Set Of Microcosms Research Articles

Cellulolytic potential of mangrove bacteria Bacillus haynesii DS7010 and the effect of anthropogenic and environmental stressors on bacterial survivability and cellulose metabolism

Cellulose degrading bacterial diversity of Bhitarkanika mangrove ecosystem, India, was uncovered and the cellulose degradation mechanism in Bacillus haynesii DS7010 under the modifiers such as pH (pCO2), salinity and lead (Pb) was elucidated in the present study. The abundance of cellulose degrading heterotrophic bacteria was found to be higher in mangrove sediment than in water. The most potential strain, B. haynesii DS7010 showed the presence of endoglucanase, exoglucanase and β-glucosidase with the maximum degradation recorded at 48 h of incubation, with 1% substrate concentration at 41 °C incubation temperature. Two glycoside hydrolase genes, celA and celB were confirmed in this bacterium. 3D structure prediction of the translated CelA and CelB proteins showed maximum similarities with glycoside hydrolase 48 (GH48) and glycoside hydrolase 5 (GH5) respectively. Native PAGE followed by zymogram assay unveiled the presence of eight isoforms of cellulase ranged from 78 kDa to 245 kDa. Among the stressors, most adverse effect was observed under Pb stress at 1400 ppm concentration, followed by pH at pH 4. This was indicated by prolonged lag phase growth, higher reactive oxygen species (ROS) production, lower enzyme activity and downregulation of celA and celB gene expressions. Salinity augmented bacterial metabolism up to 3% NaCl concentration. Mangrove leaf litter degradation by B. haynesii DS7010 indicated a substantial reduction in cellulolytic potential of the bacterium in response to the synergistic effect of the stressors. Microcosm set up with the stressors exhibited 0.97% decrease in total carbon (C%) and 0.02% increase in total nitrogen (N%) after 35 d of degradation while under natural conditions, the reduction in C and the increase in N were 4.05% and 0.2%, respectively. The findings of the study suggest the cellulose degradation mechanism of a mangrove bacterium and its resilience to the future consequences of environmental pollution and climate change.

Soil macroporosity modulates the extent of negative microbial associations during organic substance decomposition

Microbial species interactions are expected to influence the community-level properties, such as the production of extracellular enzymes and the degradation of organic substances. This work examined how microbial diversity, composition and the overall sign of microbial associations were altered with soil texture and structure following the amendment of organic substances. Two sets of microcosms (1:100 and 1:1) of a 4 × 3 factorial design were constructed, with four artificial textural classes (a sandy loam, two loams, and a (silty) clay loam) and three organics (TSB, tryptic soy broth; CA, a mixture of cellulose and humic/fulvic acids; BS, barley straw). As the ‘microbial inoculant’, an agricultural soil was added to the 1:100 and 1:1 microcosms at 1% and 50%, respectively. A few of microbial taxa were specifically enriched after soil addition of TSB, CA, or BS, but distributions across textural classes were inconsistent between microcosms or between organic amendments. Regardless, top abundant bacterial and fungal OTUs were overall negatively associated, suggesting that microbial competition for the shared resource dominated the decomposition of both simple and complex organics. Microbial associations were also modified by soil pore size distribution (PSD), being fewer negative (or more positive) in soils of greater macroporosity than in soils of lower macroporosity. The PSD-based differences in microbial associations were coordinated with PSD-based differences in the activities of exoglucanase and β-glucosidase in TSB-amended soils or soil respiration characteristics in CA-amended soils. Our results provide new insight into how soil structure regulates microbial interactions and, accordingly, the degradation of organic matter.

Stream nitrogen uptake associated with suspended sediments: A microcosm study

Despite significant advances in our understanding of nitrogen (N) removal pathways along river networks, the role of water column processes remains largely understudied. This knowledge gap not only limits our capacity to determine N transport and retention in mid-to-large rivers but also hampers our understanding of N removal processes in smaller streams during stormflow conditions, in which significant increases in suspended sediment concentrations (SSC) typically occur. High SSC in the water column can provide abundant substrate for microbial growth and water column N uptake. However, storms of different size mobilize different quantities of sediment of varying properties and sizes, which can ultimately modulate water column N uptake rates in the stream during stormflows. To assess water column N uptake associated with suspended sediment particles of different sources and sizes, we quantified assimilatory and dissimilatory N uptake rates in a set of microcosms representing a gradient of sediment properties (organic matter, N content, and microbial activity) and surface area (fine vs. coarse size) availability. Water column assimilatory uptake (Used) ranged from 12.7 to 187.8 µg N [g sediment]−1 d−1 across all sediment sources and size fractions, and was higher on average than denitrification rates (DNsed) in agricultural and stream bank sediments but not in streambed sediments (mean DNsed = 240.9 ± 99 µg·N [g sediment]−1·d−1). Sediment-bound C in suspended sediment varied among sediment sources and was directly related to Used rates, but not to DNsed rates, which were less predictable and more variable. Overall, our results showed a positive nonlinear relationship between water column N uptake and SSC, while indicating that water column N uptake may scale differently to SSC depending on sediment source, and to a lesser degree, particle size. Because low, moderate, and large storms can mobilize different quantities of sediment in the watershed of different sources and sizes, it is likely that storm size will ultimately modulate the contribution of water column uptake during storm events to whole-reach N retention.

Experimental evidence for the impact of soil viruses on carbon cycling during surface plant litter decomposition

To date, the potential impact of viral communities on biogeochemical cycles in soil has largely been inferred from correlational evidence, such as virus-driven changes in microbial abundances, viral auxiliary metabolic genes, and links with soil physiochemical properties. To more directly test the impact of soil viruses on carbon cycling during plant litter decomposition, we added concentrated viral community suspensions to complex litter decomposer communities in 40-day microcosm experiments. Microbial communities from two New Mexico alpine soils, Pajarito (PJ) and Santa Fe (SF), were inoculated onto grass litter on sand, and three treatments were applied in triplicate to each set of microcosms: addition of buffer (no added virus), live virus (+virus), or killed-virus (+killed-virus) fractions extracted from the same soil. Significant differences in respiration were observed between the +virus and +killed-virus treatments in the PJ, but not the SF microcosms. Bacterial and fungal community composition differed significantly by treatment in both PJ and SF microcosms. Combining data across both soils, viral addition altered links between bacterial and fungal diversity, dissolved organic carbon and total nitrogen. Overall, we demonstrate that increasing viral pressure in complex microbial communities can impact terrestrial biogeochemical cycling but is context-dependent.

Surfactant-aided mycoremediation of soil contaminated with polycyclic aromatic hydrocarbons

Remediation of persistent polycyclic aromatic hydrocarbons (PAHs) contaminated soil has become a major challenge in recent years. Further, conventional application of bioaugmentation strategies for PAHs remediation require continuous supply of microbial specific nutrients, which makes these processes less feasible. Hence, the present study focused on PAHs remediation using surfactants along with wood assisted fungal system in a microcosm set up. In this study, in absence of surfactants, a saturation in PAHs degradation was noted in bioaugmentation with wood assisted fungal system (BAW) with 61 ± 1.25% degradation, followed by bioaugmentation with free fungi system (BAF) (54 ± 0.46%). However, with addition of 1500 mg/L of surface-active compounds (SAC), a maximum PAHs degradation in BAW (100%) and BAF (86 ± 1.30%) strategies were noted on 21st day. Irrespective of the strategies, presence of SAC and rhamnolipids enhanced PAHs degradation by increasing the enzymes production in Trametes hirsuta when compared to Triton x-100 and sodium dodecyl sulphate (SDS). Among the detected PAHs, 100% degradation within 17 days was noted for naphthalene and acenaphthene in SAC-supplemented BAW system. Further, ecotoxicity analysis established showed the LC50 of sediment soil at 26.5 ± 0.24%, which was reduced by an average of 71% after soil remediation. Hence, the current microcosm system proved that the application of SAC with BAW enhanced the PAHs remediation rate, which supports its application in real time soil remediation.

Persistence of wastewater-associated antibiotic resistant bacteria in river microcosms

The spread of antibiotic-resistant bacteria (ARB) associated with wastewater is a significant environmental concern, but little is known about the persistence and proliferation of these organisms in receiving water bodies after discharge. To address this knowledge gap, we performed a series of microcosm experiments in which river water was amended with either untreated or treated wastewater, and the abundance of viable ciprofloxacin-, Bactrim-, and erythromycin-resistant bacteria was monitored for 72 h.Both types of wastewater amendments significantly increased the initial abundance of ARB compared to microcosms containing only river water (all p < 0.03). The increase was greatest with untreated wastewater, but that effect decreased steadily over time. In contrast, microcosms amended with treated wastewater saw a smaller initial increase and more complex temporal dynamics. Following a brief lag, ARB abundance bloomed for all three of the antibiotics that we considered. This suggests that ARB that survive wastewater treatment are particularly hardy and may proliferate in riverine conditions after a short recovery period.To determine how interactions with the native river microbial community impacted the persistence of wastewater-associated ARB, an additional set of microcosms was prepared using filter-sterilized river water. Peak abundance in these microcosms was significantly higher by 1–2 orders of magnitude compared to microcosms containing an intact river microbial community (all p < 0.05), which suggests that biotic interactions play a significant role in regulating the persistence and proliferation of ARB. The data presented in this paper are among the first available that specifically consider persistence of viable ARB and represent an important step toward understanding AR-related human health risks downstream from wastewater discharge points and following sewer overflow events. Additional studies that consider longer time scales and the interplay of biotic and abiotic variables are essential for modeling public health risks associated with wastewater inputs of ARB to rivers and other aquatic environments.

Quantitative Proteomics and Quantitative PCR as Predictors of cis-1,2-Dichlorethene and Vinyl Chloride Reductive Dechlorination Rates in Bioaugmented Aquifer Microcosms

Quantitative measurement of process-specific biomarker genes of Dehalococcoides mccartyi (Dhc) supports monitoring at chlorinated ethene contaminated sites. In this study, we varied Dhc cell abundances from ∼103 to 108 cells/mL in aquifer microcosms and correlated the corresponding reductive dehalogenase (RDase) gene and RDase protein abundances with measured reductive dechlorination (RD) rates of cis-1,2-dichloroethene (cDCE) and vinyl chloride (VC). An additional set of microcosms tested the RD rate-predictive power of the regression analyses. These efforts revealed (1) that targeted proteomics quantifies Dhc biomarker proteins (e.g., TceA and VcrA, OmeA) over a relevant range of Dhc cell densities, and (2) that protein and gene abundances can predict RD rates. Protein detection limits translated to a rate coefficient of 10–4 day–1 (0.04 year–1) for both kcDCE and kvc, which is within the range observed at sites undergoing monitored natural attenuation (MNA) (i.e., without the implementation of enhanced bioremediation treatment). Rates predicted using a combination of quantitative biomarker gene and protein measurements generally resulted in the best match with experimentally determined rate constants. These new findings provide evidence that quantitative biomarker measurements may be useful predictors of in situ RD rates, which would constitute a major advance for the cost-effective management of contaminated sites.

Effect of enhanced salinity on the chlorophyll-a concentration and partial pressure of CO2 of a sewage-fed freshwater aquaculture pond: a microcosm experiment

ABSTRACT Numerous fresh and saline-water tropical aquaculture ponds that often can be significant sources super-saturation of CO2 towards the atmosphere are gradually increasing throughout the world. The role of salinity in regulating the chlorophyll-a and dissolved pCO2 in a freshwater aquaculture pond, situated in East Kolkata Wetlands, Eastern India, was tested using a microcosm conducted during summer (April-May) and winter (December–January) months. The effects of enhanced salinity to microcosm sets of 5, 10 and 15 ppt were monitored for nine consecutive days. pH, dissolved oxygen (DO), pCO2(water), chlorophyll-a, and gross primary productivity (GPP) were measured in-situ and every day during the entire microcosm. Enhanced salinity was hypothesised to alter the pCO2(water) and chl-a dynamics of this system significantly. Increasing salinity to 5 ppt would enhance the photosynthetic potential of the existing primary producers and reduce the pCO2(water) significantly, thus boosting the CO2 sink strength. This enhanced CO2 sink strength, accompanied with increased GPP and DO, was also observed in 10 ppt, only during summer; however, low temperature was found to abate the photosynthetic response during winter. Finally, in 15 ppt treatments, drastic chlorophyll-a reduction and extreme CO2 super-saturation showed the existing phytoplankton community cannot cope with such high salinity.

On the balance between practical relevance and standardization - Testing the effects of zinc and pyrene on native nematode communities in soil microcosms

Soils are among the most densely inhabited and biodiverse habitats on our planet, and many important soil ecosystem services depend on the health condition of the native soil fauna. Anthropogenic stress such as chemical pollution acting on the native soil fauna might jeopardize these functions. Laboratory microcosm tests are an appropriate tool for assessing the risk of chemicals on the native soil fauna and can be regarded as intermediate tier tests, bridging the gap between single species toxicity tests and field testing. Nematodes are one of the most abundant and divers soil invertebrates, and as such native nematode communities might be suitable for ecotoxicological assessments in laboratory microcosm set ups. In order to test such a small-scale (30 g soil) microcosm system, two different chemicals (zinc and pyrene) were assessed in various soil types for their effects on the respective native nematode communities. Various community parameters such as total nematode density, genus richness and genus composition, as well as trait-related indices (e.g. maturity index) were monitored over a period of 8–10 weeks. The response of the nematode communities strongly varied between soil types, and these differences were more pronounced for Zn than for pyrene. Interestingly, the structure of the respective native nematode communities was shown to play a larger role for explaining the varying toxic effects than soil properties governing the bioavailability of the spiked chemicals. We demonstrated that exposure of natural nematode communities in their original soil matrix to the metal zinc and to pyrene under climatically highly controlled conditions resulted in quantitatively and qualitatively distinct responses. Upon comparison of various community indices, the maturity index was shown to be the most sensitive toxicity endpoint for all tested soils and chemicals.

Separation of Escherichia coli from natural samples for identification of sources and microcosm inoculation.

Obtaining uncultured Escherichia coli from natural waters is an important step in the study of microbes in the environment, which are critical for bacterial decay and microbial source tracking. The quality of the samples used can influence the assays, because high contaminant concentrations, differing cell ages, and physiologic states can impair results. The proposed separation is based on a three-step filtration method applied to replicates of seven samples from a sewage plant affluent, collected in different periods. Aliquots of the leachate were inoculated into microcosms, aiming to observe the cultivability of the cells. The assay resulted in colimetry values ranging between 104 and 105 cells. In the leachate, averages of 1.05% of total coliforms and 1.10% of Escherichia coli were recovered from original samples. Although enduring unfavorable temperatures, salinities, and nutritional conditions, the inoculated microcosm populations grew approximately 310 times after 24h. The final leachate contained cultivable cells in appropriate physiological states and quantities for inoculum in microcosm sets. The bacteria obtained from the leachate were also appropriate for surveys of microbial source tracking, because, in the developed procedure, organisms were separated from contaminants, while cell concentrations were sufficient for inocula.

Interaction between root hairs and soil phosphorus on rhizosphere priming of soil organic matter

We hypothesized that the rhizosphere priming effect (RPE) of soil organic matter by mutant barley lacking root hairs is dependant on a large network of symbiotic arbuscular mycorrhizal fungi (AMF). We thus predicted that fertilizing with phosphate-P would reduce AMF abundance and, in turn, reduce RPE of mutant barley. We packed microcosms with a P-responsive soil in which we grew mutant barley lacking root hairs as well as wild type barley and narrowleaf plantain, each possessing root hairs. One set of microcosms was fertilized with phosphate-P while another set was not fertilized. The plants were grown in a labelling chamber with 13C-depleted CO2. Soil respiration and δ13C of headspace CO2 were measured after 3, 4 and 5 weeks and RPE was calculated using an isotope mass balance approach. Root hair length was measured and soils were analyzed for the 16:1ω5 neutral lipid fatty acid (i.e. AMF biomarker). AMF abundance was greater, whereas RPE was lower, in mutant barley soil under low-P than under high-P conditions. In the other two plant-types, P had no effect on AMF or on RPE. As our results contradict our prediction, we propose an alternative explanation based on plant N demand under high-P.

Bioirrigation: a common mycorrhizal network facilitates the water transfer from deep-rooted pigeon pea to shallow-rooted finger millet under drought

Hydraulically lifted water can be redistributed to a neighbouring plant, a process referred to as “bioirrigation”. Facilitation of bioirrigation by beneficial microbes such as arbuscular mycorrhizal (AM) fungi that form a common mycorrhizal network (CMN) between neighbouring plants has often been suggested but is not yet well explored. In this study, we tested if the presence of a CMN can facilitate the transfer of hydraulically lifted water from pigeon pea (PP) to finger millet (FM) and ameliorate thereby the water relations of the shallow-rooted FM during drought. In a compartmented microcosm set up, PP roots were grown up to the bottom layer of the pot to access the soil moisture. Whereas FM roots were restricted into a shallow compartment, separated through a 21 μm nylon mesh, without access to the moist bottom layer. We applied deuterium labelled water to the bottom layer of the pot to test if PP can perform hydraulic lift (HL) and if hydraulically lifted water is transferred to FM via a CMN. During the drought period we also assessed the water relations of FM to determine if bioirrigation mediated through a CMN can support the water relations of FM. Application of deuterium-enriched water to the moist bottom layer of the microcosms demonstrated the capability of PP to hydraulically lift water to the drier topsoil through an insulation layer of coarse gravel. Only FM plants that were connected to PP via a CMN were able to utilize HL water. As a consequence, FM bioirrigated by PP in the presence of a CMN was able to maintain its water relations during drought conditions and showed higher rates of survival than FM plants in monoculture. Connecting the rhizosphere of two intercropping partners with a CMN can improve the water relations of shallow-rooted crops by bioirrigation. This finding has great potential for reducing drought induced crop yield loss in arid and semi-arid tropics.

PAH biodegradation by telluric saprotrophic fungi isolated from aged PAH-contaminated soils in mineral medium and historically contaminated soil microcosms

Remediation of contaminated soils is of high relevance considering losses of this limited resource in most countries through erosion or through destruction for societal purposes. Most physicochemical remediation techniques lead to soil destruction avoiding reuse of the sites and loss of soil functions including ecological services like water retention/filtration, plant needs, carbon sequestration, or atmosphere restoration. This study aims to find out efficient telluric PAH-degrading fungi to both remediate soils and preserve their functioning. Fifty telluric saprotrophic fungi were thus isolated from different aged PAH-contaminated soils sampled from four brownfields in the North of France. Thirty of these isolates were screened in a mineral medium for their ability to degrade benzo[a]pyrene (BaP) used as a model of HMW PAH. After 9 days of incubation, the remaining BaP was quantified through HPLC analysis. Then, a set of microcosms was performed with an aged PAH-contaminated non-sterile soil encompassing different approaches with bioaugmentation using mycelia of three strains pre-established on expanded clay particles and, for one of these strains, biostimulation strategies including nitrogen or nitrogen/phosphorous supplementations or aeration by stirring. After an incubation time of 30 days, remaining PAH were quantified through GC-MS and evolution of fungal populations evaluated through qPCR. Isolated Penicillium canescens, Cladosporium cladosporioides, Fusarium solani, and Talaromyces helicus degraded more than 30% of the initial 500 μg of BaP after 9 days of incubation. The three latest strains were thus inoculated in aged PAH-contaminated soil microcosms. After 30 days, PAH quantitative analyses showed that the highest degradation was obtained by bioaugmentation with T. helicus (26% of the initial total PAH content: 321.7 mg kg−1), which seems high considering an aged industrial contamination. Biostimulation approaches coupled to the inoculation of this strain did not improve the degradation. DNA quantification of the inoculated species confirmed their enrichment in the soil revealing the interest of the used inoculation strategy. We discuss bioaugmentation and biostimulation approaches in the case of the considered pollutants and soil. A strain identified as T. helicus appears interesting for its HMW PAH degradation capacities both in mineral medium with pure BaP and in industrial non-sterile soil microcosms contaminated with a hydrocarbon complex mixture. This study also confirms the efficiency of a well-studied BaP-degrading strain of F. solani. These results indicate the potentialities of the used bioaugmentation approach and underline the necessity of scale-up strategies to apply this kind of technique on site.

Degradation of a fluoroquinolone antibiotic in an urbanized stretch of the River Tiber

The widespread detection of antibiotics in terrestrial and aquatic systems has engendered significant scientific and regulatory concern. Overall, knowledge concerning the ecotoxicology and sub-lethal effects in water is scarce, but some experimental studies show that antibiotics can induce pathogen resistance and they can also have detrimental effects on natural microbial communities and their key functions.The main aim of this study was to investigate the occurrence of the biodegradation and photodegradation processes of the fluoroquinolone ciprofloxacin (CIP) in the River Tiber waters, in a stretch highly impacted from human pressure. Two set of microcosms consisting of river water containing the natural microbial community and treated with 500μg/L of CIP in absence or presence of UV-light were performed. Moreover, some microcosms were filled with river water previously sterilized and then treated with the antibiotic. The combined experimental set made it possible to evaluate if the antibiotic CIP could be photodegraded and/or biodegraded.CIP residual concentrations were measured over time by using HPLC coupled to fluorescence detection (FLD) and the effects of the antibiotic on the natural microbial community were assessed in terms of live cell abundance. The key role of light in CIP disappearance was confirmed, but also its biodegradation in natural river water was demonstrated. In fact, differently from other experiments we found a higher degradation rate (DT50=10.4d), in presence of both light and the natural river bacterial populations than in the same sterilized river water (DT50=18.4d). Moreover, even in the dark, a partial CIP biodegradation was also observed (DT50=177d). The overall results were supported by the increase in live cell numbers with the decrease of CIP concentrations both in the dark and light condition.

Response of the bacterial community in oil-contaminated marine water to the addition of chemical and biological dispersants

The use of dispersants in different stages of the oil production chain and for the remediation of water and soil is a well established practice. However, the choice for a chemical or biological dispersant is still a controversial subject. Chemical surfactants that persist long in the environment may pose problems of toxicity themselves; therefore, biosurfactants are considered to constitute an environmentally friendly and effective alternative. Nevertheless, the putative effects of such agents on the microbiomes of oil-contaminated and uncontaminated marine environments have not been sufficiently evaluated. Here, we studied the effects of the surfactant Ultrasperse II® and the surfactin (biosurfactant) produced by Bacillus sp. H2O-1 on the bacterial communities of marine water. Specifically, we used quantitative PCR and genetic fingerprint analyses to study the abundance and structure of the bacterial communities in marine water collected from two regions with contrasting climatic conditions. The addition of either chemical surfactant or biosurfactant influenced the structure and abundance of total and oil-degrading bacterial communities of oil-contaminated and uncontaminated marine waters. Remarkably, the bacterial communities responded similarly to the addition of oil and/or either the surfactant or the biosurfactant in both set of microcosms. After 30 days of incubation, the addition of surfactin enhanced the oil-degrading bacteria more than the chemical surfactant. However, no increase of hydrocarbon biodegradation values was observed, irrespective of the dispersant used. These data contribute to an increased understanding of the impact of novel dispersants on marine bacteriomes before commercial release into the environment.

Critérios Qualis A1 da Educação: a avaliação sob a perspectiva da disputa acadêmica

O objetivo deste artigo é refletir sobre os critérios do Qualis Periódico da Educação, mecanismo de avaliação dos periódicos, parte de um complexo sistema de avaliação dos programas de pós-graduação. Por meio do método documental, selecionamos como objeto de estudo os critérios A1 definidos pelo Documento de Área da Avaliação Trienal de 2013, os mais atuais da área da Educação. Com base nas discussões sociológicas da teoria de campo de Pierre Bourdieu, ao analisar cada um dos critérios, caracterizamos a revista como um agente sujeito à s regras que regem a disputa pelo capital simbólico em jogo nesse microcosmo. Ainda que na esfera da prática, o processo avaliativo seja mais complexo do que prevê os documentos oficiais, a análise realizada evidencia como os critérios adotados pela Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Capes) traduzem as disputas acadêmicas em busca de legitimidade, por meio de disposições próprias adquiridas no interior do próprio campo.

Trace element release patterns from three floodplain soils under simulated oxidized–reduced cycles

River-floodplain ecosystems are long-term sinks for certain contaminants. Fluctuations between flooding and drying are major drivers of spatial and temporal changing biogeochemical processes within floodplain soils. Even small changes of the frequency, magnitude, and timing of drying and rewetting can episodically turn those ecosystems into a source for matter. To understand such changes we investigated the effects on top soils of three hydro-geomorphological units that are typical for floodplains: depression, levee, and plateau. They show distinct characteristics regarding soil type, trace element (TE) pollution level and hydrology. In the laboratory we used an automated biogeochemical microcosm set up to simulate oxidized–reduced cycles to monitor the effects of strong fluctuating redox potential (EH), on pH, iron (Fe), manganese (Mn), sulfur (S), nitrate (NO3), dissolved organic carbon (DOC) and dissolved concentrations of arsenic (As), cadmium (Cd), copper (Cu), chromium (Cr), nickel (Ni), and zinc (Zn) in the soil solution. The results indicated different responses regarding the course of EH/pH and different release patterns of TEs for each hydro-geomorphological unit separately. Both could be mainly allocated to their explicit spatial characteristics; due to differences in its buffer capacities and to the interaction between pH-value and microbial activity. In particular, we could demonstrate that a combination of several biogeochemical factors may influence TE release or retention in floodplain soils by means of generalized additive models (GAMs). Using those, Fe and S were identified as most important factors that determined the dynamics of TEs in all three studied soils; concentrations of As, Cu, Cr, Ni, and Zn increased with increasing Fe-concentrations whereas Cd, Cu, Cr, Ni, and Zn seem correspondingly to be dependent on S that went along with the course of the oxidized–reduced cycle. Still, several uncertainties between environmental changes and TE release from floodplain soils may exist. Thus, the fate of dissolved TEs in river-floodplain ecosystems needs to be taken under serious consideration since the ecotoxicology threat of them is of undisputed risk.

Changes in microbial community structure and functioning of a semiarid soil due to the use of anaerobic digestate derived composts and rosemary plants

We studied the changes in structure and functioning of the microbial community in a degraded agricultural soil after the addition of two composts, obtained from cattle manure or pig slurry anaerobic digestate, and the use of rosemary plants for restoring soil quality.The composts were added at low or high doses to soil samples (30 or 60tha−1, respectively), which were kept in microcosms for 6months. Some soil microcosms were treated with inorganic fertiliser and other non-treated soils were used as microbiological controls. Rosemary plants, used both for their ability to grow in semi-arid regions and for the capacity of their root system to protect soil from erosion, were planted in half of the entire microcosm set up. At different times (0–180days) microbial abundance and dehydrogenase activity were measured in the various experimental treatments. Total and water-soluble soil organic carbon and nitrogen contents were assessed at 0 and 180days. With an increase in carbon and nitrogen soil content, a rise in microbial abundance was also observed in the presence of both composts. However, microbial activity was significantly influenced by the presence of rosemary, without considering the allochthonous carbon and nitrogen input. Microbial community structure and diversity were also assessed by Fluorescence In Situ Hybridization in the different treatments. The highest values for microbial community biodiversity were found in the co-presence of rosemary and at low concentrations of both composts.The overall results suggest that the use of composts together with plant species suited to Mediterranean areas seems to be an appropriate strategy for restoring soil quality and the ecosystem services provided by microorganisms.

Fungal communities are more sensitive indicators to non-extreme soil moisture variations than bacterial communities

Many studies have focused on the impact of intense drought and rain events on soil functioning and diversity, but little attention has been paid to the response of microbial communities to non-extreme soil moisture variations. However, small fluctuations of soil water content represent a common situation that ought to be examined before understanding and deciphering the impact of extreme events. Here, we tested the impact of a decrease in average soil water content and small water content fluctuations in non-extreme conditions on microbial community composition and C mineralisation rate of a temperate meadow soil. Two soil microcosm sets were incubated at high and low constant moisture and a third set was subjected to 4 short dry–wet cycles between these two soil moistures. No robust change in bacterial community composition, molecular microbial biomass, and fungal:bacterial ratio were associated with soil water content change. On the contrary, the fungal community composition rapidly alternated between states corresponding to the high and low levels of soil moisture content. In addition, gross C mineralisation was correlated with soil moisture, with a noteworthy absence of a Birch effect (C over-mineralisation) during the wetting. This study suggests that some fungal populations could coexist by occupying different moisture niches, and high fungal community plasticity would classify them as more sensitive indicators of soil moisture than bacteria. Moreover, under non-stressed conditions, the community composition did not affect metabolic performance so a future decrease in average soil moisture content should not result in a supplemental loss in soil carbon stocks by a Birch effect.

Elevated temperature may intensify the positive effects of nutrients on microbial decomposition in streams

Summary Climate change scenarios predict an increase in global temperature and alterations in precipitation regimes, which may change nutrient concentrations in waterbodies. In forested streams, decomposition of allochthonous organic matter is a key ecosystem process that is affected by the quality of plant litter entering the streams and several environmental factors, including nutrient concentrations, whose interactive effects are difficult to predict. We examined the concomitant effects of increased temperature, concentration of inorganic nutrients in stream water and litter quality on leaf decomposition and activity of microbial decomposers. Leaves of alder (Alnus glutinosa) and oak (Quercus robur), representative of high and low initial N content, respectively, were immersed in a stream (NW Portugal) to allow microbial colonisation and then were exposed in microcosms to increasing concentrations of N‐NO3 (0.09–5 mg L−1; six levels) and P‐PO4 (0.003–0.3 mg L−1; three levels) alone or in all possible combinations. One set of microcosms was kept at 12 °C, a temperature typically found in Iberian streams in autumn, and the other set at 18 °C to simulate a warming scenario. Nitrogen immobilisation was higher in alder than in oak leaves, and increased with temperature and N concentration in stream water for both leaf species. Leaf decomposition, fungal biomass accrual and reproduction were not affected by P concentration, but overall microbial activity increased asymptotically (Michaelis–Menten kinetics) with N concentration. Increased temperature led to an increase in maximum activity of fungal decomposers and to a decrease in N concentration needed to achieve it, especially in alder leaves. Under the predicted warming scenario, leaf decomposition may become faster in streams with lower nutrient levels, especially those receiving high‐quality leaf litter.