Determination of physical properties of undisturbed soil samples according to V. Novák.

The methodology described here presents the procedures for determining physical soil properties of undisturbed soil samples. Besides describing the methods for determining bulk and particle density, moisture content and porosity of the soil in detail, it also offers a way of determining soil's water holding properties when there is no pressure membrane apparatus available. This method is based on a capillary water saturation experiment and gravimetric measurements performed in different time intervals after the saturation (30 minutes, 2 hours, and 24 hours). With a few, simple to follow steps, and not using complicated and space-consuming equipment, it can be replicated in almost any laboratory, and the results are easily interpreted. The method was, and still is, widely used in the Czech Republic, and some parts of it are used as standard soil testing methods. To a lesser or greater detail, this method is described in Rejsek (1999), Valla et al. (2011), Pospísilová et al. (2016) and ÚKZÚZ (2016), and this methodology is compiled from those publications, mainly focusing (and using the same abbreviations) on the procedures described by Valla et al. (2011). The methodology described does not essentially differ from the original, but the steps here have been described to a greater detail, based on the practical experiences obtained over the years, in order to make some common mistakes less likely to happen. The methodology is further complemented with graphical illustrations for each step described in the process, making it clearer, more easily understood, and easier to replicate. Since this methodology has not been available in English so far, this guide offers a great opportunity of its replication on an international level.•Simple, cost-effective and environmentally friendly method for determining physical soil properties•Easy replication and results interpretation•Results can be obtained even in non-highly specialized soil laboratories.

Assessment of potential exposure to As, Cd, Pb and Zn in vegetable garden soils and vegetables in a mining region.

Mining and smelting activities can contaminate soils and affect farming due to high emissions and input of potentially toxic elements (PTE) into the environment. Soils (sampled from two depths) and market vegetables from vegetable gardens located within the vicinity of unconfined slag deposits from decades of mining and smelting activities in Kutná Hora, Czechia were assessed to determine to what extent they pose a health hazard to communities that use these gardens. Pseudo-total As concentrations in the soils exceeded background levels (4.5 mg kg-1) 1.9-93 times, with higher concentrations in the deeper layer. The pseudo-total concentrations of PTE in soils ranked in the order As > Zn > Cd > Pb. Phyto-available concentrations of PTE in soils were relatively low, compared to pseudo-total concentrations. Concentration of As, Cd, Pb and Zn in the vegetables exceeded guideline values, with the highest concentrations found in the fruits of cucumber, peppers, and zucchini. Despite low phyto-available PTE concentrations in soils, all the PTE concentrations in the vegetables surpassed the guidelines set by the Czech Ministry of Health and EU directive, indicating a health hazard to consumers.

Bioleaching of Manganese Oxides at Different Oxidation States by Filamentous Fungus Aspergillus niger.

This work aimed to examine the bioleaching of manganese oxides at various oxidation states (MnO, MnO·Mn2O3, Mn2O3 and MnO2) by a strain of the filamentous fungus Aspergillus niger, a frequent soil representative. Our results showed that the fungus effectively disintegrated the crystal structure of selected mineral manganese phases. Thereby, during a 31-day static incubation of oxides in the presence of fungus, manganese was bioextracted into the culture medium and, in some cases, transformed into a new biogenic mineral. The latter resulted from the precipitation of extracted manganese with biogenic oxalate. The Mn(II,III)-oxide was the most susceptible to fungal biodeterioration, and up to 26% of the manganese content in oxide was extracted by the fungus into the medium. The detected variabilities in biogenic oxalate and gluconate accumulation in the medium are also discussed regarding the fungal sensitivity to manganese. These suggest an alternative pathway of manganese oxides' biodeterioration via a reductive dissolution. There, the oxalate metabolites are consumed as the reductive agents. Our results highlight the significance of fungal activity in manganese mobilization and transformation. The soil fungi should be considered an important geoactive agent that affects the stability of natural geochemical barriers.

Aspergillus niger enhances oxalate production as a response to phosphate deficiency induced by aluminium(III).

This paper investigates Aspergillus niger's behaviour in the presence of mobile Al3+ species by evaluating the changes in oxalate exudation at various aluminium contents. When the fungus was exposed to Al3+, no significant changes in oxalate production were observed until 100 mg.L-1 aluminium was reached resulting in oxalate production decrease by 18.2%. By stripping the culture medium completely of phosphate, even more prominent decrease by 34.8% and 67.1% at 10 and 100 mg.L-1 aluminium was observed, respectively, indicating the phosphate's significance instead of Al3+ in oxalate production. Our results suggest that the low phosphate bioavailability, which most likely resulted from its interaction with Al3+, stimulated the overproduction of oxalate by A. niger. Furthermore, when the fungus was incubated in aluminium-free media supplemented with 0.1 mM of phosphate, oxalate production increased up to 281.5 µmol.g-1, while at 1.85 mM of available phosphate only 80.7 µmol.g-1 of oxalate was produced. This indicates that oxalic acid is produced by fungus not as a mean to detoxify aluminium, but as an attempt to gain access to additional phosphate.

Antimony leaching from antimony-bearing ferric oxyhydroxides by filamentous fungi and biotransformation of ferric substrate.

Ferric oxyhydroxides are natural scavengers of antimony, thus, they contribute significantly to antimony immobilization in soils and sediments. Recent studies, however, usually omit microbial influence on geochemically stable antimony-ferric oxyhydroxide association. Therefore, we have evaluated fungal contribution to antimony mobility during static cultivation of common soil fungus Aspergillus niger in presence of ferric oxyhydroxides. Our results indicate distinguished effect of fungus on antimony distribution at two different antimony concentrations that were used for antimony pre-adsorbtion onto ferric oxyhydroxides prior to the inoculation. Approximately 36% of antimony was bioextracted by fungus from antimony bearing ferric oxyhydroxide after 14-day cultivation when the 8.9 mg·L-1 antimony concentration was used for pre-adsorption. However, no statistically significant change of antimony content in ferric oxyhydroxides was observed after cultivation when initial 48 mg·L-1 antimony concentration was used for pre-adsorption. As Mössbauer spectroscopy and XRD analysis indicated, nanosized akageneite, goethite, and lepidocrocite enhanced their crystallinity during cultivation, while hematite was identified only after the cultivation. Nevertheless, presence of ferric oxyhydroxides at both initial concentrations enabled transformation of antimony into volatile derivatives, and almost 9.5% of antimony was biovolatilized after cultivation. These results contribute significantly to environmental geochemistry of antimony-ferric oxyhydroxides association and highlight the importance of microbial activity in relation to ferric component of natural geochemical barriers.

Evaluation of aluminium mobilization from its soil mineral pools by simultaneous effect of Aspergillus strains' acidic and chelating exometabolites.

This contribution investigates aluminium mobilization from main aluminium pools in soils, phyllosilicates and oxyhydroxides, by acidic and chelating exometabolites of common soil fungi Aspergillus niger and A. clavatus. Their exometabolites' acidity as well as their ability to extract aluminium from solid mineral phases differed significantly during incubation. While both strains are able to mobilize aluminium from boehmite and aluminium oxide mixture to some extent, A. clavatus struggles to mobilize any aluminium from gibbsite. Furthermore, passive and active fungal uptake of aluminium enhances its mobilization from boehmite, especially in later growth phase, with strong linear correlation between aluminium bioaccumulated fraction and increasing culture medium pH. We also provide data on concentrations of oxalate, citrate and gluconate which are synthesized by A. niger and contribute to aluminium mobilization. Compared to boehmite-free treatment, fungus reduces oxalate production significantly in boehmite presence to restrict aluminium extraction efficiency. However, in presence of high phyllosilicates' dosages, aluminium is released to an extent that acetate and citrate is overproduced by fungus. Our results also highlight fungal capability to significantly enhance iron and silicon mobility as these elements are extracted from mineral lattice of phyllosilicates by fungal exometabolites alongside aluminium.