Journal: Soil Biology and Biochemistry

DOI: https://doi.org/10.1016/j.soilbio.2026.110284

Meeting future food demands while preserving ecosystem integrity requires agricultural systems that sustain soil biodiversity. Despite its critical role in regulating soil fertility, crop resilience, and food production, the response of soil biodiversity to sustainable agricultural practices remains poorly understood, particularly across multiple groups of organisms. Here, we evaluated the effects of organic amendments, cropping pattern diversification, and microbial inoculation on soil biodiversity using 23 treatment-control pairs from 11 case studies across six Mediterranean countries and three different cropping systems. We employed an integrative methodology combining multitargeted DNA metabarcoding (16S rRNA, ITS, 18S rRNA, COI, Oligo01) and morphological identification (Macfadyen extractor and pitfall traps) to study the structural and functional diversity of soil microorganisms, microfauna, microarthropods, and macrofauna. Data from molecular methods differed between primers and from morphological data; specifically, 18S rRNA and COI yielded markedly different diversity estimates, and both underperformed morphological identification for soil fauna resolution, indicating the need for primer standardisation, increased soil input mass and methodological complementarity between molecular and morphological approaches. Overall, our results show that compost addition positively influenced prokaryotic chemoheterotrophs, epigeic Collembola, spider richness, and total macrofauna abundance, with mulching eliciting broader positive responses. Cropping pattern diversification (i.e., rotations, cover crops, intercropping) more frequently enhanced than reduced soil biodiversity metrics, with 32% of effect sizes being moderately positive compared to 24% moderately negative. Microbial inoculations had limited influence on biodiversity, consistent with their intended role of enhancing specific functions while minimising disruption to resident communities. Although positive responses to sustainable agricultural practices were more frequent than negative ones, effects were often not statistically significant and were taxon- and context-dependent, highlighting the importance of site-specific assessments.

Journal: Scientific Reports

DOI: https://doi.org/10.1038/s41598-026-38389-8

Antibiotic resistance is a growing global problem, with agricultural practices and climate change as substantial contributors to the spread of antibiotic resistance genes (ARGs) in the environment. We investigated the effect of drought and fertilization type (organic vs. mineral) on radish crop growth and soil prokaryotic communities, with special emphasis on the radish and soil resistomes, as measured by the relative abundance of ARGs and mobile genetic element (MGE)-linked genes. Manure fertilization significantly increased ARG relative abundances in soil, compared to mineral fertilization. Drought and the presence of radish plants emerged as key variables regulating the association between ARGs and MGE-linked genes. Nonetheless, despite radish being a belowground crop, no direct connection was observed between the soil and crop resistomes. These results suggest that soil moisture and fertilization strategies do not necessarily increase the risk of ARG transfer to human pathogens through crop consumption. Consequently, a robust risk assessment of the environmental resistome must account for all compartments within the transmission chain. Together, our findings highlight the complex interplay between agricultural practices and climatic factors in shaping the soil and crop resistome.

Journal: Applied Soil Ecology

DOI: https://doi.org/10.1016/j.apsoil.2026.106843

Agricultural practices can be main drivers of antibiotic resistomes in agroecosystems. The application of manure-based fertilizers, the use of biocides, and the entry of heavy metals to agricultural soils associated with fungicide and/or manure application can all influence the prevalence and dissemination of antibiotic resistance genes (ARGs) in agricultural settings. Alternative soil amendments, such as biochar, have been proposed for the mitigation of antibiotic resistance in agriculture. Here, we investigated the effects of the following treatments, individually and in combination, on soil and lettuce resistomes: (i) mineral (NPK) vs. organic (aged cow manure, non-spiked or spiked with two doses of oxytetracycline) fertilization; (ii) copper application; and (iii) biochar application. We assessed their impact on soil physicochemical and microbial properties, including prokaryotic community composition, as well as the relative abundances of ARGs and MGE-linked genes in soil and lettuce plants. The application of mineral fertilizer, oxytetracycline-spiked manure, and biochar increased the abundance of ARGs and MGE-linked genes in soil by 2- to 16-fold, along with increases in some prokaryotic families linked to ARG-harboring MGEs. In contrast, copper application reduced soil microbial activity but did not affect the soil resistome. Our findings underscore the importance of evaluating the impact of agricultural practices on soil and crop resistomes, with fertilization emerging as the practice with the greatest impact under the conditions of this study. Such assessments are critical for proposing management strategies (e.g., pre-treatment of manure-based amendments) aimed at mitigating the transfer of ARGs to potential bacterial human pathogens.

Journal: Data in Brief

DOI: https://doi.org/10.1016/j.dib.2025.112358

This article presents a dataset of antibiotic resistance gene abundances obtained when exposing soil, previously amended with oxytetracycline-spiked cow manure, to different temperatures and moisture contents as two highly relevant climate change-related variables. The absolute abundances of six antibiotic resistance genes (ARGs) and two mobile genetic element (MGE)-linked genes were determined by droplet-digital PCR. Data on soil microbial biomass carbon, the total abundance of the 16S rRNA gene, and basal respiration are also included to show the effect of the climate change-related variables on the biomass and activity of soil microbial communities. The dataset presented in this article contains raw observations (including the soil´s physicochemical characterization), as well as analysis-derived data, on the effects of climate change-related variables on the risk of antibiotic resistance occurrence and spread in soils amended with animal manure, a topic of the utmost importance given the potential links between the environmental resistome and the human resistome. The data provided in this article are of much interest to researchers dealing with the potential impact of agricultural practices (i.e., organic fertilization) on antibiotic resistance under the current scenario of climate change.This article presents a dataset of antibiotic resistance gene abundances obtained when exposing soil, previously amended with oxytetracycline-spiked cow manure, to different temperatures and moisture contents as two highly relevant climate change-related variables. The absolute abundances of six antibiotic resistance genes (ARGs) and two mobile genetic element (MGE)-linked genes were determined by droplet-digital PCR. Data on soil microbial biomass carbon, the total abundance of the 16S rRNA gene, and basal respiration are also included to show the effect of the climate change-related variables on the biomass and activity of soil microbial communities. The dataset presented in this article contains raw observations (including the soil´s physicochemical characterization), as well as analysis-derived data, on the effects of climate change-related variables on the risk of antibiotic resistance occurrence and spread in soils amended with animal manure, a topic of the utmost importance given the potential links between the environmental resistome and the human resistome. The data provided in this article are of much interest to researchers dealing with the potential impact of agricultural practices (i.e., organic fertilization) on antibiotic resistance under the current scenario of climate change.

Lurzoruko biomaren azterketa – Teknopolis (elhuyar.eus)

Un examen al bioma del suelo – Teknopolis (elhuyar.eus)

Journal: Environmental Science and Pollution Research

DOI: 10.1007/s11356-023-31550-0

The remediation of mixed contaminated soil is challenging as it often requires actions to minimize metal-induced risks while degrading organic contaminants. Here, the effectiveness of different bioremediation strategies, namely, rhizoremediation with native plant species, mycoremediation with Pleurotus ostreatus spent mushroom substrate, and biostimulation with organic by-products (i.e., composted sewage sludge and spent mushroom substrate), for the recovery of a mixed contaminated soil from an abandoned gravel pit was studied. The combination of biostimulation and rhizoremediation led to the most significant increase in soil health, according to microbial indicator values. The application of composted sewage sludge led to the highest reduction in anthracene and polychlorinated biphenyls concentrations. None of the strategies managed to decrease contamination levels below regulatory limits, but they did enhance soil health. It was concluded that the biological remediation treatments improved soil functioning in a short time, before the concentration of soil contaminants was significantly reduced.

Journal: Chemosphere

https://doi.org/10.1016/j.chemosphere.2023.138538

Mycoremediation with mushroom growth substrates can be used for the recovery of mixed contaminated soils due to the benefits derived from the physicochemical characteristics of the substrates, the activity of extracellular enzymes secreted by the fungi, and the presence of the fungal mycelia. The objective of this work was to assess the potential of Agaricus bisporus and Pleurotus ostreatus growth substrates (inoculated mushroom substrates vs. spent mushroom substrates) for the mycoremediation of soils co-contaminated with lead and lindane (g-HCH). We compared the efficiency of these mycoremediation strategies with the phytoremediation with Brassica spp. or Festuca rubra plants, in terms of both reduction in contaminant levels and enhancement of soil health. An enhanced soil health was achieved as a result of the application of mycoremediation treatments, compared to phytoremediation and control (untreated) treatments. The application of P. ostreatus inoculated substrate led to the most significant reduction in g-HCH concentration (up to 88.9% compared to corresponding controls). In the presence of inoculated mushroom substrate, P. ostreatus fruiting bodies extracted more Pb than Brassica spp. or F. rubra plants. Mycoremediation with P. ostreatus growth substrates appears a promising strategy for the recovery of the health of soils co-contaminated with Pb and g-HCH.