The biotechnological potential of the Chloroflexota phylum

In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on ecosystems and will call for greater investments in infrastructures and modern technologies. A valid approach to overcome such future challenges is the employment of sustainable bio-based technologies that explore the metabolic richness of microorganisms. Collectively, the metabolic capabilities of Chloroflexota, spanning aerobic and anaerobic conditions, thermophilic adaptability, anoxygenic photosynthesis, and utilization of toxic compounds as electron acceptors, underscore the phylum's resilience and ecological significance. These diverse metabolic strategies, driven by the interplay between temperature, oxygen availability, and energy metabolism, exemplify the complex adaptations that enabled Chloroflexota to colonize a wide range of ecological niches. In demonstrating the metabolic richness of the Chloroflexota phylum, specific members exemplify the diverse capabilities of these microorganisms: Chloroflexus aurantiacus showcases adaptability through its thermophilic and phototrophic growth, whereas members of the Anaerolineae class are known for their role in the degradation of complex organic compounds, contributing significantly to the carbon cycle in anaerobic environments, highlighting the phylum's potential for biotechnological exploitation in varying environmental conditions. In this context, the metabolic diversity of Chloroflexota must be considered a promising asset for a large range of applications. Currently, this bacterial phylum is organized into eight classes possessing different metabolic strategies to survive and thrive in a wide variety of extreme environments. This review correlates the ecological role of Chloroflexota in such environments with the potential application of their metabolisms in biotechnological approaches.

Molecular Sieve, Halloysite, Sepiolite and Expanded Clay as a Tool in Reducing the Content of Trace Elements in Helianthus annuus L. on Copper-Contaminated Soil

The aim of this study was to determine the effect of copper soil contamination on the trace element content of sunflower aerial parts and in roots. Another aim was to assess whether the introduction of selected neutralizing substances (molecular sieve, halloysite, sepiolite and expanded clay) into the soil could reduce the impact of copper on the chemical composition of sunflower plants. Copper soil contamination with 150 mg Cu²⁺ kg^-1 of soil and 10 g of each adsorbent per kg of soil were used. Soil contamination with copper caused a significant increase in the content of this element in the aerial parts (by 37%) and roots (by 144%) of sunflower. Enriching the soil with the mineral substances reduced the amount of copper in the aerial parts of sunflower. Halloysite had the greatest effect (35%), while expanded clay had the smallest effect (10%). An opposite relationship was found in the roots of this plant. In copper-contaminated objects, a decrease in the content of cadmium and iron and an increase in the concentrations of nickel, lead and cobalt in the aerial parts and roots of sunflower were observed. The applied materials reduced the content of the remaining trace elements more strongly in the aerial organs than in the roots of sunflower. Molecular sieve had the greatest reducing effect on the content of trace elements in sunflower aerial organs, followed by sepiolite, while expanded clay had the least impact. The molecular sieve also reduced the content of iron, nickel, cadmium, chromium, zinc and, especially, manganese, whereas sepiolite reduced the content of zinc, iron, cobalt, manganese and chromium in sunflower aerial parts. Molecular sieve contributed to a slight increase in the content of cobalt, while sepiolite had the same effect on the content of nickel, lead and cadmium in the aerial parts of sunflower. All materials decreased the content of chromium in sunflower roots, molecular sieve-zinc, halloysite-manganese, and sepiolite-manganese and nickel. The materials used in the experiment, especially the molecular sieve and to a lesser extent sepiolite, can be used effectively to reduce the content of copper and some other trace elements, particularly in the aerial parts of sunflower.

Potentially Toxic Elements’ Contamination of Soils Affected by Mining Activities in the Portuguese Sector of the Iberian Pyrite Belt and Optional Remediation Actions: A Review

Both sectors of the Iberian Pyrite Belt, Portuguese and Spanish, have been exploited since ancient times, but more intensively during and after the second half of the 19th century. Large volumes of polymetallic sulfide ore were extracted in open pits or in underground works, processed without environmental concerns, and the generated waste rocks and tailings were simply deposited in the area. Many of these mining sites were abandoned for years under the action of erosive agents, leading to the spread of trace elements and the contamination of soils, waters and sediments. Some of these mine sites have been submitted to rehabilitation actions, mostly using constructive techniques to dig and contain the contaminated tailings and other waste materials, but the remaining soil still needs to be treated with the best available techniques to recover its ecosystem functions. Besides the degraded physical structure and poor nutritional status of these soils, they have common characteristics, as a consequence of the pyrite oxidation and acid drainage produced, such as a high concentration of trace elements and low pH, which must be considered in the remediation plans. This manuscript aims to review the results from studies which have already covered these topics in the Iberian Pyrite Belt, especially in its Portuguese sector, considering: (i) soils’ physicochemical characteristics; (ii) potentially toxic trace elements’ concentration; and (iii) sustainable remediation technologies to cope with this type of soil contamination. Phytostabilization, after the amelioration of the soil’s properties with organic and inorganic amendments, was investigated at the lab and field scale by several authors, and their results were also considered.

Chemical Composition, Antioxidant and Anti-Inflammatory Activities of Clary Sage and Coriander Essential Oils Produced on Polluted and Amended Soils-Phytomanagement Approach

The potential of essential oils (EO), distilled from two aromatic plants—clary sage (Salvia sclarea L.) and coriander (Coriandrum sativum L.)—in view of applications as natural therapeutic agents was evaluated in vitro. These two were cultivated on a trace element (TE)-polluted soil, as part of a phytomanagement approach, with the addition of a mycorrhizal inoculant, evaluated for its contribution regarding plant establishment, growth, and biomass production. The evaluation of EO as an antioxidant and anti-inflammatory, with considerations regarding the potential influence of the TE-pollution and of the mycorrhizal inoculation on the EO chemical compositions, were the key focuses. Besides, to overcome EO bioavailability and target accession issues, the encapsulation of EO in β-cyclodextrin (β-CD) was also assessed. Firstly, clary sage EO was characterized by high proportions of linalyl acetate (51–63%) and linalool (10–17%), coriander seeds EO by a high proportion of linalool (75–83%) and lesser relative amounts of γ-terpinene (6–9%) and α-pinene (3–5%) and coriander aerial parts EO by 2-decenal (38–51%) and linalool (22–39%). EO chemical compositions were unaffected by both soil pollution and mycorrhizal inoculation. Of the three tested EO, the one from aerial parts of coriander displayed the most significant biological effects, especially regarding anti-inflammatory potential. Furthermore, all tested EO exerted promising antioxidant effects (IC₅₀ values ranging from 9 to 38 g L⁻¹). However, EO encapsulation in β-CD did not show a significant improvement of EO biological properties in these experimental conditions. These findings suggest that marginal lands polluted by TE could be used for the production of EO displaying faithful chemical compositions and valuable biological activities, with a non-food perspective.

Investigation of factors affecting phytoremediation of multi-elements polluted calcareous soil using Taguchi optimization

Growing environmental concern regarding multi elements-contaminated soils reveals the necessity of paying more attention to environmentally friendly remediation techniques such as phytoremediation. A large number of factors influences phytoremediation of potentially toxic elements (PTEs) and investigation on a variety of these factors need appropriate statistical approaches such as "Taguchi optimization" which effectively decreases time and cost of experiments. In the present study, based on the Taguchi optimization method, the effects of several biological (plant type and mycorrhizal fungi (AMF)) and chemical (chelating agents, surfactants and organic acids) factors, on the phytoremediation of soils contaminated with zinc (Zn), lead (Pb), cadmium (Cd) and nickel (Ni) were investigated. The goal was to find out the most effective factors as well as the best level for each factor. The values of dry weights in roots and aerial parts of the studied plants were in orders of maize > sorghum > sunflower and sorghum > maize > sunflower, respectively. AMF was the main factor in increasing dry weight of shoots. Inoculation of AMF caused increases in root and shoot uptake of some PTEs. RESULTS: showed that phytoremediation of PTEs is element-dependent; as Zn showed the highest translocation factor (TF) and bioconcentration factor (BCF) values, while Ni showed the lowest ones and the intermediate values belonged to Pb and Cd. These results show the diverse distribution of elements in plant parts, as Zn and Ni were mostly accumulated in shoot and root, respectively. Although different factors caused impacts on phytoremediation criteria, the role of plant type in the phytoremediation of PTEs was at the first rank. Mean TF of PTEs in sunflower was 6.3 times that of maize. Sunflower showed high TF value for the four elements and translocated most of the PTEs from root to the aerial parts demonstrating phytoextraction as the main mechanism in this plant. Maize and sorghum, however, showed low TF and accumulated most of PTEs in their roots revealing phytostabilization as the main mechanism. In general, it can be concluded that plant type was the most influential factor in the phytoremediation of PTEs followed by EDTA and AMF. Taguchi optimization revealed the appropriateness and significance of different chemical and biological treatments on phytoremediation criteria of different elements.

Keep and promote biodiversity at polluted sites under phytomanagement

The phytomanagement concept combines a sustainable reduction of pollutant linkages at risk-assessed contaminated sites with the generation of both valuable biomass for the (bio)economy and ecosystem services. One of the potential benefits of phytomanagement is the possibility to increase biodiversity in polluted sites. However, the unique biodiversity present in some polluted sites can be severely impacted by the implementation of phytomanagement practices, even resulting in the local extinction of endemic ecotypes or species of great conservation value. Here, we highlight the importance of promoting measures to minimise the potential adverse impact of phytomanagement on biodiversity at polluted sites, as well as recommend practices to increase biodiversity at phytomanaged sites without compromising its effectiveness in terms of reduction of pollutant linkages and the generation of valuable biomass and ecosystem services.

Open mining pits and heaps of waste material as the source of undesirable substances: biomonitoring of air and soil pollution in former mining area (Dubnik, Slovakia)

Moss and lichen bag technique (Dicranum sp., Hypnum sp., Polytrichum sp., Hypogymnia physodes) and activity of soil enzymes (urease, acid and alkaline phosphatase, fluorescein diacetate, ß-glucosidase) were used as bioindicators of air and soil pollution in Dubník former mining area (East Slovakia). Ten open mining pits and 8 heaps of waste material were chosen for the research purposes. Contamination factor (C_f), degree of contamination (C_d), and pollution load index (PLI) were used to evaluate the level of soil pollution and relative accumulation factor (RAF) expressed the level of air pollution by risk elements (As, Cd, Cu, Fe, Mn, Ni, Sb, Pb, Zn). Based the degree of contamination results, the study area was polluted by individual elements in the following order: Fe>Cd>As>Pb>Sb>Zn>Cu>Ni>Mn. The highest values of Mn and Ni and lower values of urease were determined in open mining pits comparing heaps of waste material. The results of PLI index confirmed extreme pollution at all sampling sites. Considering the average RAF values showed the decrease of accumulation abilities of evaluated taxa in the following order: Dicranum sp.>Hypnum sp.>Hypogymnia physodes>Polytrichum sp.

Potential Benefits and Risks for Soil Health Derived From the Use of Organic Amendments in Agriculture

The use of organic amendments in agriculture is a common practice due to their potential to increase crop productivity and enhance soil health. Indeed, organic amendments of different origin and composition (e.g., animal slurry, manure, compost, sewage sludge, etc.) can supply valuable nutrients to the soil, as well as increase its organic matter content, with concomitant benefits for soil health. However, the application of organic amendments to agricultural soil entails a variety of risks for environmental and human health. Organic amendments often contain a range of pollutants, including heavy metals, persistent organic pollutants, potential human pathogens, and emerging pollutants. Regarding emerging pollutants, the presence of antibiotic residues, antibiotic-resistant bacteria, and antibiotic-resistance genes in agricultural amendments is currently a matter of much concern, due to the concomitant risks for human health. Similarly, currently, the introduction of microplastics to agricultural soil, via the application of organic amendments (mainly, sewage sludge), is a topic of much relevance, owing to its magnitude and potential adverse effects for environmental health. There is, currently, much interest in the development of efficient strategies to mitigate the risks associated to the application of organic amendments to agricultural soil, while benefiting from their numerous advantages.

Mobile genetic elements and antibiotic resistance in mine soil amended with organic wastes

Metal resistance has been associated with antibiotic resistance due to co- or cross-resistance mechanisms. Here, metal contaminated mine soil treated with organic wastes was screened for the presence of mobile genetic elements (MGEs). The occurrence of conjugative IncP-1 and mobilizable IncQ plasmids, as well as of class 1 integrons, was confirmed by PCR and Southern blot hybridization, suggesting that bacteria from these soils have gene-mobilizing capacity with implications for the dissemination of resistance factors. Moreover, exogenous isolation of MGEs from the soil bacterial community was attempted under antibiotic selection pressure by using Escherichia coli as recipient. Seventeen putative transconjugants were identified based on increased antibiotic resistance. Metabolic traits and metal resistance of putative transconjugants were investigated, and whole genome sequencing was carried out for two of them. Most putative transconjugants displayed a multi-resistant phenotype for a broad spectrum of antibiotics. They also displayed changes regarding the ability to metabolise different carbon sources, RNA: DNA ratio, growth rate and biofilm formation. Genome sequencing of putative transconjugants failed to detect genes acquired by horizontal gene transfer, but instead revealed a number of nonsense mutations, including in ubiH, whose inactivation was linked to the observed resistance to aminoglycosides. Our results confirm that mine soils contain MGEs encoding antibiotic resistance. Moreover, they point out the role of spontaneous mutations in achieving low-level antibiotic resistance in a short time, which was associated with a trade-off in the capability to metabolise specific carbon sources.