Analysis of the diversity of substrate utilisation of soil bacteria exposed to Cd and earthworm activity using generalised additive models

Recover of Soil Microbial Community Functions in Beech and Turkey Oak Forests After Coppicing Interventions

Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15-20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change.

Microbial response to Nature-Based Solutions in urban soils: A comprehensive analysis using Biolog® EcoPlates™

The study presents a comprehensive examination of changes in soil microbial functional diversity (hereafter called microbial activity) following the implementation of Nature-Based Solutions (NBS) in urban areas. Utilizing the Biolog® EcoPlates™ technique, the study explored variations in microbial diversity in urban soil under NBSs implementation across timespan of two years. Significant differences in microbial activity were observed between control location and those with NBS implementations, with seasonal variations playing a crucial role. NBS positively impacted soil microbial activity especially at two locations: infiltration basin and wild flower meadow showing the most substantial increase after NBS implementation. The study links rainfall levels to microbial functional diversity, highlighting the influence of climatic conditions on soil microbiome. The research investigates also the utilization of different carbon sources by soil microorganisms, shedding light on the specificity of substrate utilization across seasons and locations. The results demonstrate that NBSs implementations lead to changes in substrate utilization patterns, emphasizing the positive influence of NBS on soil microbial communities. Likewise, biodiversity indices, such as Shannon-Weaver diversity (H'), Shannon Evenness Index (E), and substrate richness index (S), exhibit significant variations in response to NBS. Notably, NBS implementation positively impacted H' and E indexes, especially in infiltration basin and wild flower meadow, underlining the benefits of NBS for enhancing microbial diversity. The obtained results demonstrated valuable insight into the dynamic interactions between NBS implementation and soil microbial activity. The findings underscore the potential of NBS to positively influence soil microbial diversity in urban environments, contributing to urban sustainability and soil health. The study emphasizes the importance of monitoring soil microbial activity to assess the effectiveness of NBS interventions and guides sustainable urban development practices.

Detection of Changes in Soil Microbial Community Physiological Profiles in Relation to Forest Types and Presence of Antibiotics Using BIOLOG EcoPlate

Soil is home to microbiota with diverse metabolic activities. These microorganisms play vital roles in many ecological processes. Thus, the assessment of microbial functional diversity is an important quality indicator of soil ecosystems. In this study, we collected soil samples from three distinct forest habitats, i.e., an agroforest, a primary forest (PF), and a secondary forest, within the Angat Watershed Reservation in Bulacan, Northern Philippines. Community-level physiological profiling (CLPP) was done with the BIOLOG EcoPlate™ to analyze the responses of the soil microbial communities from the three forest habitats in the absence or presence of antibiotics. The BIOLOG EcoPlate represents 31 utilizable carbon sources. Based on the CLPP analysis, soil samples from the PF showed significantly higher utilization of most carbon sources than the other forest types (p < 0.05). Thus, less disturbed forest types constitute more functionally diverse microbial communities. The presence of antibiotics significantly decreased the carbon utilization patterns of the soil microbial communities (p < 0.05), indicating the possible use of CLPP in monitoring contamination in soil.

Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis

Microbial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 μm. Such small bacteria can show genomic reductions and metabolic dependencies with other bacteria. However, so far, no study has investigated if such bacteria exist in terrestrial environments like soil. Here, we isolated soil bacteria that passed through a 0.1-μm filter. The complete genome of one of the isolates was sequenced and the bacterium was identified as Hylemonella gracilis. A set of coculture assays with phylogenetically distant soil bacteria with different cell and genome sizes was performed. The coculture assays revealed that H. gracilis grows better when interacting with other soil bacteria like Paenibacillus sp. AD87 and Serratia plymuthica. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct cell-cell contact. Our study indicates that in soil there are bacteria that can pass through a 0.1-μm filter. These bacteria may have been overlooked in previous research on soil microbial communities. Such small bacteria, exemplified here by H. gracilis, can induce transcriptional and metabolomic changes in other bacteria upon their interactions in soil. In vitro, the studied interspecific interactions allowed utilization of growth substrates that could not be utilized by monocultures, suggesting that biochemical interactions between substantially different sized soil bacteria may contribute to the symbiosis of soil bacterial communities. IMPORTANCE Analysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 μm. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments such as soil. Here, we show that such bacteria also exist in soil. The isolated bacteria were identified as Hylemonella gracilis. Coculture assays with phylogenetically different soil bacteria revealed that H. gracilis grows better when cocultured with other soil bacteria. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct contact. Our study revealed that bacteria are present in soil that can pass through 0.1-μm filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities.

Structural and functional characteristics of soil microbial communities in response to different ecological risk levels of heavy metals

Objective

The potential ecological risk index (RI) is the most commonly used method to assess heavy metals (HMs) contamination in soils. However, studies have focused on the response of soil microorganisms to different concentrations, whereas little is known about the responses of the microbial community structures and functions to HMs at different RI levels.

Methods

Here, we conducted soil microcosms with low (L), medium (M) and high (H) RI levels, depending on the Pb and Cd concentrations, were conducted. The original soil was used as the control (CK). High-throughput sequencing, qPCR, and Biolog plate approaches were applied to investigate the microbial community structures, abundance, diversity, metabolic capacity, functional genes, and community assembly processes.

Result

The abundance and alpha diversity indices for the bacteria at different RI levels were significantly lower than those of the CK. Meanwhile, the abundance and ACE index for the fungi increased significantly with RI levels. Acidobacteria, Basidiomycota and Planctomycetes were enriched as the RI level increased. Keystone taxa and co-occurrence pattern analysis showed that rare taxa play a vital role in the stability and function of the microbial community at different RI levels. Network analysis indicates that not only did the complexity and vulnerability of microbial community decrease as risk levels increased, but that the lowest number of keystone taxa was found at the H level. However, the microbial community showed enhanced intraspecific cooperation to adapt to the HMs stress. The Biolog plate data suggested that the average well color development (AWCD) reduced significantly with RI levels in bacteria, whereas the fungal AWCD was dramatically reduced only at the H level. The functional diversity indices and gene abundance for the microorganisms at the H level were significantly lower than those the CK. In addition, microbial community assembly tended to be more stochastic with an increase in RI levels.

Conclusion

Our results provide new insight into the ecological impacts of HMs on the soil microbiome at different risk levels, and will aid in future risk assessments for Pb and Cd contamination.

Impact of eight widely consumed antibiotics on the growth and physiological profile of natural soil microbial communities

Antibiotics' (ATBs) occurrence in soil ecosystems has a relevant effect in the structure and functionality of edaphic microbial communities, mainly because of their amendment with manure and biosolids that alter their key ecological functions. In this study, the impact of eight widely consumed ATBs on a natural soil microbial community, characterized through 16 S rRNA gene sequencing, was evaluated. Changes induced by the ATBs in the growth of the soil microbiota and in the community-level physiological profiling (CLPP), using Biolog EcoPlates™, were measured as endpoint. The eight assayed ATBs lead to a significant decrease in the growth of soil microbial communities in a dose-dependent way, ordered by its effect as follows: chloramphenicol > gentamycin > erythromycin > ampicillin > penicillin > amoxicillin > tetracycline > streptomycin. Chloramphenicol, gentamycin, and erythromycin adversely affected the physiological profile of the soil community, especially its ability to metabolize amino acids, carboxylic and ketonic acids and polymers. The analysis of the relationship between the physico-chemical properties of ATBs, as well as their mechanism of action, revealed that, except for the aminoglycosides, each ATB is influenced by a different physico-chemical parameters, even for ATBs of the same family. Significant effects were detected from 100 μg mL to 1, concentrations that can be found in digested sludge, biosolids and even in fertilized soils after repeated application of manure, so cumulative and long-term effects of these antibiotics on soil environment cannot be ruled out.

Microbial-assisted soil chromium immobilization through zinc and iron-enriched rice husk biochar

Soil chromium toxicity usually caused by the tannery effluent compromises the environment and causes serious health hazards. The microbial role in strengthening biochar for its soil chromium immobilization remains largely unknown. Hence, this study evaluated the effectiveness of zinc and iron-enriched rice husk biochar (ZnBC and FeBC) with microbial combinations to facilitate the chromium immobilization in sandy loam soil. We performed morphological and molecular characterization of fungal [Trichoderma harzianum (F1), Trichoderma viride (F2)] and bacterial [Pseudomonas fluorescence (B1), Bacillus subtilis (B2)] species before their application as soil ameliorants. There were twenty-five treatments having ZnBC and FeBC @ 1.5 and 3% inoculated with bacterial and fungal isolates parallel to wastewater in triplicates. The soil analyses were conducted in three intervals each after 20, 30, and 40 days. The combination of FeBC 3%+F2 reduced the soil DTPA-extractable chromium by 96.8% after 40 days of incubation (DAI) relative to wastewater. Similarly, 92.81% reduction in chromium concentration was achieved through ZnBC 3%+B1 after 40 DAI compared to wastewater. Under the respective treatments, soil Cr(VI) retention trend increased with time such as 40 > 30 > 20 DAI. Langmuir adsorption isotherm verified the highest chromium adsorption capacity (41.6 mg g⁻¹) with FeBC 3% at 40 DAI. Likewise, principal component analysis (PCA) and heat map disclosed electrical conductivity-chromium positive, while cation exchange capacity-chromium and pH-organic matter negative correlations. PCA suggested the ZnBC-bacterial while FeBC-fungal combinations as effective Cr(VI) immobilizers with >70% data variance at 40 DAI. Overall, the study showed that microbes + ZnBC/FeBC resulted in low pH, high OM, and CEC, which ultimately played a role in maximum Cr(VI) adsorption from wastewater applied to the soil. The study also revealed the interrelation and alternations in soil dynamics with pollution control treatments. Based on primitive soil characteristics such as soil metal concentration, its acidity, and alkalinity, the selection criteria can be set for treatments application to regulate the soil properties. Additionally, FeBC with Trichoderma viride should be tested on the field scale to remediate the Cr(VI) toxicity.

Metabolic Diversity of Xylariaceous Fungi Associated with Leaf Litter Decomposition

Fungi in the family Xylariaceae are primary agents of leaf litter decomposition. However, the diversity of carbon source utilization by xylariaceous fungi and the relative effects on this from environmental and phylogenetic factors are largely unknown. This study assessed the metabolic diversity and redundancy of xylariaceous fungi, associated with leaf litter decomposition, by measuring their in vitro capacity to utilize multiple carbon sources. The work identified the relative influences of geographic and climatic sources, as well as the taxonomic and phylogenetic relatedness, of the fungi. Using Biolog EcoPlate^TM, 43 isolates belonging to Nemania, Xylaria, Nodulisporium, Astrocystis, and Hypoxylon, isolated from Castanopsis sieboldii leaf litter at eight sites in Japan, were found to have the capacity to utilize a variety of carbohydrates, amino acids/amines, carboxylic acids, and polymers. The genera of xylariaceous fungi and their origins significantly affected their metabolic diversity and utilization of carbon sources. Variation partitioning demonstrated that dissimilarities in carbon utilization among fungal isolates were mostly attributable to site differences, especially climatic factors: mean annual temperature and precipitation, and maximum snow depth. Moreover, xylariaceous isolates that originated from adjacent sites tended to have similar patterns of carbon source utilization, suggesting metabolic acclimation to local environmental conditions.

Metabolic plasticity of Salmonella enterica as adaptation strategy in river water

The survival of Salmonella in subtropical river water depends on genetic and metabolic reorganization for the expression of alternative metabolic pathways in response to starvation, which allows Salmonella to use environmental carbon sources (C-sources). However, knowledge regarding the metabolic plasticity of Salmonella serotypes for C-source utilization when exposed to these conditions remains unclear. The aim of this study was to evaluate the metabolic response and level of environmental C-source consumption by environmental Salmonella (Oranienburg and Saintpaul) and clinical Salmonella (Typhi) serotypes by comparing laboratory growth against exposure to river water conditions. Metabolic characterization was performed using a Biolog® EcoPlate^TM containing 31 C-sources. The results obtained under laboratory growth conditions showed that environmental serotypes used 74.1% of the C-sources, whereas the clinical serotype used 45.1%. In contrast, in river water, all strains used up to 96.7% of the C-sources. Salmonella exposure to river water increases its capacity to use environmental C-sources.

Phylloplane Biodiversity and Activity in the City at Different Distances from the Traffic Pollution Source

The phylloplane is an integrated part of green infrastructure which interacts with plant health. Taxonomic characterization of the phylloplane with the aim to link it to ecosystem functioning under anthropogenic pressure is not sufficient because only active microorganisms drive biochemical processes. Activity of the phylloplane remains largely overlooked. We aimed to study the interactions among the biological characteristics of the phylloplane: taxonomic diversity, functional diversity and activity, and the pollution grade. Leaves of Betula pendula were sampled in Moscow at increasing distances from the road. For determination of phylloplane activity and functional diversity, a MicroResp tool was utilized. Taxonomic diversity of the phylloplane was assessed with a combination of microorganism cultivation and molecular techniques. Increase of anthropogenic load resulted in higher microbial respiration and lower DNA amount, which could be viewed as relative inefficiency of phylloplane functioning in comparison to less contaminated areas. Taxonomic diversity declined with road vicinity, similar to the functional diversity pattern. The content of Zn in leaf dust better explained the variation in phylloplane activity and the amount of DNA. Functional diversity was linked to variation in nutrient content. The fraction of pathogenic fungi of the phylloplane was not correlated with any of the studied elements, while it was significantly high at the roadsides. The bacterial classes Gammaproteobacteria and Cytophagia, as well as the Dothideomycetes class of fungi, are exposed to the maximal effect of distance from the highway. This study demonstrated the sensitivity of the phylloplane to road vicinity, which combines the effects of contaminants (mainly Zn according to this study) and potential stressful air microclimatic conditions (e.g., low relative air humidity, high temperature, and UV level). Microbial activity and taxonomic diversity of the phylloplane could be considered as an additional tool for bioindication.

Structural Selectivity of PAH Removal Processes in Soil, and the Effect of Metal Co-Contaminants

Polycyclic aromatic hydrocarbons (PAHs) form a convenient structural series of molecules with which to examine the selectivity exerted on their removal by soil microbiota. It is known that there is an inverse relationship between PAH molecular size and degradation rates in soil. In this paper, we look at how the magnitude of the slope for this relationship, m, can be used as an indicator of the effect of metal co-contaminants on degradation rates across a range of PAH molecular weights. The analysis utilises data collected from our previous microcosm study (Deary, M.E.; Ekumankama, C.C.; Cummings, S.P. Development of a novel kinetic model for the analysis of PAH biodegradation in the presence of lead and cadmium co-contaminants. Journal of Hazard Materials 2016, 307, 240–252) in which we followed the degradation of the 16 US EPA PAHs over 40 weeks in soil microcosms taken from a high organic matter content woodland soil. The soil was amended with a PAH mixture (total concentration of 2166 mg kg−1) and with a range of metal co-contaminant concentrations (lead, up to 782 mg kg−1; cadmium up to 620 mg kg−1; and mercury up to 1150 mg kg−1). It was found that the magnitude of m increases in relation to the applied concentration of metal co-contaminant, indicating a more adverse effect on microbial communities that participate in the removal of higher molecular weight PAHs. We conclude that m is a useful parameter by which we might measure the differential effects of environmental contaminants on the PAH removal. Such information will be useful in planning and implementing remediation strategies.

Macromolecular composition and substrate range of three marine fungi across major cell types

Marine fungi exist as three major cell types: unicellular yeasts, filamentous hyphae and zoosporic early-diverging forms, such as the Chytridiomycota (chytrids). To begin to understand the ecological and biogeochemical influence of these cell types within the wider context of other plankton groups, cell size and macromolecular composition must be assessed across all three cell types. Using a mass-balance approach to culture, we describe quantitative differences in substrate uptake and subsequent macromolecular distribution in three model marine fungi: the yeast Metschnikowia zobellii, the filamentous Epicoccum nigrum and chytrid Rhizophydium littoreum. We compared these model cell types with select oleaginous phytoplankton of specific biotechnological interest through metanalysis. We hypothesise that fungal cell types will maintain a significantly different macromolecular composition to one another and further represent an alternative grazing material to bacterioplankton and phytoplankton for higher trophic levels. Assessment of carbon substrate range and utilisation using phenotype arrays suggests that marine fungi have a wide substrate range. Fungi also process organic matter to an elevated-lipid macromolecular composition with reduced-protein content. Because of their size and increased lipid composition compared to other plankton groups, we propose that fungi represent a compositionally distinct, energy-rich grazing resource in marine ecosystems. We propose that marine fungi could act as vectors of organic matter transfer across trophic boundaries, and supplement our existing understanding of the microbial loop and carbon transfer in marine ecosystems.

Evaluating the metabolic functional profiles of the microbial community and alfalfa (Medicago sativa) traits affected by the presence of carbon nanotubes and antimony in drained and waterlogged sediments

Antimony (Sb) is the ubiquitous re-emerging contaminant greatly accumulated in sediments which has been revealed risky to ecological environment. However, the impacts of Sb (III/V) on microbes and plants in sediments, under different water management with presence of engineering materials are poorly understood. This study conducted sequential incubation of sediments (flooding, draining and planting) with presence of multiwall carbon nanotubes (MWCNTs) and Sb to explore the influence on microbial functional diversity, Sb accumulation and alfalfa traits. Results showed that water management and planting led to greater impacts of sediment enzyme activities and microbial community metabolic function and bioavailable Sb fractions (defined as sum of acid-soluble fraction and reducible fraction, F1 + F2). Available fractions of Sb (V) showed higher correlation to microbial metabolism (r = 0.933) than that of Sb (III) (r = -0.480) in planting stage. MWCNTs with increasing concentrations (0.011%, w/w) positively correlated to microbial community metabolic function in planting stage whereas resulted in decreasing of Sb (III/V) concentrations in alfalfa, although 0.01% MWCNT led to increase of Sb (V) and decrease of Sb (V) by 50.97% and 32.68% respectively. This study provided information for investigating combined ecological impacts of heavy metal and engineering materials under different water managing sediments.

Organic waste amendments for restoration of physicochemical and biological productivity of mine spoil dump for sustainable development

Rehabilitation of degraded lands due to mining and other activities requires rebuilding of the appropriate soil structure and microbial integrity. Organic wastes, in particular plant-based materials, play a vital role in restoration of degraded land when used as amendments for topsoil integrated with microbe-assisted phytoremediation. In this present study, a biotechnological approach using the combination of organic waste amendments, i.e., ETP (effluent treatment plant), sludge from sugarcane and paper industry, and the press mud respectively along with microbial and fungal inoculum isolated from the soil rhizosphere have been applied to study the influence on fertility and productivity of mine spoil from manganese and coal dumps. The organic amendments applied as 100-ton ha^-1 and application of biofertilizers boosted the survival of plants such as Tectona grandis (Teak), Dalbergia sisso (North Indian rosewood), Phyllanthus emblica (Indian gooseberry), Gmelina arborea (Gamhar), and Acacia auriculiformis (Earpod wattle) from 80 to 100% with robust growth and development during the short span of 25 years. The physicochemical attributes of soil and the microbial count also increased significantly. The pH of mine soil dumps slightly shifted toward alkaline conditions (7.4 to 7.8) whereas bulk density, porosity, and the water holding capacity were greatly improved. Other than this, the nutrient status of mine dump soil and the plants such as available nitrogen, phosphorus, potassium and the organic carbon content in soil were improvised to a greater extent simultaneously decreasing the available manganese concentration. The findings of the study assure a better land reclamation and restoration approach.

Spatio-temporal variations in the physiological profiles of streambed bacterial communities: implication of wastewater treatment plant effluents

The effluents of wastewater treatment plants (WWTPs) represent a complex mixture of nutrients and toxic substances, thus, the potential exists for the effluents to significantly impact the biochemical characteristics and bacterial communities of the receiving water. We examined spatial and seasonal patterns, and the impact of effluents on microbial biomass, bacterial community structure, and metabolic diversity on a fourth-order stream. We took triplicate sediment samples at five different locations along a 5000 m transect over three sampling periods. We quantified bacterial community structure as community-level physiological profiles and microbial biomass with phospholipid phosphate analysis. Our findings highlight the worrisome impacts of effluents on microbial biomass and bacterial metabolic diversity on the receiving water. Microbial biomass was significantly higher at the WWTP outfall compared to upstream and downstream sites and correlated positively with sediment physicochemical parameters. Furthermore, our data revealed significant spatial differences in bacterial community structure in the context of WWTP impact. High nutrient availability (lower carbon/nitrogen ratios) at the outfall increased site-specific bacterial metabolic diversity in winter but decreased the same in fall. Seasonal changes in the sedimentary microbial biomass and bacterial carbon substrate utilization were evident regardless of the spatial variations or impacts of the wastewater effluents. Communities in fall showed more versatile substrate utilization patterns than the winter communities. These results suggest that WWTP effluents significantly increased microbial biomass and highlight its mixed effects on bacterial community structure and metabolic diversity. Also, our data underscore a close association between sedimentary physicochemical parameters and the associated microbial functional activities.

The Biolog EcoPlate™ Technique for Assessing the Effect of Metal Oxide Nanoparticles on Freshwater Microbial Communities

The application of Biolog EcoPlate™ for community-level physiological profiling of soils is well documented; however, the functional diversity of aquatic bacterial communities has been hardly studied. The objective of this study was to investigate the applicability of the Biolog EcoPlate™ technique and evaluate comparatively the applied endpoints, for the characterisation of the effects of metal oxide nanoparticles (MONPs) on freshwater microbial communities. Microcosm experiments were run to assess the effect of nano ZnO and nano TiO2 in freshwater at 0.8-100 mg/L concentration range. The average well colour development, substrate average well colour development, substrate richness, Shannon index and evenness, Simpson index, McIntosh index and Gini coefficient were determined to quantify the metabolic capabilities and functional diversity. Comprehensive analysis of the experimental data demonstrated that short-term exposure to TiO2 and ZnO NPs affected the metabolic activity at different extent and through different mechanisms of action. TiO2 NPs displayed lower impact on the metabolic profile showing up to 30% inhibition. However, the inhibitory effect of ZnO NPs reached 99% with clearly concentration-dependent responses. This study demonstrated that the McIntosh and Gini coefficients were well applicable and sensitive diversity indices. The parallel use of general metabolic capabilities and functional diversity indices may improve the output information of the ecological studies on microbial communities.

Effects of the insecticide fipronil in freshwater model organisms and microbial and periphyton communities

Fipronil is a broad-spectrum insecticide whose release in the environment damages many non-target organisms. This study evaluated the toxicity of fipronil at two biological levels using in vivo conditions and environmentally relevant concentrations: the first based on two model organisms (aquatic invertebrate Daphnia magna and the unicellular freshwater alga Chlamydomonas reinhardtii) and a second based on three natural communities (river periphyton and freshwater and soil microbial communities). The physicochemical properties of fipronil make it apparently unstable in the environment, so its behaviour was followed with high performance liquid chromatography (HPLC) under the different test conditions. The most sensitive organism to fipronil was D. magna, with median lethal dose (LC₅₀) values from 0.07 to 0.38 mg/L (immobilisation test). Toxicity was not affected by the media used (MOPS or river water), but it increased with temperature. Fipronil produced effects on the photosynthetic activity of C. reinhardtii at 20 °C in MOPS (EC₅₀ = 2.44 mg/L). The freshwater periphyton presented higher sensitivity to fipronil (photosynthetic yield EC₅₀ of 0.74 mg/L) in MOPS and there was a time-dependent effect (toxicity increased with time). Toxicity was less evident when periphyton and C. reinhardtii tests were performed in river water, where the solubility of fipronil is poor. Finally, the assessment of the metabolic profiles using Biolog EcoPlates showed that bacteria communities were minimally affected by fipronil. The genetic identification of these communities based on 16S rRNA gene sequencing revealed that many of the taxa are specialists in degrading high molecular weight compounds, including pesticides. This work allows us to better understand the impact of fipronil on the environment at different levels of the food chain and in different environmental conditions, a necessary point given its presence in the environment and the complex behaviour of this compound.

Comparison of microbial community structure and function in sediment between natural regenerated and original mangrove forests in a National Nature Mangrove Reserve, South China

Mangrove has been destroyed and reforestation is often undertaken, but whether a regenerated forest could restore its ecological function is not clear. This study compares microbial community structure and function in sediment of the 17-years old natural regenerated mangrove forest (Y17) with the original forest (Y74). No significant differences in phospholipid fatty acid (PLFA) profiles and microbial metabolism of most carbon substrates were found between these two forests. However, activities of dehydrogenase, protease, cellulase and phosphatase were lower in Y17 than Y74, and some specific microbial functions were also different. Both forests exhibited significant seasonal differences in enzyme activities and microbial characteristics, but such difference was larger in Y17 than Y74, indicating the regenerated forest was more sensitive to season. Correspondence analysis based on PLFA profiles and enzyme activities revealed the microbial community in Y17 was comparable to Y74, suggesting sediment microbial characteristics in natural regenerated mangroves could be restored.

The Status of Soil Microbiome as Affected by the Application of Phosphorus Biofertilizer: Fertilizer Enriched with Beneficial Bacterial Strains

Regarding the unfavourable changes in agroecosystems resulting from the excessive application of mineral fertilizers, biopreparations containing live microorganisms are gaining increasing attention. We assumed that the application of phosphorus mineral fertilizer enriched with strains of beneficial microorganisms contribute to favourable changes in enzymatic activity and in the genetic and functional diversity of microbial populations inhabiting degraded soils. Therefore, in field experiments conditions, the effects of phosphorus fertilizer enriched with bacterial strains on the status of soil microbiome in two chemically degraded soil types (Brunic Arenosol - BA and Abruptic Luvisol - AL) were investigated. The field experiments included treatments with an optimal dose of phosphorus fertilizer (without microorganisms - FC), optimal dose of phosphorus fertilizer enriched with microorganisms including Paenibacillus polymyxa strain CHT114AB, Bacillus amyloliquefaciens strain AF75BB and Bacillus sp. strain CZP4/4 (FA100) and a dose of phosphorus fertilizer reduced by 40% and enriched with the above-mentioned bacteria (FA60). The analyzes performed included: the determination of the activity of the soil enzymes (protease, urease, acid phosphomonoesterase, β-glucosidase), the assessment of the functional diversity of microorganisms with the application of BIOLOGTM plates and the characterization of the genetic diversity of bacteria, archaea and fungi with multiplex terminal restriction fragment length polymorphism and next generation sequencing. The obtained results indicated that the application of phosphorus fertilizer enriched with microorganisms improved enzymatic activity, and the genetic and functional diversity of the soil microbial communities, however these effects were dependent on the soil type.

Long-term effects of grain husk and paper fibre sludge biochar on acidic and calcareous sandy soils - A scale-up field experiment applying a complex monitoring toolkit

Biochar is produced from a wide range of organic materials by pyrolysis, specifically for improvement of poor quality soils. One of the main issues nowadays in studying biochar as soil amendment is to upscale experiments and move from short-term, laboratory conditions to long-term field trials. This paper presents a long-term field study, being the final step of a scale-up technology development, on grain husk and paper fibre sludge biochar application for soil improvement with focus on two degraded soil types of a temperate region. The effects of biochar on an acidic and a calcareous sandy agricultural soil were studied applying a complex approach including physico-chemical, biological and ecotoxicological methods. Our study demonstrated that the applied biochar had positive direct and indirect influences on the acidic sandy soil, but these effects were different in terms of extent and time. 30 t/ha biochar addition improved the pH of the acidic sandy soil by 24% and also increased significantly the nutrient concentrations (P₂O₅ by 68%, K₂O by 11% and organic matter by 33%), and the water-holding capacity after 30 months. Furthermore, biochar addition improved also the microbiological activity and diversity in the acidic sandy soil. Biochar application did not induce any negative effects. Biochar had no toxic effect on the plants and the biochar-treated soil provided a more liveable habitat for soil living animals than the untreated acidic sandy soil. The favourable biochar-mediated influences on soil properties were manifested mainly in the acidic sandy soil, proving that the biochar-related advantages have to be verified for different soil types. The benefits of grain husk and paper fibre sludge biochar application in an acidic sandy soil were confirmed on the long term by the applied tiered approach.

Hydrological variations shape diversity and functional responses of streambed microbes

Microbiota inhabiting the intermittent streambeds mediates several in-stream processes that are essential for ecosystem function. Reduced stream discharge caused by the strengthened intermittency and increased duration of the dry phase is a spreading global response to changes in climate. Here, the impacts of a 5-month desiccation, one-week rewetting and punctual storms, which interrupted the dry period, were examined. The genomic composition of total (DNA) and active (RNA) diversity, and the community level physiological profiles (CLPP) were considered as proxies for functional diversity to describe both prokaryotes and eukaryotes inhabiting the surface and hyporheic streambeds. Comparisons between the genomic and potential functional responses helped to understand how and whether the microbial diversity was sensitive to the environmental conditions and resource acquisition, such as water stress and extracellular enzyme activities, respectively. RNA expression showed the strongest relationship with the environmental conditions and resource acquisition, being more responsive to changing conditions compared to DNA diversity, especially in the case of prokaryotes. The DNA results presumably reflected the legacy of the treatments because inactive, dormant, or dead cells were included, suggesting a slow microbial biomass turnover or responses of the microbial communities to changes mainly through physiological acclimation. On the other hand, microbial functional diversity was largely explained by resources acquisition, such as metrics of extracellular enzymes, and appeared vulnerable to the hydrological changes and duration of desiccation. The data highlight the need to improve the functional assessment of stream ecosystems with the application of complementary metrics to better describe the streambed microbial dynamics under dry-rewet stress.

Long-term exposure of activated sludge in chemostats leads to changes in microbial communities composition and enhanced biodegradation of 4-chloroaniline and N-methylpiperazine

Exposure history and adaptation of the inoculum to chemicals have been shown to influence the outcome of ready biodegradability tests. However, there is a lack of information about the mechanisms involved in microbial adaptation and the implication thereof for the tests. In the present study, we investigated the impact of a long-term exposure to N-methylpiperazine (NMP) and 4-chloroaniline (4CA) of an activated sludge microbial community using chemostat systems. The objective was to characterize the influence of adaptation to the chemicals on an enhanced biodegradation testing, following the OECD 310 guideline. Cultures were used to inoculate the enhanced biodegradability tests, in batch, before and after exposure to each chemical independently in chemostat culture. Composition and diversity of the microbial communities were characterised by 16s rRNA gene amplicon sequencing. Using freshly sampled activated sludge, NMP was not degraded within the 28 d frame of the test while 4CA was completely eliminated. However, after one month of exposure, the community exposed to NMP was adapted and could completely degrade it. This result was in complete contrast with that from the culture exposed for 3 months to 4CA. Long term incubation in the chemostat system led to a progressive loss of the initial biodegradation capacity of the community, as a consequence of the loss of key degrading microorganisms. This study highlights the potential of chemostat systems to induce adaptation to a specific chemical, ultimately resulting in its biodegradation. At the same time, one should be critical of these observations as the dynamics of a microbial community are difficult to maintain in chemostat, as the loss of 4CA biodegradation capacity demonstrates.

Grapevine Phyllosphere Community Analysis in Response to Elicitor Application against Powdery Mildew

The reduction of antimicrobial treatments and mainly the application of environmentally friendly compounds, such as resistance elicitors, is an impelling challenge to undertake more sustainable agriculture. We performed this research to study the effectiveness of non-conventional compounds in reducing leaf fungal attack and to investigate whether they influence the grape phyllosphere. Pathogenicity tests were conducted on potted Vitis vinifera "Nebbiolo" and "Moscato" cultivars infected with the powdery mildew agent (Erysiphe necator) and treated with three elicitors. Differences in the foliar microbial community were then evaluated by community-level physiological profiling by using Biolog^TM EcoPlates, high throughput sequencing of the Internal Transcribed Spacer (ITS) region, and RNA sequencing for the viral community. In both cultivars, all products were effective as they significantly reduced pathogen development. EcoPlate analysis and ITS sequencing showed that the microbial communities were not influenced by the alternative compound application, confirming their specific activity as plant defense elicitors. Nevertheless, "Moscato" plants were less susceptible to the disease and presented different phyllosphere composition, resulting in a richer viral community, when compared with the "Nebbiolo" plants. The observed effect on microbial communities pointed to the existence of distinct genotype-specific defense mechanisms independently of the elicitor application.

Impact of the Biological Cotreatment of the Kalina Pond Leachate on Laboratory Sequencing Batch Reactor Operation and Activated Sludge Quality

Hauling landfill leachate to offsite urban wastewater treatment plants is a way to achieve pollutant removal. However, the implementation of biological methods for the treatment of landfill leachate can be extremely challenging. This study aims to investigate the effect of blending wastewater with 3.5% and 5.5% of the industrial leachate from the Kalina pond (KPL) on the performance of sequencing batch reactor (SBR) and capacity of activated sludge microorganisms. The results showed that the removal efficiency of the chemical oxygen demand declined in the contaminated SBR from 100% to 69% and, subsequently, to 41% after the cotreatment with 3.5% and 5.5% of the pollutant. In parallel, the activities of the dehydrogenases and nonspecific esterases declined by 58% and 39%, and 79% and 81% after 32 days of the exposure of the SBR to 3.5% and 5.5% of the leachate, respectively. Furthermore, the presence of the KPL in the sewage affected the sludge microorganisms through a reduction in their functional capacity as well as a decrease in the percentages of the marker fatty acids for different microbial groups. A multifactorial analysis of the parameters relevant for the wastewater treatment process confirmed unambiguously the negative impact of the leachate on the operation, activity, and structure of the activated sludge.

Ecotoxicity of a new biopesticide produced by Lavandula luisieri on non-target soil organisms from different trophic levels

Plant-based biopesticides have become an eco-friendly alternative to synthetic pesticides by reducing the undesired environmental impacts and side-effects on human health. However, their effects on the environment and especially on non-target organisms have been little studied. This study analyses the ecotoxicological effects of the extract of Lavandula luisieri on soil non-target organisms from different trophic levels: the earthworm Eisenia fetida, the plant Allium cepa and a natural-soil microbial community whose taxonomy was analysed through 16S rRNA gene sequencing. The extract tested is the hydrolate -product from a semi industrial steam distillation process- of a Spanish pre-domesticated variety of L. luisieri. This hydrolate has been recently shown to have bionematicide activity against the root-knot nematode Meloidogyne javanica. A previous study showed that the main components of the hydrolate are camphor and 2,3,4,4-Tetramethyl-5-methylidenecyclopent-2-en-1-one. Hydrolate caused acute toxicity (LC₅₀ 2.2% v/v) on A. cepa, while only a slight toxicity on E. fetida (LC₅₀ > 0.4 mL/g). All the concentrations tested (from 1 to 100% v/v) caused a significant decrease in bacterial growth (LC₅₀ 9.8% v/v after 120 h of exposure). The physiological diversity of the community was also significantly altered, except in the case of the lowest concentration of hydrolate (1% v/v). The ability of soil microbial communities to use a variety of carbon sources increased for all substrates at the highest concentrations. These results show that both the plants and bacterial communities of the soil can be affected by the application of biopesticides based on these hydrolates, which highlights the need for a more detailed risk assessment during the development of plant-based products.

Comprehensive Evaluation of Soil Near Uranium Tailings, Beishan City, China

To evaluate the impact of uranium tailings on soil composition and soil microbial, six soil samples at different distance from the uranium tailings (Beishan City, China) were collected for further analysis. Concentrations of radionuclides (²³⁸U and ²³²Th), heavy metals (Mn, Cd, Cr, Ni, Zn, and Pb) and organochlorine pesticide were determined by ICP-MS and GC, they were significantly higher than those of the control. And the Average Well Color Development as well as the Shannon, the Evenness, and the Simpson index were calculated to evaluate the soil microbial diversity. The carbon utilization model of soil microbial community was also analyzed by Biolog-eco. All results indicated that uranium tailings leaded to excessive radionuclides and heavy metals, and decreased the diversity of the soil microbial community. Our study will provide a valuable basis for soil quality evaluation around uranium tailing repositories and lay a foundation for the management and recovery of uranium tailings.

Ecotoxicological assessment of soils polluted with chemical waste from lindane production: Use of bacterial communities and earthworms as bioremediation tools

An ecotoxicological survey of soils that were polluted with wastes from lindane (γ-HCH) production assessed the effects of organochlorine compounds on the metabolism of microbial communities and the toxicity of these compounds to a native earthworm (Allolobophora chlorotica). Furthermore, the bioremediation role of earthworms as facilitators of soil washing and the microbial degradation of these organic pollutants were also studied. Soil samples that presented the highest concentrations of ε-HCH, 2,4,6-trichlorophenol, pentachlorobenzene and γ-HCH were extremely toxic to earthworms in the short term, causing the death of almost half of the population. In addition, these soils inhibited the heterotrophic metabolic activity of the microbial community. These highly polluted samples also presented substances that were able to activate cellular detoxification mechanisms (measured as EROD and BFCOD activities), as well as compounds that were able to cause endocrine disruption. A few days of earthworm activity increased the extractability of HCH isomers (e.g., γ-HCH), facilitating the biodegradation of organochlorine compounds and reducing the intensity of endocrine disruption in soils that had low or medium contamination levels.

Influence of red mud on soil microbial communities: Application and comprehensive evaluation of the Biolog EcoPlate approach as a tool in soil microbiological studies

Red mud can be applied as soil ameliorant to acidic, sandy and micronutrient deficient soils. There are still knowledge gaps regarding the effects of red mud on the soil microbial community. The Biolog EcoPlate technique is a promising tool for community level physiological profiling. This study presents a detailed evaluation of Biolog EcoPlate data from two case studies. In experiment "A" red mud from Ajka (Hungary) was mixed into acidic sandy soil in soil microcosms at 5-50 w/w%. In experiement "B" red mud soil mixture was mixed into low quality subsoil in a field experiment at 5-50 w/w%. According to average well color development, substrate average well color development and substrate richness 5-20% red mud increased the microbial activity of the acidic sandy soil over the short term, but the effect did not last for 10months. Shannon diversity index showed that red mud at up to 20% did not change microbial diversity over the short term, but the diversity decreased by the 10th month. 30-50% red mud had deteriorating effect on the soil microflora. 5-20% red mud soil mixture in the low quality subsoil had a long lasting enhancing effect on the microbial community based on all Biolog EcoPlate parameters. However, 50% red mud soil mixture caused a decrease in diversity and substrate richness. With the Biolog EcoPlate we were able to monitor the changes of the microbial community in red mud affected soils and to assess the amount of red mud and red mud soil mixture applicable for soil treatment in these cases.

Effects of 18 pharmaceuticals on the physiological diversity of edaphic microorganisms

Pharmaceutical residues can enter the terrestrial environment through the application of recycled water and contaminated biosolids to agricultural soils, were edaphic microfauna can would be threatened. This study thus assessed the effect of 18 widely consumed pharmaceuticals, belonging to four groups: antibiotics, non-steroidal anti-inflammatory drugs (NSAIDs), blood lipid-lowering agents (BLLA) and β-blockers, on the physiology of soil microbial communities from a ecological crop field. Biolog EcoPlates, containing 31 of the most common carbon sources found in forest and crop soils, were used to calculate both the averaged well colour development (AWCD), as an indicator of the entire capacity of degrading carbon sources, and the diversity of carbon source utilization, as an indicator of the physiological diversity. The results show that pharmaceuticals impact microbial communities by changing the ability of microbes to metabolize different carbon sources, thus affecting the metabolic diversity of the soil community. The toxicity of the pharmaceuticals was inversely related to the log K_ow; indeed, NSAIDs were the least toxic and antibiotics were the most toxic, while BLLA and β-blockers presented intermediate toxicity. The antibiotic sulfamethoxazole imposed the greatest impact on microbial communities at concentrations from 100 mg/L, followed by the other two antibiotics (trimethoprim and tetracycline) and the β-blocker nadolol. Other chemical parameters (i.e. melting point, molecular weight, pK_a or solubility) had little influence on toxicity. Microbial communities exposed to pharmaceuticals having similar physicochemical characteristics presented similar physiological diversity patterns of carbon substrate utilization. These results suggest that the repeated amendment of agricultural soils with biosolids or sludges containing pharmaceutical residuals may result in soil concentrations of concern regarding key ecological functions (i.e. the carbon cycle).

Four years of experimental warming do not modify the interaction between subalpine shrub species

Climate warming can lead to changes in alpine plant species interactions through modifications in environmental conditions, which may ultimately cause drastic changes in plant communities. We explored the effects of 4 years of experimental warming with open-top chambers (OTC) on Vaccinium myrtillus performance and its interaction with neighbouring shrubs at the Pyrenean treeline ecotone. We examined the effects of warming on height, above-ground (AG) and below-ground (BG) biomass and the C and N concentration and isotope composition of V. myrtillus growing in pure stands or in stands mixed with Vaccinium uliginosum or Rhododendron ferrugineum. We also analysed variations in soil N concentrations, rhizosphere C/N ratios and the functional diversity of the microbial community, and evaluated whether warming altered the biomass, C and N concentration and isotope composition of V. uliginosum in mixed plots. Our results showed that warming induced positive changes in the AG growth of V. myrtillus but not BG, while V. uliginosum did not respond to warming. Vaccinium myrtillus performance did not differ between stand types under increased temperatures, suggesting that warming did not induce shifts in the interaction between V. myrtillus and its neighbouring species. These findings contrast with previous studies in which species interactions changed when temperature was modified. Our results show that species interactions can be less responsive to warming in natural plant communities than in removal experiments, highlighting the need for studies involving the natural assembly of plant species and communities when exploring the effect of environmental changes on plant-plant interactions.

Influence of global change-related impacts on the mercury toxicity of freshwater algal communities

The climatic-change related increase of temperatures, are expected to alter the distribution and survival of freshwater species, ecosystem functions, and also the effects of toxicants to aquatic biota. This study has thus assessed, as a first time, the modulating effect of climate-change drivers on the mercury (Hg) toxicity of freshwater algal photosynthesis. Natural benthic algal communities (periphyton) have been exposed to Hg under present and future temperature scenarios (rise of 5 °C). The modulating effect of other factors (also altered by global change), as the quality and amount of suspended and dissolved materials in the rivers, has been also assessed, exposing algae to Hg in natural river water or a synthetic medium. The EC50 values ranged from the 0.15-0.74 ppm for the most sensitive communities, to the 24-40 ppm for the most tolerant. The higher tolerance shown by communities exposed to higher Hg concentrations, as Jabarrella was in agreement with the Pollution Induced Community Tolerance concept. In other cases, the dominance of the invasive diatom Didymosphenia geminata explained the tolerance or sensitivity of the community to the Hg toxicity. Results shown that while increases in the suspended solids reduced Hg bioavailability, changes in the dissolved materials - such as organic carbon - may increase it and thus its toxic effects on biota. The impacts of the increase of temperatures on the toxicological behaviour of periphyton (combining both changes at species composition and physiological acclimation) would be certainly modulated by other effects at the land level (i.e., alterations in the amount and quality of dissolved and particulate substances arriving to the rivers).