor shaping the bacterial community structure, while less influence was noticed for the farming condition. The bacterial communities exhibited specific metabolic capacities, a large range of carbon sources being used at the FR stage. The identified OTUs specifically more abundant represent indicators providing useful information on soil condition, potential tools for the management of soil bacterial communities. [ABSTRACT FROM AUTHOR]

In San Luis Potosí, Mexico, the exploitation of minerals has historically been carried out as an activity that has left in its path environmental liabilities, with high concentrations of heavy metals. These metals have undergone weathering by rain and wind and have moved closer to inhabited locations as is the case of Cerro de San Pedro (CSP) and Villa de la Paz (VDP). The objective of this study is to show the biological alteration of soils due to the presence of heavy metals and metalloids like Cadmium (Cd), Copper (Cu), Lead (Pb) and Arsenic (As) and to find the relationship between contamination and risk indexes. Soil samples were obtained from sites with historical records of mining activity and their surroundings. Several analyses were performed, such as pH levels, organic matter, electrical conductivity, clays, heavy metals and As. Moreover, Community Level Physiological profiling (CLPP) were conducted. The obtained evidence showed high levels of contamination by As and heavy metals in both sites (CSP: 6485.1 mg/Kg of Pb and pH of 4.4; VDP: 7188.2 mg/Kg of As and pH of 7.8). According to the Metal Pollution Index (MPI), 607.0 in CSP and 1050.5 in VDP, presented a high environmental risk, apart from, risk to human health (SQGQI) 35.8 in CSP and 131.5 in VDP. At the same time, CLPPs showed that microbiological communities were selective in taking up substrate groups, in the following order: Carbohydrates > Polymers > Carboxylic acids > Amino acids > Amines/Amides. However, a positive correlation in CSP was only found between both indexes and Amines/Amides (r = 0.46, p

Community level physiological profiles (CLPPs) were used to characterize soils with two contrasting no‐till agricultural practices in terms of crop rotation, looking for differences in soil physiology according to management: 'good agricultural practices (GAP), based on crop rotation, and monocropping agriculture considered as poor agricultural practices (PAP); soils from nearby natural environments (NE) were used as reference. Soils from productive fields of the central Argentine Pampas were sampled in summer and winter. Treatments were replicated at four places along a 400‐km east–west transect, between longitudinal parallels 31° to 33°S. The CLPPs assay was based on either basal respiration or substrate‐induced respiration using different C sources, with or without additional nitrogen as a mineral amendment, to mimic fertilizer application effects. CLPPs allowed discrimination between soils with different agricultural practices, despite the differences in the texture and mineralogy of the soils at each replicate site. NE soils were significantly different to agriculture soils based on 70% of the estimated CLPPs parameters. The differences between GAP and PAP soils by CLPPs data were supported by 50% of the estimated parameters in winter and only by 12.5% of them in summer. The Euclidean distance between GAP and PAP increased 102% in winter compared with summer. Additional N to the incubation did not significantly modify the result. Coumaric and propionic acids appeared to be good substrates for discrimination between different agriculture practices by CLPPs. [ABSTRACT FROM AUTHOR]

Conservation Agriculture approach could be strategic for Soil Quality (SQ) conservation under the Mediterranean conditions of Southern Europe's environments. In this study, we reported the results obtained during a 2-year field experiment (split-plot design) of a 7-year experiment started in 2010–2011, combining two tillage practices (Conventional Tillage (CT) and Zero Tillage (ZT)) with two crop sequences (Wheat monocropping (WW) and Wheat-Faba bean (WF)). SQ was monitored through the selection of some chemical, physical, and biological indicators measured by both visual – Visual Soil Assessment (VSA) – and standard field or laboratory measurements. ZT produced higher values for some VSA indicators, i.e., 'soil structure and consistence' and 'earthworms counts', as well as for soil organic carbon content (0.84 vs. 0.75% in ZT and CT, respectively). CT+WW and CT+WF treatments released significantly higher CO2 fluxes of 35% and 41% than ZT+WW and ZT+WF, respectively. No clear effect of soil tillage practices on community-level physiological profiles was observed; conversely, WF induced higher values of well-color development, richness (R), and Shannon–Weaver index (H) than WW. Under dry Mediterranean areas, ZT practices, especially when combined with the other conservation principles (i.e., crop rotation), seem to ameliorate several SQ indicators already after 7-year period of adoption, allowing a positive trend for soil preservation. [ABSTRACT FROM AUTHOR]

Soil microbial functional diversity under maize grown in different agricultural management practices was determined using the Biolog EcoPlates and other microbial and biochemical methods. Comparisons of substrate utilization and the diversity indices showed differences in community composition of microorganisms related to different cultivation techniques and seasons. The soil samples collected in spring were characterized by statistically significant lower indices of biological activity in comparison to the soil collected from the flowering stage of maize. The soils collected in spring from the plots with full tillage had a similarly high biological activity as the soils obtained from maize flowering season. The principal component of PC analysis, showed the strong correlation between the parameters of soil quality and biodiversity indicators. Selected indicators of soil microbial diversity explained 71.51% of biological variability in soils. Based on the PC analysis, two major groups of soils have been indicated. Management practices and seasons were two important factors affecting soil microbial communities.

The impacts of long-term polycyclic aromatic hydrocarbons (PAHs) and heavy metal pollution on soil microbial communities functioning were studied in soils taken from an old coke plant. The concentrations of PAHs in the tested soils ranged from 171 to 2137 mg kg-1. From the group of tested heavy metals, concentrations of lead were found to be the highest, ranging from 57 to 3478 mg kg-1, while zinc concentrations varied from 247 to 704 mg kg-1 and nickel from 10 to 666 mg kg-1. High dehydrogenase, acid and alkaline phosphatase activities were observed in the most contaminated soil. This may indicate bacterial adaptation to long-term heavy metal and hydrocarbon contamination. However, the Community Level Physiological Profiles (CLPPs) analysis showed that the microbial functional diversity was reduced and influenced to a higher extent by some metals (Pb, Ni), moisture and conductivity than by PAHs.

A transgenic high-methionine soybean ZD91 and its non-transgenic parental soybean ZD were investigated to evaluate the potential negative impact of transgene on the microbial community in soil. The Biolog-ECO plate method was used to evaluate the functional diversity and activity of rhizosphere microbial communities at four growth stages of the soybean each year from 2012 to 2013. Results indicated that there was no difference between ZD and ZD91 in the functional diversity of microbial communities in rhizosphere soil. Besides, plant growth stage had stronger effect than cultivar. It was concluded that transgenic soybean ZD91 did not alter the functional diversity of microbial communities in rhizosphere soil.

Agricultural intensification has increased food production by reducing crop diversity and increasing fertilization and crop protection. Unfortunately, intensification has also reduced soil ecosystem services. Diversifying crop rotations could be a feasible alternative to promote positive feedbacks between soil biota and soil properties. Here, we investigated the impact of diversifying crop rotations on functional composition and diversity of the heterotrophic soil bacterial communities. We studied three frequent rotations with a total number of crops ranging from two to four. Before the experiment, all plots were cultivated with soybean. In the first experimental year, the crop sequences were (1) fallow/soybean, (2) barley/soybean, and (3) field pea/maize. In the second year, all plots were subjected to a wheat/soybean double crop. The experiment was replicated in three locations of the Rolling Pampa (Argentina). Soil and plant sampling took place immediately after the soybean harvest, in the second year. The most diverse rotation (field pea/maize, wheat/soybean) showed the highest standing biomass and litter and the most metabolically diverse and active soil microbial community (P ≤ 0.05). In turn, metabolic diversity was positively associated with plant and litter biomass (r 2  = 0.7) and with soil pH (r 2  = 0.72). Our results revealed that crop rotation affects soil metabolic bacterial diversity and activity (P ≤ 0.05). The most diverse rotation (four different crops) had also the most diverse and active soil microbial biota, concomitantly with a higher plant biomass production and soil pH. Because soil microbial activity and metabolic diversity detected in specific rotations potentially contribute to soil aggregate formation and other soil properties intimately related with nutrient cycling and plant production, the negative effect of agricultural intensification could be attenuated by designing specific and more diverse crop rotations. [ABSTRACT FROM AUTHOR]

Recently, concern over environmental and health effects of massive use of antibiotics has led to the growth of bio-control agent application. Poly-β-hydroxybutyrate (PHB) is a natural polymer that can be depolymerized into water-soluble short-chain fatty acid monomers and acts as a microbial control agent. In this study, the effects of the addition of PHB to the diet of Siberian sturgeon fingerlings by 2% and 5% were investigated. Community Level Physiological Profile (CLPP) was used to analyze anaerobic bacterial metabolic diversity in Siberian sturgeon fingerlings hindgut by using Biolog™ Ecoplate microplates. The results indicated that PHB increased metabolic activity in anaerobic bacteria in sturgeon hindgut. Also Lorenz curve and the Shannon index of Biolog™ Ecoplate data revealed that anaerobic metabolic potential of the bacterial community was different in the PHB-treated fishes compared with the control situation.

In the global change context, the basal respiration (BR), the estimated number of bacterial spores (SP) and the community level physiological profiles (CLPPs) were investigated in three different Mediterranean soils following different hydric and thermic stress scenarios. The treatments consisted in an increasing number (1, 2, 4, and 7) of drying-rewetting (DRWc) or freezing-thawing cycles (FTc) at 20, 40 or −20 °C. The results highlighted that the different soils responded differently to the same treatment and that the three variables considered were weakly related one to each another. In almost all soils and modalities, the BR increased significantly during the first cycles before decreasing during the last. With regards to SP, it appeared that, for a given soil, the capacity of microbial communities to sporulate and/or germinate can be considerably more influenced by the temperature rather than by the hydric stress. Finally, the CLPPs literally collapsed with the treatment at 40 °C, irrespective of the soil considered. This suggested a progressive replacement of the catabolically diversified original bacterial communities by another showing lower functional diversities. [ABSTRACT FROM AUTHOR]

The properties of alas soils were studied in short-term isolation (4-5 years). According to the speed of the response to the isolation of degraded pastures, components of the cryoarid-alas ecosystem form the following decreasing series: above-ground vegetation-functional range of cultivated soil microbial community-colony-forming units-underground phytomass, total mobile soil carbon, and nitrification activity. The response rates, respectively, are equal to 1, 4, 5, and over 5 years. The biodynamic features of degraded grasslands in the early years of isolation indicate that these ecosystems have a high regenerative potential. The high activity of autotrophic nitrification indicates a continuing imbalance in the circulation of substances in the isolated area. [ABSTRACT FROM AUTHOR]

The aim of the present work was to assess the influence of organic amendment applications compared to mineral fertilization on soil microbial activity and functional diversity. The field experiment was set up on a soil classified as an Eutric Cambisol developed from loess (South-East Poland). Two doses of both dairy sewage sludge (20 Mg·ha−1 and 26 Mg·ha−1) and of mineral fertilizers containing the same amount of nutrients were applied. The same soil without any amendment was used as a control. The soil under undisturbed native vegetation was also included in the study as a representative background sample. The functional diversity (catabolic potential) was assessed using such indices as Average Well Color Development (AWCD), Richness (R) and Shannon–Weaver index (H). These indices were calculated, following the community level physiological profiling (CLPP) using Biolog Eco Plates. Soil dehydrogenase and respiratory activity were also evaluated. The indices were sensitive enough to reveal changes in community level physiological profiles due to treatment effects. It was shown that dairy sewage amended soil was characterized by greater AWCD, R, H and dehydrogenase and respiratory activity as compared to control or mineral fertilized soil. Analysis of variance (ANOVA) and principal component analysis (PCA) were used to depict the differences of the soil bacterial functional diversity between the treatments.

Lichens are a symbiotic association between a fungus and a green alga or a cyanobacterium, or both. They can grow in practically any terrestrial environment and play crucial roles in ecosystems, such as assisting in soil formation and degrading soil organic matter. In their thalli, they can host a wide diversity of non-photoautotrophic microorganisms, including bacteria, which play important functions and are considered key components of the lichens. In this work, using the BioLog® EcoPlate system, we studied the consumption kinetics of different carbon-sources by microbial communities associated with the thallus and the substrate of Peltigera lichens growing in a Chilean temperate rain forest dominated by Nothofagus pumilio. Based on the similarity of the consumption of 31 carbon-sources, three groups were formed. Among them, one group clustered the microbial metabolic profiles of almost all the substrates from one of the sampling sites, which exhibited the highest levels of consumption of the carbon-sources, and another group gathered the microbial metabolic profiles from the lichen thalli with the most abundant mycobiont haplotypes. These results suggest that the lichen thallus has a higher impact on the metabolism of its microbiome than on the microbial community of its substrate, with the latter being more diverse in terms of the metabolized sources and whose activity level is probably related to the availability of soil nutrients. However, although significant differences were detected in the microbial consumption of several carbon-sources when comparing the lichen thallus and the underlying substrate, d-mannitol, l-asparagine, and l-serine were intensively metabolized by both communities, suggesting that they share some microbial groups. Likewise, some communities showed high consumption of 2-hydroxybenzoic acid, d-galacturonic acid, and itaconic acid; these could serve as suitable sources of microorganisms as bioresources of novel bioactive compounds with biotechnological applications.

The predicted increases in drought in many forest ecosystems may alter soil microbial community diversity and activity, which may further depend on tree species richness. Shifts in microbial community composition and activity could engender changes in ecosystem function, notably, in soil greenhouse gas emissions and C storage. Using soils from mono-specific and mixed three-species forest stands from across Europe, we performed a microcosm experiment to test how soil microbial taxonomic and catabolic diversity are affected by repeated drying-rewetting (DRW) cycles and tree species mixing. We used Illumina sequencing and MicroResp™ analyses to explore community-level changes between microbial functional groups. DRW decreased bacterial richness and carbon substrate use diversity and increased fungal Shannon diversity. Additionally, microbial communities exposed to DRW changed their consumption of 11 out of 15 substrates significantly, suggesting microbial functional shifts. The legacy effect of tree species mixing influenced the structure of the microbial communities (i.e. taxonomic differential abundance) although, community weighted mean (CWM) values of absorptive root traits appeared to affect more strongly microbial richness, relative abundance, and Shannon diversity. No significant tree species mixing:DRW interaction was found for most microbial variables, except for the use of certain substrates and potentially differential abundance. Our data from a laboratory experiment with soils from different forest ecosystems underline that drought may cause shifts in microbial taxonomic and catabolic diversity, while tree species influences primarily taxonomic diversity through root traits. • Drying-rewetting decreased bacterial richness and increased fungal Shannon diversity. • Drying-rewetting changed microbial consumption of certain substrates considerably. • Tree species mixing legacy effects influenced taxonomic differential abundance. • Root trait legacy affected microbial richness, abundance, and diversity. • Tree species mixing:drying-rewetting interaction not generally found. [ABSTRACT FROM AUTHOR]

Rock outcrop ecosystems, such as limestone cedar glades (LCGs), are known for their rare and endemic plant species adapted to high levels of abiotic stress. Soils in LCGs are thin (< 25 cm), soil-moisture conditions fluctuate seasonally between xeric and saturated, and summer soil temperatures commonly exceed 48 °C. The effects of these stressors on soil microbial communities (SMC) remain largely unstudied, despite the importance of SMC-plant interactions in regulating the structure and function of terrestrial ecosystems. SMC profiles and functional diversity were characterized in LCGs using community level physiological profiling (CLPP) and plate-dilution frequency assays (PDFA). Most-probable number (MPN) estimates and microbial substrate-utilization diversity (H) were positively related to soil thickness, soil organic matter (OM), soil water content, and vegetation density, and were diminished in alkaline soil relative to circumneutral soil. Soil nitrate showed no relationship to SMCs, suggesting lack of N-limitation. Canonical correlation analysis indicated strong correlations between microbial CLPP patterns and several physical and chemical properties of soil, primarily temperature at the ground surface and at 4-cm depth, and secondarily soil-water content, enabling differentiation by season. Thus, it was demonstrated that several well-described abiotic determinants of plant community structure in this ecosystem are also reflected in SMC profiles. [ABSTRACT FROM AUTHOR]

Contamination of coastal environments is often due to a complex mixture of pollutants, sometimes in trace levels, that may have significant effects on diversity and function of organisms. The aim of this study was to evaluate the short-term dynamics of bacterioplankton exposed to natural and artificial mixtures of contaminants. Bacterial communities from a southwestern Mediterranean ecosystem, lagoon and the bay (offshore) of Bizerte were exposed to i) elutriate from resuspension of contaminated sediment, and ii) an artificial mixture of metals and herbicides mimicking the contamination observed during sediment resuspension. Elutriate incubation as well as artificial spiking induced strong enrichments in nutrients (up to 18 times), metals (up to six times) and herbicides (up to 20 times) relative to the in situ concentrations in the offshore station, whereas the increases in contaminants were less marked in the lagoon station. In the offshore waters, the artificial mixture of pollutants provoked a strong inhibition of bacterial abundance, production and respiration and significant modifications of the potential functional diversity of bacterioplankton with a strong decrease of the carbohydrate utilization. In contrast, incubation with elutriate resulted in a stimulation of bacterial activities and abundances, suggesting that the toxic effects of pollutants were modified by the increase in nutrient and DOM concentrations due to the sediment resuspension. The effects of elutriate and the artificial mixture of pollutants on bacterial dynamics and the functional diversity were less marked in the lagoon waters, than in offshore waters, suggesting a relative tolerance of lagoon bacteria against contaminants. [ABSTRACT FROM AUTHOR]

Land application of intensive swine farm wastewater has raised serious environmental concerns due to the accumulation and microbially mediated transformation of large amounts of swine wastewater organic C (SWOC). Therefore, the study of SWOC mineralization and dynamics of wastewater microorganisms is essential to understand the environmental impacts of swine wastewater application. We measured the C mineralization of incubated swine wastewaters with high (wastewater H) and low (wastewater L) organic C concentrations. The dynamics of bacteria metabolic profile and community structure were also investigated. The results showed that SWOC mineralization was properly fitted by the two-simultaneous reactions model. The initial potential rate of labile C mineralization of wastewater H was 46% higher than that of wastewater L, whereas the initial potential rates of recalcitrant C mineralization of wastewaters H and L were both around 23 mg L-1 d-1. The bacterial functional and structural diversities significantly decreased for both the wastewaters during SWOC mineralization, and were all negatively correlated to specific UV absorbance (SUVA254; P < 0.01). The bacteria in the raw wastewaters exhibited functional similarity, and both metabolic profile and community structure changed with the mineralization of SWOC, mainly under the influence of SUVA254 (P < 0.001). These results suggested that SWOC mineralization was characterized by rapid mineralization of labile C and subsequent slow decomposition of recalcitrant C pool, and the quality of SWOC varied between the wastewaters with different amounts of organic C. The decreased bio-availability of dissolved organic matter affected the dynamics of wastewater bacteria during SWOC mineralization. [ABSTRACT FROM AUTHOR]

Disposal of oil sludge, a hazardous waste, is currently a prevalent environmental issue. In this study, two field-scale biopiles were constructed to explore the temporal changes of microbial metabolic characteristics during the biotreatment of aged oil sludge. Bulking agent was mixed thoroughly with oily sludge to form a treated pile. The BIOLOG™ system was used to analyze the community level physiological parameters, including microbial metabolic activity, diversity, and variance. In comparison with the control, the community level physiological parameters of the treated pile were dramatically improved. Microbial metabolic activity of the treated pile was improved by 25.06% calculated from the maximums during the treatment. Microbial diversity index (Shannon index) ranges were improved from 1.64-3.02 (control pile) to 2.34-3.14 (treated pile). The numbers of petroleum-degrading bacteria and the total heterotrophic bacteria were correlated with the environmental temperature, and microbial metabolic characteristics in the treated pile revealed the distinctive carbon resources selection with the addition of cotton stalk. Temporal microbial metabolic characteristics, which have important effect on bioremediation, were revealed in this study. [ABSTRACT FROM AUTHOR]

Highlights: [•] Region level analysis of soil biological quality in commercial olive orchards in Spain. [•] Biolog EcoPlate and API ZYM assays were useful as functional soil indicators. [•] Orchard soil samples were adequately classified in their respective farm management. [•] Olive orchards under organic management showed better soil biological quality. [ABSTRACT FROM AUTHOR]

Abstract: Four biopiles were constructed for the bioremediation of total petroleum hydrocarbons (TPHs) in aged oily sludge by indigenous microorganisms. Three biopiles were treated with bulking agent, nutrients or their combination with the fourth pile serving as the control. Responses of microbial community level physiological profiles (CLPPs) to these biostimulation strategies were estimated, and variances among three layers within each biopile were evaluated. Microbial metabolic activity and diversity and the numbers of two species of bacteria were significantly enhanced by the addition of bulking agent, which also made the layers more homogeneous. In contrast, the application of large amounts of nutrients had a suppressing effect on the microbes. After 220days, 49.62% of TPHs were removed from the middle layer of the bulking agent pile, whereas only 20.44% were removed from the inner layer of the control. This study aims to provide experience to improve the remediation efficiency of future investigations. [Copyright &y& Elsevier]

The aim of the present work was to assess the influence of organic amendment applications compared to mineral fertilization on soil microbial activity and functional diversity. The field experiment was set up on a soil classified as an Eutric Cambisol developed from loess (South-East Poland). Two doses of both dairy sewage sludge (20 Mg•ha-1 and 26 Mg•ha-1) and of mineral fertilizers containing the same amount of nutrients were applied. The same soil without any amendment was used as a control. The soil under undisturbed native vegetation was also included in the study as a representative background sample. The functional diversity (catabolic potential) was assessed using such indices as Average Well Color Development (AWCD), Richness (R) and Shannon-Weaver index (H). These indices were calculated, following the community level physiological profiling (CLPP) using Biolog Eco Plates. Soil dehydrogenase and respiratory activity were also evaluated. The indices were sensitive enough to reveal changes in community level physiological profiles due to treatment effects. It was shown that dairy sewage amended soil was characterized by greater AWCD, R, H and dehydrogenase and respiratory activity as compared to control or mineral fertilized soil. Analysis of variance (ANOVA) and principal component analysis (PCA) were used to depict the differences of the soil bacterial functional diversity between the treatments. [ABSTRACT FROM AUTHOR]

Aims: Postfire logging recoups the economic value of timber killed by wildfire, but whether such forest management activity supports or impedes forest recovery in stands differing in structure from historic conditions remains unclear. The aim of this study was to determine the impact of mechanical logging after wildfire on soil bacterial and fungal communities and other measures influencing soil productivity. Methods: We compared soil bacterial and fungal communities and biogeochemical responses of 1) soils compacted, and 2) soils compacted and then subsoiled, to 3) soils receiving no mechanical disturbance, across seven stands, 1-3 years after postfire logging. Results: Compaction decreased plant-available N on average by 27% compared to no mechanical disturbance, while subsoiling decreased plant-available P (Bray) on average by 26% compared to the compacted and non-mechanically disturbed treatments. Neither bacterial nor fungal richness significantly differed among treatments, yet distinct separation by year in both bacterial and fungal community composition corresponded with significant increases in available N and available P between the first and second postharvest year. Conclusions: Results suggest that nutrients critical to soil productivity were reduced by mechanical applications used in timber harvesting, yet soil bacteria and fungi, essential to mediating decomposition and nutrient cycling, appeared resilient to mechanical disturbance. Results of this study contribute to the understanding about impacts of harvesting fire-killed trees and bear consideration along with the recovery potential of a site and the impending risk of future fire in stands with high densities of fire-killed trees. [ABSTRACT FROM AUTHOR]

Abstract: Because of their rapidly changing vegetation dynamics and harsh environmental conditions, roadside prairies in semi-arid regions represent an exceptional study system in which to investigate the effects of plant-soil interactions on ecosystem functioning. We conducted a two-year field experiment on two roadside embankments in semi-arid central Spain differing in construction age to answer the following questions: (i) do commonly used restoration treatments (hydroseeding, fertilization and irrigation) affect soil microbial functional diversity and processes related to soil functioning (basal respiration, total N and P and in situ N availability rate)? (ii) what portion of plant effects on processes related to soil functioning is mediated indirectly by microbial functional diversity? Except for a small and negative irrigation effect on the microbial functional diversity in the three-year old site, the restoration treatments employed did not affect this variable. Fertilization increased plant diversity, an effect likely mediated by the enhanced soil nutrient availability with this treatment at early stages of secondary succession. In contrast, hydroseeding did not affect processes related to soil functioning. The total effect of the plant community on these processes was higher than that of the microbial functional diversity alone, suggesting that the studied slopes are to the greater extent regulated by plants. However, soil microbes are a key proximate influence in the system, as the indirect effects of plant community on soil functioning processes mediated by soil microbes represented 37–41% of the total plant effects observed. Our results indicate that the restoration of recently built slopes can potentially be improved with treatments that promote plant compositional shifts, such as fertilization, or alter soil function, such as the enhancement of soil microbial functional diversity. They also highlight that plant-soil interactions are an important process that can be manipulated for restoration purposes in early-successional stages, especially in nutrient-poor semi-arid ecosystems. [Copyright &y& Elsevier]

Abstract: Soil microbial communities are of crucial importance for the functioning of ecosystems developing in post-mining areas. The objective of this study was to compare the properties of microbial communities in mine soils reclaimed for forestry and in mine soils developing under vegetation from natural succession. Soil samples were taken from a degraded site prior to reclamation (MS), a site after 2 years of lupine cultivation (LUP), reclaimed post-mining sites afforested with Scots pine (R6, R20, R28), post-mining sites with spontaneously developing pine forest stands (S6, S20, S27) and two natural pine forest stands (F30, F100). The examined microbial properties included basal respiration (RESP), microbial biomass (C mic), C mic-to-C org ratio, potential nitrogen mineralization rate (Min_N) and community-level physiological profiles (CLPPs) studied using Biolog® Ecoplates. The lowest C mic, RESP and Min_N values were determined in soil MS (C mic =26.5mgkg−1, RESP=1.06μg C-CO2 g−1 24h−1, Min_N=5.2μgNkg−1 24h−1). Among the reclaimed mine soils the most biologically active was R6 (C mic =89.2mgkg−1, RESP=7.28μg C-CO2 g−1 24h−1, Min_N=213.2μgNkg−1 24h−1). C mic, RESP and Min_N gradually increased with soil age in S6, S20 and S27. Cluster analysis of CLPPs revealed a distinct difference between the natural forest soils and the mine soils. Among the mine soils, the least physiologically diverse was MS. In the successional mine soils, the metabolic abilities developed gradually with soil age. The CLPPs of the youngest successional mine soils resembled more the profiles of soil MS than those of natural forest soils whereas for the youngest reclaimed mine soils the opposite was the case. The results indicate that reclamation measures not only boost the gross microbial properties but also promote rapid development of metabolic abilities characteristic of natural forest soil microbial communities. [Copyright &y& Elsevier]

Abstract: Soils from a long term experiment, established in 1972, incorporating replicated treatments of burning every 2 and 4years with control plots were sampled in 2005 to determine the changes in microbial community structure, measured using phospholipid fatty acids (PLFAs) and functional diversity measured using multiple substrate induced respiration (SIR) tests (MicroResp™). Microbial biomass (total PLFA) in the 2year burn treatments was 50% less than both the control and 4-year burn treatments. There was also concomitantly less respiratory activity which mirrored the known changes in soil C and substrate quality. Contrary to other studies soil bacterial PLFAs were reduced as much as fungal PLFAs in the 2-year burn and the short term (6h) SIR of arginine, lysine, galactose and trehalose were significantly inhibited in the 2-year burn soils. The data suggest that a 4-year burn is a more sustainable practice for maintaining the original structure and function of the forest belowground ecosystem. [Copyright &y& Elsevier]

Background, Aims and Scope. Soil microbial community diversity has been suggested as a way of assessing the 'health or 'quality of soils. While molecular (genetic) or biochemical (phenotypic) measurements of microbial diversity have their place, functional diversity is popular in that it relates to the activity of the soil microflora, particularly in the carbon cycle. Community Level Physiological Profiles (CLPPs) are usually assessed by carbon substrate utilization. The aim here is to review the various methods available for CLPP assessment. Main Features. The original method for CLPP determination was based upon the Biolog plate with its range of 95 carbon substrates and many studies have been employing this over the past 15 years. However, a number of criticisms have been leveled at the method, principally that it relies upon the growth of an extracted microbial population, which may not represent the true functioning of the whole soil. A multiple carbon-source, substrate induced respiration method (multi-SIR) was developed that did measure the response of the whole soil community without the need for growth but it did not have the convenience of the microtitre plate format. MicroResp™ was designed to overcome the deficiencies in both methods and we have applied it to a range of media including mineral and organic soils, sediments and litter. In addition we have adapted the method to the testing of a wide range of carbon substrates such as hydrocarbons, terpenes and pesticides. Results. The MicroResp™ technique covers the middle road of relevance and convenience, being a 'whole soil method in a flexible microtitre plate format. It also has the advantage that it can be adapted for the use of radiolabelled (14C) substrates, which increases the specificity and sensitivity of the assay. A few direct comparisons between MicroResp™ have been made. We have found that its discriminatory ability compares favourably with Biolog while other users have reported it to be superior to the multiple SIR approach. A number of laboratories around the world are now utilizing MicroResp™ and reporting good sensitivity to changes to the microbial community due to such varied factors as age of forest rehabilitation, heavy metal treatment, hydrocarbon exposure, salinity, peatland vegetation, cropping system and tree clone type. Discussion. A comparison of the available methods reveals that each has its advantages and drawbacks. The choice of method may depend upon the particular hypotheses or questions. Conclusions. MicroResp™ offers a convenient, rapid and sensitive method for the determination of Community Level Physiological Profiles. Its application in a number of case studies has demonstrated its utility and advantages over other methods though its full potential for characterizing soil activity is yet to be realized. Perspectives. Increasing awareness of the environmental pressures on soils and the need to monitor soil health has resulted in a range of potential indicators. Microbial functional diversity is one such indicator that seeks to characterize a core soil attribute. The availability of rapid methods for its assessment will aid our understanding of such pressures on basic soil functioning. [ABSTRACT FROM AUTHOR]

Abstract: The aim of the present work was to assess the response of microbial functional diversity to organic soil amendment and the relationship between the microbial functional diversity and soil carbon availability. Household solid waste compost, horse and rabbit manure and chicken manure were applied at two doses. The same undisturbed soil type (Vertic Argiudoll) was used as reference. Soil suspensions were applied to Biolog EcoPlate™ and average color development (AWCD), richness (R) and Shannon–Weaver index (H) were calculated. The amendment incorporation resulted in significant increases (p <0.05) in AWCD, R and H compared to the unamended plots. The regression functions showed linear relationships when R and H were related to soil organic carbon (R 2 =0.77 and 0.72, respectively). Principal component analysis allowed the differentiation of treatments from the control and the undisturbed sites. The Biolog EcoPlate assay was sensitive to changes in the short term due to management practices. [Copyright &y& Elsevier]

We studied the effects of applying different composts (urban organic waste, green waste, manure and sewage sludge), mineral fertilizer and compost plus mineral fertilizer on chemical, biological and soil microbiological parameters over a 12-year period. The organic C and total N levels in soils were increased by all compost and compost + N treatments. Microbial biomass C was significantly ( P ≤ 0.05) increased for some compost treatments. In addition, basal respiration and the metabolic quotient (qCO2) were significantly higher in all soils that had received sewage sludge compost. The Shannon diversity index ( H), based on community level physiological profiling, showed a higher consumption of carbon sources in soils treated with compost and compost + N compared with the control. The utilization of different guilds of carbon sources varied amongst the treatments (compost, compost + N or mineral fertilizer). Cluster analysis of polymerase chain reaction-denaturing gradient gel electrophoresis patterns showed two major clusters, the first containing the mineral fertilization and compost treatments, and the second, the composts + N treatments. No differences in bacterial community structure could be determined between the different types of compost. However, the results suggest that long-term compost treatments do have effects on the soil biota. The results indicate that the effects on the qCO2 may be due to shifts in community composition. In this study, it was not possible to distinguish with certainty between the effects of different composts except for compost derived from sewage sludge. [ABSTRACT FROM AUTHOR]

Community level physiological profiles (CLPPs) have been implemented in many European soil monitoring programmes as a rapid tool for the assessment of the functional properties of soil microbial communities. However, this technique has not been harmonized among different laboratories. In this experiment, the changes of the CLPPs after storage of three Mediterranean forest soils were characterised for two sampling depths. The methods to store the samples were cooling, freezing and room temperature storage. Data presented in this study provide evidence that substantial changes can occur to the soil microbial community functions, regardless of the kind of storage. Changes in functional diversity and substrate evenness depended on the profile and sampling depth. The rate of consumption of the groups of substrates, however, shifted towards an enhanced utilisation of carboxylic acids, phenols and/or amines after 1 month storage at 4°C, regardless of the profile or sampling depth. This was attributed to the physical disruption of soil aggregates and exposure of relatively recalcitrant occluded organic matter. These effects levelled out during 1-year storage. The great sensitivity of CLPPs to storage treatment suggests to take care for immediate analysis after sampling. In case fresh samples are not available, freezing is recommended as a convenient alternative; in that case, however, the kinetic approach is required for data analysis. [Copyright &y& Elsevier]

Two sandstone-derived soils under pure stands of silver fir (Abies alba Mill.) and European beech (Fagus sylvatica L.) were studied to determine if the fine earth (<2 mm material) and two size-classes of porous rock fragments (>2 mm material) supported different microbial communities. Samples from three soil horizons (A, Bw, and BC) were analysed under both optical and scanning electron microscopes. Small stones (2–10 mm in average diameter) appeared more altered than larger ones (40–60 mm) and the effects of weathering became more obvious with shallower depth. In both soils, numerous hyphae and other living forms were observed on the surface of the stones from the A and Bw horizons; this contrasted with the stones from the BC horizon, which showed little or no colonisation. The microbial community of each fraction was characterised using Biolog-Community Level Physiological Profiles (CLPP) and phospholipid fatty acid analyses (PLFA) for samples in the A and B horizons. Significant potential microbial activity (C source utilisation) was associated with rock fragments, from the A horizon and, to a lesser extent, the B, although this was lower than for the equivalent fine earth fraction. The microbial colonisation of the stones appeared inversely related with their size and sampling depth. The PLFA analysis showed not only quantitative differences in the microbial biomass between horizons and size-fractions but also highlighted that the communities differed between soils, horizons (for the sole beech soil) and fractions. These findings demonstrate that by considering rock fragments as a microbiologically inert fraction and discarding them before analysis, as usually is done, can lead to an incomplete picture of both the total amount and, perhaps more importantly, the structure of soil microbial community. [Copyright &y& Elsevier]

In San Luis Potosí, Mexico, the exploitation of minerals has historically been carried out as an activity that has left in its path environmental liabilities, with high concentrations of heavy metals. These metals have undergone weathering by rain and wind and have moved closer to inhabited locations as is the case of Cerro de San Pedro (CSP) and Villa de la Paz (VDP). The objective of this study is to show the biological alteration of soils due to the presence of heavy metals and metalloids like Cadmium (Cd), Copper (Cu), Lead (Pb) and Arsenic (As) and to find the relationship between contamination and risk indexes. Soil samples were obtained from sites with historical records of mining activity and their surroundings. Several analyses were performed, such as pH levels, organic matter, electrical conductivity, clays, heavy metals and As. Moreover, Community Level Physiological profiling (CLPP) were conducted. The obtained evidence showed high levels of contamination by As and heavy metals in both sites (CSP: 6485.1 mg/Kg of Pb and pH of 4.4; VDP: 7188.2 mg/Kg of As and pH of 7.8). According to the Metal Pollution Index (MPI), 607.0 in CSP and 1050.5 in VDP, presented a high environmental risk, apart from, risk to human health (SQGQI) 35.8 in CSP and 131.5 in VDP. At the same time, CLPPs showed that microbiological communities were selective in taking up substrate groups, in the following order: Carbohydrates > Polymers > Carboxylic acids > Amino acids > Amines/Amides. However, a positive correlation in CSP was only found between both indexes and Amines/Amides (r = 0.46, p < 0.05), and in VDP the D -Galactonic acid-γ-Lactone with the MPI (r = 0.49, p < 0.05), and with the SQGQI (r = 0.45, p < 0.05). Although this behavior was not homogeneous, it was possible to find negative correlations between both indexes and the AWCD with other substrates, influenced by the physicochemical characteristics presented in each studied site. Consequently, according to our findings, a combined effect between the physicochemical characteristics, As, and heavy metals took place, on the metabolic activity, causing alterations to soil functions. • Soil contaminated with mine wastes has high concentrations of toxic elements compared to the reference sites. • As and heavy metal concentrations in contaminated sites represent a high potential risk for human and environmental health. • Long-term contaminated enviroments altered the metabolic activity and physicochemical properties in soil. • Substrate consumption assays are useful to study physiological responses of microbes in these environments. [ABSTRACT FROM AUTHOR]

Lichens are a symbiotic association between a fungus and a green alga or a cyanobacterium, or both. They can grow in practically any terrestrial environment and play crucial roles in ecosystems, such as assisting in soil formation and degrading soil organic matter. In their thalli, they can host a wide diversity of non-photoautotrophic microorganisms, including bacteria, which play important functions and are considered key components of the lichens. In this work, using the BioLog® EcoPlate system, we studied the consumption kinetics of different carbon-sources by microbial communities associated with the thallus and the substrate of Peltigera lichens growing in a Chilean temperate rain forest dominated by Nothofagus pumilio. Based on the similarity of the consumption of 31 carbon-sources, three groups were formed. Among them, one group clustered the microbial metabolic profiles of almost all the substrates from one of the sampling sites, which exhibited the highest levels of consumption of the carbon-sources, and another group gathered the microbial metabolic profiles from the lichen thalli with the most abundant mycobiont haplotypes. These results suggest that the lichen thallus has a higher impact on the metabolism of its microbiome than on the microbial community of its substrate, with the latter being more diverse in terms of the metabolized sources and whose activity level is probably related to the availability of soil nutrients. However, although significant differences were detected in the microbial consumption of several carbon-sources when comparing the lichen thallus and the underlying substrate, d-mannitol, l-asparagine, and l-serine were intensively metabolized by both communities, suggesting that they share some microbial groups. Likewise, some communities showed high consumption of 2-hydroxybenzoic acid, d-galacturonic acid, and itaconic acid; these could serve as suitable sources of microorganisms as bioresources of novel bioactive compounds with biotechnological applications. [ABSTRACT FROM AUTHOR]