Use of metal-reducing bacteria for bioremediation of soil contaminated with mixed organic and inorganic pollutants

The European trees phyllosphere characteristics and its potential in air bioremediation

The air pollution remediation is naturally carried out by plants. Their overground parts called phyllosphere are a type of a natural filter on which pollutants can be adsorb. Moreover, microbial communities living in phyllosphere perform a variety of biochemical processes removing also chemical pollutants. As their pollution is nowadays a burning issue especially for highly developed countries, the development of effective and ecological technologies for air treatment are of the utmost importance. The use of phyllosphere bacteria in the process of air bioremediation is a promising technology. This article reviews the role of phyllospheric bacteria in air bioremediation processes especially linked with the moderate climate plants. Research results published so far indicate that phyllosphere bacteria are able to metabolize the air pollutants but their potential is strictly determined by plant-phyllospheric bacteria interaction. The European tree species most commonly used for this purpose are also presented. The collected information filled the gap in the practical use of tree species in air bioremediation in the moderate climate zone.

A Biochemical Deconstruction-Based Strategy to Assist the Characterization of Bacterial Electric Conductive Filaments

Periplasmic nanowires and electric conductive filaments made of the polymeric assembly of c-type cytochromes from Geobacter sulfurreducens bacterium are crucial for electron storage and/or extracellular electron transfer. The elucidation of the redox properties of each heme is fundamental to the understanding of the electron transfer mechanisms in these systems, which first requires the specific assignment of the heme NMR signals. The high number of hemes and the molecular weight of the nanowires dramatically decrease the spectral resolution and make this assignment extremely complex or unattainable. The nanowire cytochrome GSU1996 (~42 kDa) is composed of four domains (A to D) each containing three c-type heme groups. In this work, the individual domains (A to D), bi-domains (AB, CD) and full-length nanowire were separately produced at natural abundance. Sufficient protein expression was obtained for domains C (~11 kDa/three hemes) and D (~10 kDa/three hemes), as well as for bi-domain CD (~21 kDa/six hemes). Using 2D-NMR experiments, the assignment of the heme proton NMR signals for domains C and D was obtained and then used to guide the assignment of the corresponding signals in the hexaheme bi-domain CD. This new biochemical deconstruction-based procedure, using nanowire GSU1996 as a model, establishes a new strategy to functionally characterize large multiheme cytochromes.

Interactions between organic matter and Fe oxides at soil micro-interfaces: Quantification, associations, and influencing factors

Iron (Fe) oxides are widely recognized to prevent the degradation of organic matter (OM) in environments, thereby promoting the persistence of organic carbon (OC) in soils. Thus, discerning the association mechanisms of Fe oxides and OC interactions is key to effectively influencing the dynamics and extent of organic C cycling in soils. Previous studies have focused on i) quantifying Fe oxide-bound organic carbon (Fe-OC) in individual environments, ii) investigating the distribution and adsorption capacity of Fe-OC, and iii) assessing the redox cycling and transformation of Fe-OC. Furthermore, the widespread application of high-tech instrumentation and methods has greatly contributed to a better understanding of the mechanism of organic mineral assemblages in the past few decades. However, few literature reviews have comprehensively summarized Fe-OC distributions, associations, and characteristics in soil-plant systems. Here, studies investigating the Fe-OC contents among different environments are reviewed. In addition, the mechanisms and processes related to OM transformation dynamics occurring at mineral-organic interfaces are also described. Recent studies have highlighted that diverse interactions occur between Fe oxides and OC, with organic compounds adhering to Fe oxides due to their huge specific surfaces area and active reaction sites. Moreover, we also review methods for understanding Fe-OC interactions at micro-interfaces. Lastly, developmental prospects for understanding coupled Fe-OC geochemical processes in soil environments at molecular- and nano-scales are outlined. The summary suggests that combined advanced techniques and methods should be used in future research to explore micro-interfaces and in situ descriptions of organic mineral assemblages. This review also suggests that future studies need to consider the functional and spatial complexity that is typical of soil/sediment environments where Fe-OC interactions occur.

Mobilization of contaminants: Potential for soil remediation and unintended consequences

Land treatment has become an essential waste management practice. Therefore, soil becomes a major source of contaminants including organic chemicals and potentially toxic elements (PTEs) which enter the food chain, primarily through leaching to potable water sources, plant uptake, and animal transfer. A range of soil amendments are used to manage the mobility of contaminants and subsequently their bioavailability. Various soil amendments, like desorbing agents, surfactants, and chelating agents, have been applied to increase contaminant mobility and bioavailability. These mobilizing agents are applied to increase the contaminant removal though phytoremediation, bioremediation, and soil washing. However, possible leaching of the mobilized pollutants during soil washing is a major limitation, particularly when there is no active plant uptake. This leads to groundwater contamination and toxicity to plants and soil biota. In this context, the present review provides an overview on various soil amendments used to enhance the bioavailability and mobility of organic and inorganic contaminants, thereby facilitating increased risk when soil is remediated in polluted areas. The unintended consequences of the mobilization methods, when used to remediate polluted sites, are discussed in relation to the leaching of mobilized contaminants when active plant growth is absent. The toxicity of targeted and non-targeted contaminants to microbial communities and higher plants is also discussed. Finally, this review work summarizes the existing research gaps in various contaminant mobilization approaches, and prospects for future research.

Changes of bacterial community in arable soil after short-term application of fresh manures and organic fertilizer

The application of animal manure is highly recommended in agricultural production. However, the effect of different kinds of manures on bacterial community in farmland still remains unclear. In this study, a short-term field experiment was conducted to investigate the rapid effects of pig manure (PM), chicken manure (CM) and organic fertilizer (OF, composted by pig manure) application on soil physicochemical properties and soil bacterial community. The results showed that the application of CM and OF significantly increased soil bacterial richness (p < 0.05), mainly correlated with the increase of soil total nitrogen. Compared with CM and PM, OF had the greatest disturbance to soil bacterial structure. And total phosphorus showed the highest correlation with bacterial community. Meanwhile, the application of OF reduced the relative abundance of Actinobacteria, the organic matter synthetic bacteria, and Nitrospirae, the nitrifying bacteria, by 17.18% and 40.00%, respectively. 16S functional prediction analysis results shows that the application of OF increased the relative abundance of genes encoding Ribulose-1,5-bisphosphate carboxylase/oxyg (RuBsiCO), the genes involved in soil Calvin cycling, by 20.51%, and increased the relative abundance of genes encoding nitrous-oxide reductase by 44.86%. In conclusion, Short-term application of OF had greater disturbance to soil bacteria than CM and PM, and it had a significant influence on soil functional bacteria and genes involved in soil carbon and nitrogen cycling.

Effect of sterilization on cadmium immobilization and bacterial community in alkaline soil remediated by mercapto-palygorskite

Cadmium (Cd) pollution in alkaline soil in some areas of northern China has seriously threatened wheat production and human health. However, there are still few effective amendments for alkaline soil, and the mechanism of amendments with a good immobilization effect remains unclear. In this study, soil sterilization experiments were conducted to investigate the effects of soil microorganisms on the immobilization of a novel amendment-mercapto palygorskite (MPAL) in Cd-contaminated alkaline soils. The results showed that the mercapto on the MPAL surface was not affected by autoclaving. Compared with the control, the available Cd concentration in 0.025% MPAL treatments decreased by 18.80-29.23% after 1 d of aging and stabled after 10 d of aging. Importantly, the immobilization of MPAL on Cd in sterilized soil was significantly better than that in natural soil due to the changes in Cd fractions. Compared with MPAL-treated natural soil, exchangeable Cd fraction and carbonate-bound Cd fraction in MPAL-treated sterilized soil decreased by 20.79-27.09% and 20.05-26.45%, while Fe/Mn oxide-bound Cd fraction and organic matter-bound Cd fraction increased by 17.77-22.68% and 18.85-27.32%. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis found that the potential functions of the microbial community in normal and sterilized soil were different significantly. Soil sterilization increased the soil pH and decreased the arylsulfatase activity, but did not change the soil zeta potential and available sulfur. The changes in Cd fractions in MPAL-treated sterilized soil may be related to the reduction in the bacterial community and the changes in function microbial, but not to the soil properties. In addition, MPAL application had little effects on the bacterial community, soil pH value, zeta potential, available sulfur, and arylsulfatase. These results showed that the immobilization of MPAL on Cd in alkaline soil was stable and effective, and was not affected by soil sterilization and soil microorganism reduction.

The Transcriptomic Landscape of Cupriavidus metallidurans CH34 Acutely Exposed to Copper

Bacteria are increasingly used for biotechnological applications such as bioremediation, biorecovery, bioproduction, and biosensing. The development of strains suited for such applications requires a thorough understanding of their behavior, with a key role for their transcriptomic landscape. We present a thorough analysis of the transcriptome of Cupriavidus metallidurans CH34 cells acutely exposed to copper by tagRNA-sequencing. C. metallidurans CH34 is a model organism for metal resistance, and its potential as a biosensor and candidate for metal bioremediation has been demonstrated in multiple studies. Several metabolic pathways were impacted by Cu exposure, and a broad spectrum of metal resistance mechanisms, not limited to copper-specific clusters, was overexpressed. In addition, several gene clusters involved in the oxidative stress response and the cysteine-sulfur metabolism were induced. In total, 7500 transcription start sites (TSSs) were annotated and classified with respect to their location relative to coding sequences (CDSs). Predicted TSSs were used to re-annotate 182 CDSs. The TSSs of 2422 CDSs were detected, and consensus promotor logos were derived. Interestingly, many leaderless messenger RNAs (mRNAs) were found. In addition, many mRNAs were transcribed from multiple alternative TSSs. We observed pervasive intragenic TSSs both in sense and antisense to CDSs. Antisense transcripts were enriched near the 5' end of mRNAs, indicating a functional role in post-transcriptional regulation. In total, 578 TSSs were detected in intergenic regions, of which 35 were identified as putative small regulatory RNAs. Finally, we provide a detailed analysis of the main copper resistance clusters in CH34, which include many intragenic and antisense transcripts. These results clearly highlight the ubiquity of noncoding transcripts in the CH34 transcriptome, many of which are putatively involved in the regulation of metal resistance.

Bioremediation Options for Heavy Metal Pollution

BACKGROUND

Rapid industrialization and anthropogenic activities such as the unmanaged use of agro-chemicals, fossil fuel burning and dumping of sewage sludge have caused soils and waterways to be severely contaminated with heavy metals. Heavy metals are non-biodegradable and persist in the environment. Hence, remediation is required to avoid heavy metal leaching or mobilization into environmental segments and to facilitate their extraction.

OBJECTIVES

The present work briefly outlines the environmental occurrence of heavy metals and strategies for using microorganisms for bioremediation processes as reported in the scientific literature.

METHODS

Databases were searched from different libraries, including Google Scholar, Medline and Scopus. Observations across studies were then compared with the standards for discharge of environmental pollutants.

DISCUSSION

Bioremediation employs microorganisms for removing heavy metals. Microorganisms have adopted different mechanisms for bioremediation. These mechanisms are unique in their specific requirements, advantages, and disadvantages, the success of which depends chiefly upon the kind of organisms and the contaminants involved in the process.

CONCLUSIONS

Heavy metal pollution creates environmental stress for human beings, plants, animals and other organisms. A complete understanding of the process and various alternatives for remediation at different steps is needed to ensure effective and economic processes.

COMPETING INTERESTS

The authors declare no competing financial interests.

Soil Microbial Forensics

Soil microbial forensics can be defined as the study of how microorganisms can be applied to forensic investigations. The field of soil microbial forensics is of increasing interest and applies techniques commonly used in diverse disciplines in order to identify microbes and determine their abundances, complexities, and interactions with soil and surrounding objects. Emerging new techniques are also providing insights into the complexity of microbes in soil. Soil may harbor unique microbes that may reflect specific physical and chemical characteristics indicating site specificity. While applications of some of these techniques in the field of soil microbial forensics are still in early stages, we are still gaining insight into how microorganisms may be more robustly used in forensic investigations.

Development and applications of a DNA labeling method with magnetic nanoparticles to study the role of horizontal gene transfer events between bacteria in soil pollutant bioremediation processes

Horizontal gene transfers are critical mechanisms of bacterial evolution and adaptation that are involved to a significant level in the degradation of toxic molecules such as xenobiotic pesticides. However, understanding how these mechanisms are regulated in situ and how they could be used by man to increase the degradation potential of soil microbes is compromised by conceptual and technical limitations. This includes the physical and chemical complexity and heterogeneity in such environments leading to an extreme bacterial taxonomical diversity and a strong redundancy of genes and functions. In addition, more than 99 % of soil bacteria fail to develop colonies in vitro, and even new DNA-based investigation methods (metagenomics) are not specific and sensitive enough to consider lysis recalcitrant bacteria and those belonging to the rare biosphere. The objective of the ANR funded project “Emergent” was to develop a new culture independent approach to monitor gene transfer among soil bacteria by labeling plasmid DNA with magnetic nanoparticles in order to specifically capture and isolate recombinant cells using magnetic microfluidic devices. We showed the feasibility of the approach by using electrotransformation to transform a suspension of Escherichia coli cells with biotin-functionalized plasmid DNA molecules linked to streptavidin-coated superparamagnetic nanoparticles. Our results have demonstrated that magnetically labeled cells could be specifically retained on micromagnets integrated in a microfluidic channel and that an efficient selective separation can be achieved with the microfluidic device. Altogether, the project offers a promising alternative to traditional culture-based approaches for deciphering the extent of horizontal gene transfer events mediated by electro or natural genetic transformation mechanisms in complex environments such as soil.

Fate of Cd during microbial Fe(III) mineral reduction by a novel and Cd-tolerant Geobacter species

Fe(III) (oxyhydr)oxides affect the mobility of contaminants in the environment by providing reactive surfaces for sorption. This includes the toxic metal cadmium (Cd), which prevails in agricultural soils and is taken up by crops. Fe(III)-reducing bacteria can mobilize such contaminants by Fe(III) mineral dissolution or immobilize them by sorption to or coprecipitation with secondary Fe minerals. To date, not much is known about the fate of Fe(III) mineral-associated Cd during microbial Fe(III) reduction. Here, we describe the isolation of a new Geobacter sp. strain Cd1 from a Cd-contaminated field site, where the strain accounts for 10(4) cells g(-1) dry soil. Strain Cd1 reduces the poorly crystalline Fe(III) oxyhydroxide ferrihydrite in the presence of at least up to 112 mg Cd L(-1). During initial microbial reduction of Cd-loaded ferrihydrite, sorbed Cd was mobilized. However, during continuous microbial Fe(III) reduction, Cd was immobilized by sorption to and/or coprecipitation within newly formed secondary minerals that contained Ca, Fe, and carbonate, implying the formation of an otavite-siderite-calcite (CdCO3-FeCO3-CaCO3) mixed mineral phase. Our data shows that microbially mediated turnover of Fe minerals affects the mobility of Cd in soils, potentially altering the dynamics of Cd uptake into food or phyto-remediating plants.

Assessment of biochar and iron filing amendments for the remediation of a metal, arsenic and phenanthrene co-contaminated spoil

Sites contaminated with mixtures of metals, metalloids and organics are difficult to remediate as each contaminant type may require a different treatment. Biochar, with high metal sorption capacity, used singly and in combination with iron filings, is investigated in microcosm trials to immobilise metal(loid)s within a contaminated spoil, thereby enabling revegetation and degradation of organic pollutants. A mine spoil, contaminated with heavy metals, arsenic and spiked with phenanthrene was treated with either 1%w/w biochar, 5%w/w iron or their combination, enhancing phenanthrene degradation by 44-65%. Biochar treatment reduced Cu leaching and enabled sunflower growth, but had no significant effect on As mobility. Iron treatment reduced Cu and As leaching but negatively impacted soil structure and released high levels of Fe causing sunflower plant mortality. The combined treatment reduced both Cu and As leaching and enabled sunflower growth suggesting this could be a useful approach for treating co-contaminated sites.