Soil microorganisms represent one of the largest biodiversity reservoirs. However, most low-abundance, slow-growing or dormant microorganisms in soils are difficult to capture with traditional enrichment culture methods. These types of microorganisms represent a valuable “microbial seed bank”. To better exploit and utilize this “microbial dark matter”, we developed a novel strategy that integrates single-cell-level isolation with microfluidics technology and culture with resuscitation-promoting factor (Rpf) to isolate biphenyl-degrading bacteria from four typical soils (paddy soil, red soil, alluvial soil and black soil) in eastern China. Multitudinous bacteria were successfully isolated and cultured; some of the identified clades have not been previously linked to biphenyl biodegradation, such as Actinotalea, Curtobacterium and Rothia. Soil microcosmic experiments validated that some bacteria are responsible for biphenyl degradation in soil. In addition, genomic sequencing and Illumina MiSeq sequencing of 16S rRNA genes indicated that exogenous Rpf mainly promotes the recovery and growth of bacteria containing endogenous Rpf-encoding genes. In summary, this study provides a novel strategy for capturing target functional microorganisms in soils, indicates potential bioresources for the bioremediation of contaminated soils, and enhances our current understanding of the mechanisms involved in the response to exogenous Rpf.

This study evaluated three biochars derived from bioenergy by-products — manure-based anaerobic digestate (DIG), distillers’ grains (DIS), and a mixture thereof (75G25S) — as amendments to stabilize Hg in contaminated floodplain soil under long-term saturated (up to 200 d) and cyclic drying and rewetting conditions. Greater total Hg (THg) removal (72 to nearly 100%) and limited MeHg production (<65 ng L⁻¹) were observed in digestate-based biochar-amended systems under initial saturated conditions. Drying and rewetting resulted in limited THg release, increased aqueous MeHg, and decreased solid MeHg in digestate-based biochar-amended systems. Changes in Fe and S chemistry as well as microbial communities during drying and rewetting potentially affected MeHg production. Digestate-based biochars may be more effective as amendments to control Hg release and minimize MeHg production in floodplain soils under long-term saturated and drying and rewetting conditions compared to distillers’ grains biochar.

Enhancing metals phytoextraction using gentile mobilizing agents might be an appropriate approach to increase the phytoextraction efficiency and to shorten the phytoremediation duration. The effect of sulfur-impregnated organoclay (SIOC) on the redistribution of potentially toxic elements (PTEs) among their geochemical fractions in soils and their plant uptake has not yet been studied. Therefore, our aim is to investigate the role of different SIOC application doses (1%, 3% and 5%) on operationally defined geochemical fractions (soluble + exchangeable; bound to carbonate; manganese oxide; organic matter; sulfide; poorly- and well-crystalline Fe oxide; and residual fraction) of Cd, Cr, Cu, Ni, Pb, and Zn, and their accumulation by pea (Pisum sativum) and corn (Zea mays) in a greenhouse pot experiment using a polluted floodplain soil. The SIOC caused a significant decrease in soil pH, and an increase in organic carbon and total sulfur content in the soil. The addition of SIOC increased significantly the soluble + exchangeable fraction and bioavailability of the metals. The SIOC leads to a transformation of the residual, organic, and Fe-Mn oxide fractions of Cd, Cu, Ni, and Zn to the soluble + exchangeable fraction. The SIOC addition increased the potential mobile (non-residual) fraction of Cr and Pb. The SIOC increased the sulfide fraction of Cr, Ni, and Zn, while it decreased the same fraction for Cd, Cu, and Pb. The effect of SIOC on the redistribution of metal fractions increased with enhancing application dosages. Pea accumulated more metals than corn with greater accumulation in the roots than shoots. Application of the higher dose of SIOC promoted the metals accumulation by roots and their translocation to shoots of pea and corn. Our results suggest the potential suitability of SIOC for enhancing the phytomanagement of PTEs polluted soils and reducing the environmental risk of these pollutants.

Mining activities have contaminated many riverine floodplains with arsenic (As). When floodplain soils become anoxic under water-saturated conditions, As can be released from the solid phase. Several microbially-driven As solubilization processes and numerous influential factors were recognized in the past. However, the interplay and relative importance of soil properties and the influence of environmental factors such as temperature remain poorly understood, especially considering the (co)variation of soil properties in a floodplain. We conducted anoxic microcosm experiments at 10, 17.5, and 25 °C using 65 representative soils from the mining-impacted Ogosta River floodplain in Bulgaria. To investigate the processes of As solubilization and its quantitative variation we followed the As and Fe redox dynamics in the solid and the dissolved phase and monitored a range of other solution parameters including pH, Eh, dissolved organic C, and dissolved Mn. We related soil properties to dissolved As observed after 20 days of microcosm incubation to identify key soil properties for As solubilization. Our results evidenced reductive dissolution of As-bearing Fe(III)-oxyhydroxides as the main cause for high solubilization. The availability of nutrients, most likely organic C as the source of energy for microorganisms, was found to limit this process. Following the vertical nutrient gradient common in vegetated soil, we observed several hundred μM dissolved As after 1–2 weeks for some topsoils (0–20 cm), while for subsoils (20–40 cm) with comparable total As levels only minor solubilization was observed. While high Mn contents were found to inhibit As solubilization, the opposite applied for higher temperature (Q10 2.3–6.1 for range 10–25 °C). Our results suggest that flooding of nutrient-rich surface layers might be more problematic than water-saturation of nutrient-poor subsoil layers, especially in summer floodings when soil temperature is higher than in winter or spring.

Arsenic contamination of floodplain soils is extensive and additional fresh arsenic inputs to the pedosphere from human activities are ongoing.We investigate the cumulative effects of repetitive soil redox cycles, which occur naturally during flooding and draining, on a calcareous fluvisol, the native microbial community and arsenic mobility following a simulated contamination event.We show through bioreactor experiments, spectroscopic techniques and modelling that repetitive redox cycling can decrease arsenic mobility during reducing conditions by up to 45%. Phylogenetic and functional analyses of the microbial community indicate that iron cycling is a key driver of observed changes to solution chemistry. We discuss probable mechanisms responsible for the arsenic immobilisation observed in-situ. The proposed mechanisms include, decreased heterotrophic iron reduction due to the depletion of labile particulate organic matter (POM), increases to the proportion of co-precipitated vs. aqueous or sorbed arsenic with α-FeOOH/Fe(OH)3 and potential precipitation of amorphous ferric arsenate.

Analytical techniques used to assess the environmental risk of contamination from polycyclic aromatic hydrocarbons (PAHs) typically consider only abiotic sample parameters. Supercritical fluid extraction and sorption enthalpy experiments previously suggested slow desorption rates for PAH compounds in two coal-contaminated floodplain soils. In this study, the actual PAH availability for aerobic soil microorganisms was tested in two series of soil-slurry experiments. The experimental conditions supported microbial degradation of phenanthrene if it was weakly sorbed onto silica gel. Native coals and coal-derived particles in two soils effectively acted as very strong sorbents and prevented microbial PAH degradation. The long history of PAH exposure and degree of coal contamination apparently had no influence on the capability of the microbial soil community to overcome constraints of PAH availability. Within the context of the experimental conditions and the compounds chosen, our results confirm that coal-bound PAHs are not bioavailable and hence of low environmental concern.

Present study reports the laboratory and field scale application of different organic and inorganic amendments to immobilize cadmium (Cd) and lead (Pb) in a co-contaminated alluvial paddy soil. For that purpose, lime, biochar, Fe-biochar and two composite amendments (CA) composed of biochar, lime, sepiolite and zeolite (CA1: composite amendment 1) and manure, lime and sepiolite (CA2: composite amendment 2) were firstly tested in an incubation experiment to ameliorate Cd and Pb co-contaminated alluvial soil. It was observed that liming and CA2 elevated the soil pH and reduced DTPA extractable Cd and Pb in the incubated soil leading to higher metal immobilization. Therefore, efficiency of lime and CA2 was further investigated in field conditions with mid rice as the test crop to evaluate field scale immobilization and precise application rate for the tested soil type. DTPA and CaCl₂ extractable Cd (46 and 51%) and Pb (68 and 70%) in field soil were decreased with applied treatments. Speciation of Cd and Pb also promoted conversion of metal exchangeable contents to less-available forms. Activated functional groups on amendments’ surface (_OH bonding, C_O and CO, -O-H, Si–O–Si, carboxylic and ester groups) sequestered metals by precipitation, adsorption, ion exchange or electro static attributes. Application of lime at 2400 kg/acre (T4) and CA2 at 1200 kg/acre was more effective in reducing rice shoot and grains metal contents. Moreover, obtained results in terms of pH, extractable content, speciation and yield, and microanalysis of amendments highlights the remarkable efficiency of lime and composite amendment to sorb Cd and Pb providing the key evidence of these amendments for metals immobilization and environmental remediation. Considering these results, lime and CA2 are potential amendments for co-contaminated rice field especially in context of alluvial soil.

We aimed to assess the dynamics of pore water concentrations of Cd, Co, Cu, Ni, Zn and their controlling factors (EH, pH, DOC, Fe, Mn, and SO42−) in a contaminated floodplain soil under different flood-dry-cycles. Two parallel undisturbed groundwater lysimeters (mean values presented) were used for long term (LT; 94 days) and short term (ST; 21 days) flood-dry-cycles. Reducing conditions under LT lead to low EH and pH, while DOC, Co, Fe, Mn, and Ni increased. Cadmium, Cu, Zn, and SO42− increased under oxidizing conditions during ST. Cobalt and Ni revealed a similar behavior which seem to governed by EH/pH, Mn, Fe, and DOC. Cadmium, Cu, and Zn reveal a similar fate; their dynamics were affected by EH/pH, DOC, and SO42−. Our findings suggest that a release of Cd, Cu, Co, Fe, Mn, Ni, and Zn under different flood-dry-cycles can assumed what might create potential environmental risks in using metal-enriched floodplain soils.

Environmental pollution by mercury (Hg) is a considerable environmental problem world-wide. Due to the occurrence of Hg volatilization from their soils, floodplains can function as an important source of volatile Hg. Soil temperature and soil water content related to flood dynamics are considered as important factors affecting seasonal dynamics of total gaseous mercury (TGM) fluxes. We quantified seasonal variations of TGM fluxes and conducted a laboratory microcosm experiment to assess the effect of temperature and moisture on TGM fluxes in heavily polluted floodplain soils. Observed TGM emissions ranged from 10 to 850 ng m−2 h−1 and extremely exceeded the emissions of non-polluted sites. TGM emissions increased exponentially with raised air and soil temperatures in both field (R2: 0.49–0.70) and laboratory (R2: 0.99) experiments. Wet soil material showed higher TGM fluxes, whereas the role of soil water content was affected by sampling time during the microcosm experiments. Warmer environmental conditions result in higher Hg volatilization rates from floodplain soils.

Mercury biomagnification on the South River floodplain (Virginia, USA) was modeled at two locations along a river reach previously modeled for methylmercury movement through the aquatic trophic web. This provided an opportunity to compare biomagnification in adjoining trophic webs. Like the aquatic modeling results, methylmercury-based models provided better prediction than those for total mercury. Total mercury Food Web Magnification Factors (FWMF, fold per trophic level) for the two locations were 4.9 and 9.5. Methylmercury FWMF for the floodplain locations were higher (9.3 and 25.1) than that of the adjacent river (4.6). Previous speculation was not resolved regarding whether the high mercury concentrations observed in floodplain birds was materially influenced by river prey consumption by riparian spiders and subsequent spider movement into the trophic web of the adjacent floodplains. Results were consistent with a gradual methylmercury concentration increase from contaminated floodplain soil, to arthropod prey, and finally, to avian predators.