Reflections and Insights on the Evolution of the Biological Remediation of Contaminated Soils

The field of soil biological remediation was initially focused on the use of microorganisms. For organic contaminants, biostimulation and bioaugmentation were the strategies of choice. For heavy metals, bioremediation was centered on the feasibility of using microorganisms to reduce metal toxicity. Partly due to the impossibility to degrade metals, phytoremediation emerged proposing the use of plants to extract them (phytoextraction) or reduce their bioavailability (phytostabilization). Later, microbial-assisted phytoremediation addressed the inoculation of plant growth-promoting microorganisms to improve phytoremediation efficiency. Similarly, plant-assisted bioremediation examined the stimulatory effect of plant growth on the microbial degradation of soil contaminants. The combination of plants and microorganisms is nowadays often recommended for mixed contaminated soils. Finally, phytomanagement emerged as a phytotechnology focused on the use of plants and associated microorganisms to decrease contaminant linkages, maximize ecosystem services, and provide economic revenues. Although biological remediation methods have been in use for decades, the truth is that they have not yet yielded the expected results. Here, we claim that much more research is needed to make the most of the many ways that microorganisms have evolutionary developed to access the contaminants and to better understand the soil microbial networks responsible, to a great extent, for soil functioning.This work was supported by the European Union through the Interreg SUDOE Program (Project Phy2SUDOE SOE4/P5/E1021)

A case for the importance of following antibiotic resistant bacteria throughout the soil food web

It is necessary to complement next-generation sequencing data on the soil resistome with theoretical knowledge provided by ecological studies regarding the spread of antibiotic resistant bacteria (ARB) in the abiotic and, especially, biotic fraction of the soil ecosystem. Particularly, when ARB enter agricultural soils as a consequence of the application of animal manure as fertilizer, from a microbial ecology perspective, it is important to know their fate along the soil food web, that is, throughout that complex network of feeding interactions among members of the soil biota that has crucial effects on species richness and ecosystem productivity and stability. It is critical to study how the ARB that enter the soil through the application of manure can reach other taxonomical groups (e.g., fungi, protists, nematodes, arthropods, earthworms), paying special attention to their presence in the gut microbiomes of mesofauna-macrofauna and to the possibilities for horizontal gene transfer of antibiotic resistant genes.This work was supported by MCIN/AEI/10.13039/501100011033 (PID2020-116495RB-I00), Basque Government (IT1578-22), and Euskampus – JRL Environmental Antibiotic Resistance

Contextualization of the Bioeconomy Concept through Its Links with Related Concepts and the Challenges Facing Humanity

The concept of bioeconomy is a topic of debate, confusion, skepticism, and criticism. Paradoxically, this is not necessarily a negative thing as it is encouraging a fruitful exchange of information, ideas, knowledge, and values, with concomitant beneficial effects on the definition and evolution of the bioeconomy paradigm. At the core of the debate, three points of view coexist: (i) those who support a broad interpretation of the term bioeconomy, through the incorporation of all economic activities based on the production and conversion of renewable biological resources (and organic wastes) into products, including agriculture, livestock, fishing, forestry and similar economic activities that have accompanied humankind for millennia; (ii) those who embrace a much narrower interpretation, reserving the use of the term bioeconomy for new, innovative, and technologically-advanced economic initiatives that result in the generation of high-added-value products and services from the conversion of biological resources; and (iii) those who stand between these two viewpoints. Here, to shed light on this debate, a contextualization of the bioeconomy concept through its links with related concepts (biotechnology, bio-based economy, circular economy, green economy, ecological economics, environmental economics, etc.) and challenges facing humanity today is presented

Soil Enzyme Activities as Bio Indicators of Soil pH and Fertility in Temperate Grassland

In recent years, biological indicators are being used to estimate the continued capacity of a given soil to function (i.e., soil health). After all, biological processes are intimately linked with the maintenance of soil structure and fertility, being more sensitive to changes in the soil than conventional physicochemical parameters. Soil enzymes, as mediators and catalysts of vital soil functions, offer great potential as integrative indicators of soil health (Dick et al., 1996). The main aim of the current work was to study the potential of soil enzyme activities as biological (more precisely, biochemical) indicators of soil physicochemical properties as well as of soil fertility in different temperate grasslands

La esencia de los seres vivos

La Biología es la ciencia que trata de los seres vivos. De esta definición se deriva que la persona que profesa la Biología, como parte de unos mínimos principios deontológicos profesionales, tiene la obligación de entender qué es un ser vivo. La comprensión del "ser", esencia o naturaleza, de los seres vivos es un tema de enorme complejidad. No obstante, para el lego en la materia esta cuestión puede parecer trivial, pues todos creemos que no tiene mayor dificultad reconocer un ser vivo de un objeto inanimado

Antibiotic Resistance in Agricultural Soil and Crops Associated to the Application of Cow Manure-Derived Amendments from Conventional and Organic Livestock Farms

he application of organic amendments to agricultural soil can enhance crop yield, while improving the physicochemical and biological properties of the recipient soils. However, the use of manure-derived amendments as fertilizers entails environmental risks, such as the contamination of soil and crops with antibiotic residues, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). In order to delve into these risks, we applied dairy cow manure-derived amendments (slurry, fresh manure, aged manure), obtained from a conventional and an organic farm, to soil. Subsequently, lettuce and wheat plants were grown in the amended soils. After harvest, the abundance of 95 ARGs and MGE-genes from the amended soils and plants were determined by high-throughput qPCR. The structure of soil prokaryotic communities was determined by 16S rRNA amplicon sequencing and qPCR. The absolute abundance of ARGs and MGE-genes differed between treatments (amended vs. unamended), origins of amendment (conventional vs. organic), and types of amendment (slurry vs. fresh manure vs. aged manure). Regarding ARG-absolute abundances in the amendments themselves, higher values were usually found in slurry vs. fresh or aged manure. These abundances were generally higher in soil than in plant samples, and higher in wheat grain than in lettuce plants. Lettuce plants fertilized with conventional amendments showed higher absolute abundances of tetracycline resistance genes, compared to those amended with organic amendments. No single treatment could be identified as the best or worst treatment regarding the risk of antibiotic resistance in soil and plant samples. Within the same treatment, the resistome risk differed between the amendment, the amended soil and, finally, the crop. In other words, according to our data, the resistome risk in manure-amended crops cannot be directly inferred from the analysis of the amendments themselves. We concluded that, depending on the specific question under study, the analysis of the resistome risk should specifically focus on the amendment, the amended soil or the cropThis work has been financially supported by the Basque Government (projects: URAGAN and KONTRAE-Elkartek-KK-2020-00007) and the Spanish Ministry of Science and Innovation (project: PRADA PID2019-110055RB-C21). LJ was the recipient of a predoctoral fellowship from the Department of Economic Development and Infrastructure of the Basque Governmen

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.J.U. was the recipient of a predoctoral fellowship from the Department for Economic Development and Infrastructures of the Basque Governmen

Agricultural Soils Amended with Thermally-Dried Anaerobically-Digested Sewage Sludge Showed Increased Risk of Antibiotic Resistance Dissemination

The application of sewage sludge (SS) to agricultural soil can help meet crop nutrient requirements and enhance soil properties, while reusing an organic by-product. However, SS can be a source of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), resulting in an increased risk of antibiotic resistance dissemination. We studied the effect of the application of thermally-dried anaerobically-digested SS on (i) soil physicochemical and microbial properties, and (ii) the relative abundance of 85 ARGs and 10 MGE-genes in soil. Soil samples were taken from a variety of SS-amended agricultural fields differing in three factors: dose of application, dosage of application, and elapsed time after the last application. The relative abundance of both ARGs and MGE-genes was higher in SS-amended soils, compared to non-amended soils, particularly in those with a more recent SS application. Some physicochemical parameters (i.e., cation exchange capacity, copper concentration, phosphorus content) were positively correlated with the relative abundance of ARGs and MGE-genes. Sewage sludge application was the key factor to explain the distribution pattern of ARGs and MGE-genes. The 30 most abundant families within the soil prokaryotic community accounted for 66% of the total variation of ARG and MGE-gene relative abundances. Soil prokaryotic alpha-diversity was negatively correlated with the relative abundance of ARGs and MGE-genes. We concluded that agricultural soils amended with thermally-dried anaerobically-digested sewage sludge showed increased risk of antibiotic resistance dissemination.This work has been financially supported by the Basque Government (projects: URAGAN and KONTRAE-Elkartek-KK2020-00007) and the Spanish Ministry of Science and Innovation (project: PRADA PID2019-110055RB-C21). LJ was the recipient of a predoctoral fellowship from the Department of Economic Development and Infrastructure of the Basque Government

The Application of Nanoscale Zero-Valent Iron Promotes Soil Remediation While Negatively Affecting Soil Microbial Biomass and Activity

The use of nanoscale zero-valent iron (nZVI) particles for soil remediation is gaining increased attention. However, there are concerns about the potential adverse effects of nZVI on soil microbial communities and, hence, soil quality. The objective of this study was to assess the impact of the application of nZVI on soil microbial parameters (as bioindicators of soil quality) during the nanoremediation of soil artificially contaminated with lindane (10 mg gamma-HCH kg(-1) DW soil) and zinc (1,500 mg Zn kg(-1) DW soil). nZVI particles were also applied to non-contaminated soil. The following nZVI doses were applied twice: 0, 0.25, 0.5, 1, and 2 mg nZVI g(-1) DW soil. Nine weeks after nZVI application, the following parameters were determined in soil samples: lindane concentration, extractable Zn concentration, microbial biomass carbon (C-MB), bacterial and fungal abundance (gene copy numbers by qPCR), enzyme activities (beta-glucosidase, beta-glucosaminidase, xylosidase, acid phosphatase, arylsulphatase, and Leu-aminopeptidase) and bacterial richness by ARISA profiles. The application of nZVI reduced lindane and extractable Zn concentrations following a dose-dependent pattern. The presence of contaminants reduced soil microbial biomass and activity. The application of nZVI negatively affected the microbial quality of the contaminated soil but not of the non-contaminated soil. This observation might reflect a "stress-on-stress" effect, i.e., the already stressed microbial populations present in the contaminated soil were more sensitive to the application of nZVI (a second stress) than those present in the non-contaminated soil.This work was supported by the Spanish Ministry of Economy, Industry and Competitiveness through NANORRIZORREM-2 Project (AGL2016-76592-R)