► Mineralisation of toxic pollutants can be higher in soil than in water. ► Ciprofloxacin affects the microbial communities and activities in soil. ► Toxicity of ciprofloxacin is reduced in soil due ...to sorption processes. ► Despite the buffering capacity of soil, ciprofloxacin remains active. ► Ciprofloxacin resistance can develop in soils contaminated with this antibiotic.
While antibiotics are frequently found in the environment, their biodegradability and ecotoxicological effects are not well understood. Ciprofloxacin inhibits active and growing microorganisms and therefore can represent an important risk for the environment, especially for soil microbial ecology and microbial ecosystem services. We investigated the biodegradation of
14C-ciprofloxacin in water and soil following OECD tests (301B, 307) to compare its fate in both systems. Ciprofloxacin is recalcitrant to biodegradation and transformation in the aqueous system. However, some mineralisation was observed in soil. The lower bioavailability of ciprofloxacin seems to reduce the compound's toxicity against microorganisms and allows its biodegradation. Moreover, ciprofloxacin strongly inhibits the microbial activities in both systems. Higher inhibition was observed in water than in soil and although its antimicrobial potency is reduced by sorption and aging in soil, ciprofloxacin remains biologically active over time. Therefore sorption does not completely eliminate the effects of this compound.
Fungal-bacterial interactions are highly diverse and contribute to many ecosystem processes. Their emergence under common environmental stress scenarios however, remains elusive. Here we use a ...synthetic microbial ecosystem based on the germination of Bacillus subtilis spores to examine whether fungal and fungal-like (oomycete) mycelia reduce bacterial water and nutrient stress in an otherwise dry and nutrient-poor microhabitat. We find that the presence of mycelia enables the germination and subsequent growth of bacterial spores near the hyphae. Using a combination of time of flight- and nanoscale secondary ion mass spectrometry (ToF- and nanoSIMS) coupled with stable isotope labelling, we link spore germination to hyphal transfer of water, carbon and nitrogen. Our study provides direct experimental evidence for the stimulation of bacterial activity by mycelial supply of scarce resources in dry and nutrient-free environments. We propose that mycelia may stimulate bacterial activity and thus contribute to sustaining ecosystem functioning in stressed habitats.
The formation of soil organic matter (SOM) very much depends on microbial activity. Even more, latest studies identified microbial necromass itself being a significant source of SOM and found ...microbial products to initiate and enhance the formation of long-term stabilized SOM. The objectives of this study were to investigate the microbial contribution to SOM in pools of different stability and its impact on SOM quality. Hence, four arable soils of widely differing properties were density-fractionated into free and occluded particulate organic matter (fPOM, oPOM < 1.6 g cm−3 and oPOM < 2.0 g cm−3) and mineral associated organic matter (MOM > 2.0 g cm−3) by using sodium polytungstate. These fractions were characterized by in-source pyrolysis-field ionization mass spectrometry (Py-FIMS). Main SOM compound classes of the fractions were determined and further SOM properties were derived (polydispersity, thermostability). The contribution of microbial derived input to arable soil OM was estimated from the hexose to pentose ratio of the carbohydrates and the ratio of C4–C26 to C26–C36 fatty acids. Additionally, selected samples were investigated by scanning electron microscopy (SEM) for visualizing structures as indicators for the origin of OM. Results showed that, although the samples differed significantly regarding soil properties, SOM composition was comparable and almost 50% of identifiable SOM compounds of all soils types and all density fractions were assigned to phenols, lignin monomers and alkylaromatics. Most distinguishing were the high contents of carbohydrates for the MOM and of lipids for the POM fractions. Qualitative features such as polydispersity or thermostability were not in general assignable to specific compounds, density fractions or different mean residence times. Only the microbial derived part of the soil carbohydrates could be shown to be correlated with high SOM thermostability (r2 = 0.63**, n=39). Microbial derived carbohydrates and fatty acids were both enriched in the MOM, showing that the relative contribution of microbial versus plant-derived input to arable SOM increased with density and therefore especially increased MOM thermostability. Nevertheless, the general microbial contribution to arable SOM is suggested to be high for all density fractions; a mean proportion of about 1:1 was estimated for carbohydrates. Despite biomolecules released from living microorganisms, SEM revealed that microbial mass (biomass and necromass) is a considerable source for stable SOM which is also increasing with density.
•Microbial mass was identified as a significant source for SOM.•Microbial contribution to arable soils OM was especially high for mineral associated OM.•Microbial derived carbohydrates correlated with SOM thermostability.
Forest soils constitute a major carbon pool in the context of the global carbon cycle. Although ectomycorrhizal fungi (EMF) are responsible for a large part of the input of carbon into this pool, ...information on the transformation of EMF biomass into soil organic matter (SOM) is scarce. In order to quantitatively analyze the contribution of EMF biomass to SOM formation, we incubated a typical forest arenosol with 13C-labeled fungal biomass from the ectomycorrhizal basidiomycete Laccaria bicolor in a closed bioreactor system for 231 d, enabling the establishment of a full mass balance for the turnover. rDNA fragments specific for the genus Laccaria disappeared after 28 d, indicating death and decay of the organism. The amount of 13C PLFA as a proxy for living biomass decreased to roughly 10% of the initial value in the course of the experiment, again suggesting efficient disintegration of the fungal organism. After 231 d, however, 63.5% of the initially added 13C had been converted to SOM and 52% belonged to the non-living fraction. The analysis of 13CO2 formation (36.5% of the initially added label) suggested two-pool exponential kinetics with k1 = 0.0615 d−1 for the easily degradable and k2 = 0.0005 d−1 for the stable fraction (pool sizes 74% and 26% of the initially added label, respectively). When compared to the degradation of bacterial biomass in agricultural soils, the pool of readily degradable fungal biomass was considerably smaller and the half-lives of both pools (readily degradable and persistent C) were markedly higher for fungal biomass. In summary, our data allow the conclusion that EMF biomass is a significant source of SOM in forest ecosystems.
•A full mass balance for EMF-derived 13C in a forest soil was set up.•After 231 d, 64% of the added C remained in soil and 36% were mineralized.•The degradation kinetics differed from studies with bacterial derived biomass.•EMF necromass is a potential significant contributor to SOM formation.
Morphology and physiology of fish embryos undergo dramatic changes during their development until the onset of feeding, supplied only by endogenous yolk reserves. For obtaining an insight how these ...restructuring processes are reflected by body mass related parameters, dry weights (dw), contents of the elements carbon and nitrogen and lipid and protein levels were quantified in different stages within the first four days of embryo development of the zebrafish (Danio rerio). The data show age dependent changes in tissue composition. Dry weights decreased significantly from 79μgdw/egg at 0hours post fertilization (hpf) to 61 μgdw/egg after 96 hpf. The amounts of total carbon fluctuated between 460 mg g-1 and 540 mg g-1 dw, nitrogen was at about 100 mg g-1 dw and total fatty acids were between 48-73 mg g-1 dw. In contrast to these parameters that remained relatively constant, the protein content, which was 240 mg g-1 at 0 hpf, showed an overall increase of about 40%. Comparisons of intact eggs and dechorionated embryos at stages prior to hatching (24, 30, 48 hpf) showed that the differences seen for dry weight and for carbon and nitrogen contents became smaller at more advanced stages, consistent with transition of material from the chorion to embryo tissue. Further, we determined the effect of 2,4-dinitrophenol at a subacutely toxic concentration (14 μM, LC10) as a model chemical challenge on the examined body mass related parameters. The compound caused significant decreases in phospholipid and glycolipid fatty acid contents along with a decrease in the phospholipid fatty acid unsaturation index. No major changes were observed for the other examined parameters. Lipidomic studies as performed here may thus be useful for determining subacute effects of lipophilic organic compounds on lipid metabolism and on cellular membranes of zebrafish embryos.
Catalytic activity of microbial communities maintains the services and functions of soils. Microbial communities require energy and carbon for microbial growth, which they obtain by transforming ...organic matter (OM), oxidizing a fraction of it and transferring the electrons to various terminal acceptors. Quantifying the relations between matter and energy fluxes is possible when key parameters such as reaction enthalpy (
), energy use efficiency (related to enthalpy) (EUE), carbon use efficiency (CUE), calorespirometric ratio (CR), carbon dioxide evolution rate (CER), and the apparent specific growth rate (
) are known. However, the determination of these parameters suffers from unsatisfying accuracy at the technical (sample size, instrument sensitivity), experimental (sample aeration) and data processing levels thus affecting the precise quantification of relationships between carbon and energy fluxes. To address these questions under controlled conditions, we analyzed microbial turnover processes in a model soil amended using a readily metabolizable substrate (glucose) and three commercial isothermal microcalorimeters (MC-Cal/100P, TAM Air and TAM III) with different sample sizes meaning varying volume-related thermal detection limits (
) (0.05
mW L
). We conducted aeration experiments (aerated and un-aerated calorimetric ampoules) to investigate the influence of oxygen limitation and thermal perturbation on the measurement signal. We monitored the CER by measuring the additional heat caused by CO
absorption using a NaOH solution acting as a CO
trap. The range of errors associated with the calorimetrically derived
, EUE, and CR was determined and compared with the requirements for quantifying CUE and the degree of anaerobicity (
. Calorimetrically derived
and EUE were independent of the instrument used. However, instruments with a low
yielded the most accurate results. Opening and closing the ampoules for oxygen and CO
exchange did not significantly affect metabolic heats. However, regular opening during calorimetrically derived CER measurements caused significant measuring errors due to strong thermal perturbation of the measurement signal. Comparisons between experimentally determined CR, CUE,
, and modeling indicate that the evaluation of CR should be performed with caution.
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•Maize litter addition stimulated microbial activity and turnover of MCPA.•Litter altered the soil microbiome and MCPA degraders.•Mainly fungi and Gram-negative bacteria involved in ...MCPA degradation.•Litter promoted the formation of biogenic non-extractable residues (bioNERs).•Most bioNERs were found at the 2–5 mm of litter-amended treatment.
Amendment of soils with plant residues is common practice for improving soil quality. In addition to stimulated microbial activity, the supply of fresh soluble organic (C) from litter may accelerate the microbial degradation of chemicals in soils. Therefore, the aim of this study was to test whether the maize litter enhances degradation of 4-chloro-2-methylphenoxyacetic acid (MCPA) and increases formation of non-toxic biogenic non-extractable residues (bioNERs). Soil was amended with 13C6-MCPA and incubated with or without litter addition on the top. Three soil layers were sampled with increasing distance from the top: 0–2 mm, 2–5 mm and 5–20 mm; and the mass balance of 13C6-MCPA transformation determined.
Maize litter promoted microbial activity, mineralization of 13C6-MCPA and bioNER formation in the upper two layers (0–2 and 2–5 mm). The mineralization of 13C6-MCPA in soil with litter increased to 27% compared to only 6% in the control. Accordingly, maize addition reduced the amount of extractable residual MCPA in soil from 77% (control) to 35% of initially applied 13C6-MCPA. While non-extractable residues (NERs) were <6% in control soil, litter addition raised NERs to 21%. Thereby, bioNERs comprised 14% of 13C6-MCPA equivalents. We found characteristic differences of bioNER formation with distance to litter. While total NERs in soil at a distance of 2–5 mm were mostly identified as 13C-bioNERs (97%), only 45–46% of total NERs were assigned to bioNERs in the 0–2 and 5–20 mm layers. Phospholipid fatty acid analysis indicated that fungi and Gram-negative bacteria were mainly involved in MCPA degradation. Maize-C particularly stimulated fungal activity in the adjacent soil, which presumably facilitated non-biogenic NER formation. The plant litter accelerated formation of both non-toxic bioNERs and non-biogenic NERs. More studies on the structural composition of non-biogenic NERs with toxicity potential are needed for future recommendations on litter addition in agriculture.
Abstract
Studying bacterial adhesion to mineral surfaces is crucial for understanding soil properties. Recent research suggests that minimal coverage of sand particles with cell fragments ...significantly reduces soil wettability. Using atomic force microscopy (AFM), we investigated the influence of hypertonic stress on
Pseudomonas fluorescens
adhesion to four different minerals in water. These findings were compared with theoretical XDLVO predictions. To make adhesion force measurements comparable for irregularly shaped particles, we normalized adhesion forces by the respective cell-mineral contact area. Our study revealed an inverse relationship between wettability and the surface-organic carbon content of the minerals. This relationship was evident in the increased adhesion of cells to minerals with decreasing wettability. This phenomenon was attributed to hydrophobic interactions, which appeared to be predominant in all cell–mineral interaction scenarios alongside with hydrogen bonding. Moreover, while montmorillonite and goethite exhibited stronger adhesion to stressed cells, presumably due to enhanced hydrophobic interactions, kaolinite showed an unexpected trend of weaker adhesion to stressed cells. Surprisingly, the adhesion of quartz remained independent of cell stress level. Discrepancies between measured cell–mineral interactions and those calculated by XDLVO, assuming an idealized sphere-plane geometry, helped us interpret the chemical heterogeneity arising from differently exposed edges and planes of minerals. Our results suggest that bacteria may have a significant impact on soil wettability under changing moisture condition.
The understanding of microbial interactions and trophic networks is a prerequisite for the elucidation of the turnover and transformation of organic materials in soils. To elucidate the incorporation ...of biomass carbon into a soil microbial food web, we added ¹³C-labeled Escherichia coli biomass to an agricultural soil and identified those indigenous microbes that were specifically active in its mineralization and carbon sequestration. rRNA stable isotope probing (SIP) revealed that uncultivated relatives of distinct groups of gliding bacterial micropredators (Lysobacter spp., Myxococcales, and the Bacteroidetes) lead carbon sequestration and mineralization from the added biomass. In addition, fungal populations within the Microascaceae were shown to respond to the added biomass after only 1 h of incubation and were thus surprisingly reactive to degradable labile carbon. This RNA-SIP study identifies indigenous microbes specifically active in the transformation of a nondefined complex carbon source, bacterial biomass, directly in a soil ecosystem.
Our understanding of the interactions between minerals, organic matter, and microorganisms at so-called biogeochemical interfaces in soil is still hampered by the inherent complexity of these ...systems. Artificial soil maturation experiments can help to bridge a gap in complexity between simple abiotic sorption experiments and larger-scale field experiments. By controlling other soil-forming factors, the effect of a particular variable can be identified in a simplified system. Here, we review the findings of a series of artificial soil incubation experiments with the aim of revealing general trends and conclusions. The artificial soils were designed to determine the effect of mineral composition and charcoal presence on the development of abiotic and biotic soil properties during maturation. In particular, the development of soil aggregates, organic matter (OM) composition and turnover, sorption properties, and the establishment of microbial community composition and function were considered. The main objectives of the research were to determine (1) how surface properties and sorption of chemicals modify biogeochemical interfaces; (2) how much time is required to form aggregates from mixtures of pure minerals, OM, and a microbial inoculum; and (3) how the presence of different mineral and charcoal surfaces affects aggregation, OM turnover, and the development of microbial community composition.
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