Jessica Cuartero Monino

Scopus Publications

Air-drying of soil preserves microbial and faunal eDNA abundance and diversity regardless of land-use type or management intensity
Xingguo Han, Jessica Cuartero, Verena Koppe, Seraina Nohl, Astrid Sneyders, Karen Vancampenhout, Beat Frey, Aline Frossard
Soil Biology and Biochemistry, 2026
Soil biodiversity monitoring requires standardized and practical sample storage methods, particularly for large-scale surveys. Yet, the influence of the soil storage conditions on eDNA-based assessments of microbial and faunal communities remains a key concern. Here, we assessed whether air-drying of soils at room temperature alters microbial (prokaryotes, fungi, micro-eukaryotes) and faunal (nematodes, annelids, micro-arthropods) abundance and diversity compared to freezing at –20 °C across different land-use types and management intensities through quantitative polymerase chain reaction (qPCR) and multi-marker DNA metabarcoding. We sampled topsoil (0 – 10 cm) from 42 sites of the Swiss Central Plateau spanning forests, grasslands, arable lands, orchards, wetlands, and urban areas. Forests, grasslands and arable lands were sampled in sites varying in management intensities. Across land-use types and management intensities, air-drying of soil followed by four to eight weeks of storage at room temperature or at –20 °C and freezing soil directly yielded comparable gene abundances, alpha-diversity, and community structure for all microbial and faunal groups. Moreover, microbial and faunal community structure were consistently shaped by land-use types and soil physicochemical variables regardless of the soil storage method used. These findings demonstrate that air-drying is a cost-effective and reliable method for short-term storing soil samples in large-scale biodiversity monitoring without compromising data quality. • Air-dried and frozen soils were compared from lands with management intensities. • Both soils yielded comparable microbial and faunal eDNA abundance and diversity. • Microbial and faunal communities were consistently shaped by environmental factors.
Reduced Tillage Intercropping With Thymus hyemalis Reshapes the Rare Soil Microbiome and Co-Occurrence Networks in a Semi-Arid Almond Orchard
Jessica Cuartero, Beat Frey, Margarita Ros, Jose Antonio Pascual, Virginia Sánchez‐Navarro, Loredana Canfora, Onurcan Özbolat, Marcos Egea‐Cortines, Antonella Lamontanara, Carolina Boix‐Fayos, Maria Martinez‐Mena, Maria Almagro, Elvira Diaz‐Pereira, Raul Zornoza
Journal of Sustainable Agriculture and Environment, 2026
Environmentally friendly farming practices are gaining interest, and intercropping is a promising option to protect soil health, yet its effects on orchard microbiomes and functions remain underexplored. In this study, we assessed a 3‐year intercropping assay of Capparis spinosa (D1) and Thymus hyemalis (D2) with almond and reduced tillage in a semi‐arid Mediterranean orchard. Soil bacterial and fungal communities were profiled by metabarcoding (16S rRNA gene for bacteria/archaea and ITS region for fungi), functional potential was inferred from gene‐abundance proxies and co‐occurrence networks were constructed to evaluate alterations in microbial connectivity. Both intercropping treatments along with reduced tillage altered the soil microbial composition and enriched plant growth–promoting genera (e.g., Amycolatopsis , Bosea , Dyadobacter , Janthinobacterium , Leifsonia ) and AMF ( Glomeromycota ), but effects were stronger in D2. Reduced tillage and intercropping with T. hyemalis increased the richness of less abundant bacteria, increased the abundance of functional potential linked to nitrogen fixation, cellulolysis, and fermentation. It also reconfigured co‐occurrence networks toward higher connectivity with more module hubs – patterns consistent with greater functional stability. Overall, T. hyemalis intercropping with reduced tillage enhanced beneficial soil microbiota and higher functional potential than C. spinosa . Long‐term monitoring is essential to ensure that the beneficial effects of intercropping persist and translate into real agronomic gains. For farmers, intercropping with thyme offers a valuable strategy to improve soil health and potential functionality while also generating additional income through products like essential oils—all without compromising almond orchard productivity. This dual benefit supports more sustainable and profitable farming in semi‐arid regions.
Increased carbon inputs alter soil microbial genetic potential for biogeochemical cycling in Arctic ecosystems
Jessica Cuartero, Carla Perez-Mon, Weihong Qi, Beat Stierli, Beat Frey, Gilda Varliero
Communications Earth and Environment, 2025
Global warming is transforming High Arctic ecosystems, yet the effects of northward vegetation expansion on soil microbial functions remain unclear. A four-year field experiment in northern Greenland was conducted to study these impacts. We investigate how plant litter affects the active layer and thawing permafrost soils by transplanting the latter from deeper soil layers and supplementing active layer soils with Arctic shrub litter. Litter amendment altered the soils’ functional potential, including the enrichment of genes linked to ion and lipid transport, metabolism and secondary metabolite production, ultimately enhancing microbial growth and respiration. Significant alterations were observed in carbon (C) and nitrogen (N) cycling genes, marked by an enhancement of CAZymes related to the breakdown of specific C substrates such as cellulose, hemicellulose, pectin, murein and chitin. Litter amendment also shifted the microbial N-cycling potential towards increased N mineralization and assimilation of organic and inorganic N, suggesting an increased incorporation of N into microbial biomass. Without litter amendment, few C- and N-metabolism pathways changed, mainly affecting auxiliary activities and lignin breakdown due to permafrost thawing. These findings highlight the importance of monitoring High Arctic vegetation expansion, as it may impact C degradation and greenhouse gas emissions more than permafrost thaw alone.
The effect of sustainable management practices on the bacterial community in different European croplands
J. Cuartero, B. Frey, R. Zornoza, V. Sánchez-Navarro, L. Canfora, O. Özbolat, M. Egea-Cortines, R. Farina, H. Fritze, T. Tuomivirta, K. Lång, R. Lemola, J. Álvaro-Fuentes, E. Huerta-Lwanga, J.A. Pascual, M. Ros
Applied Soil Ecology, 2025
Currently, monitoring Europe's soils is crucial since over 60 % of these soils are experiencing different types of degradation, which can potentially affect food production. Recently, a shift toward sustainable soil management has occurred. This shift away from conventional management is postulated to increase soil microbial diversity. However, it is unclear whether sustainable management can shift bacterial community across Europe. The Diverfarming project uses case studies to explore how diversified cropping systems with low-input practices can increase soil fertility, sequester carbon, and increase microbial diversity under differing climate conditions. To explore this, we employed metabarcoding sequencing to amplify the 16S rRNA region and soil chemical properties to assess the effects of organic amendment, rotation/intercropping and diversification with reduced tillage compared to conventional systems in different case studies. We observed that richness and Shannon index were mainly affected by climate and soil chemical properties but not by diversification. However, diversification changed the microbial community and enhanced potential microbial functionality, especially diversification of organic amendments, which also increase total organic carbon and nitrogen. We identified specific bacterial taxa associated with diversification, such as Rubrobacter , MND1 , Pontibacter and Sphingomonas , highlighting the potential benefits of some species of these genera in diversification management ecosystems.
The potential bioavailability of phosphorus and the microbial community involved in agro-industrial composts as organic amendments or growing media
Lady Johanna Bohórquez-Sandoval, Alicia Hernandez-Lara, José Antonio Gómez-Morte, Jessica Cuartero, José Francisco García-Molano, José Antonio Pascual, Margarita Ros
Journal of Environmental Management, 2025
Harnessing agro-industrial residues through composting is gaining importance as a means of phosphorus recovery, as is its reutilization as plant available phosphorus. This research seeks to analyze various combinations of agroindustrial waste and observe the microbial communities contributing to the availability of this element for plants. Six composts were used with different proportions of agroindustrial waste. Phosphorus fractionation was carried out, and the available phosphorus was determined. The molecules involved in phosphorus mineralization and solubilization, alkaline phosphatase activity, organic acids, and microbial communities were also determined. Finally, the potential phosphorus genes (Inorganic P solubilization genes (gcd, ppx, ppqC), and Organic P mineralization genes (phoA, phoD, phnL, phnl, phnJ, phnP, phnH, and phnG)) present in the analyzed composts were established. Compost X2B, composed of vineyard and tomato residues, demonstrated superior performance in providing available phosphorus compared to other composts. This was determined by microbial communities harboring genes involved in the phosphorus cycle, facilitating phosphorus availability. • Agro-industrial waste composts boost phosphorus availability, mainly as IP. • Lysobacter, Cellvibrio and Bacillus enhance phosphorus availability for plants. • Compost microorganisms harbor genes involved in the phosphorus cycle. • A mixture of vineyard waste and tomato waste significantly promotes AVP.
Alley Cropping Can Potentially Alter the Nitrogen and Carbon Soil Cycles and Increase the Abundance of Beneficial Bacteria in a Mediterranean Citrus Orchard
Margarita Ros, Jessica Cuartero, Onurcan Özbolat, Virginia Sánchez‐Navarro, Marcos Egea‐Cortines, Maria Almagro, María Hurtado‐Navarro, Maria Martinez‐Mena, Jose Antonio Pascual, Raúl Zornoza
Journal of Sustainable Agriculture and Environment, 2025
Monocrop of mandarin leading to reduced soil biodiversity and functionality that must be changed to a sustainable agriculture practice such as alley cropping. In this study an attempt has been made to assess how two different alley cropping strategies promote soil bacterial diversity, microbial activities and the abundance of beneficial bacteria. Three treatments were established: (i) mandarin monoculture (MC); (ii) mandarin diversified with barley/vetch (summer) and with fava bean (winter) for 3 consecutive years (DIV1); and (iii) mandarin diversified with fava bean, purslane and cowpea (DIV2). Results reveal that alley cropping did not significantly affect alfa‐diversity indices, but beta‐diversity showed significant differences among the three treatments, indicating changes in the bacterial community. Specific genera such as Haliangium, Microbacterium, Pseudonocardia, Solirubrobacter and Sphingomonas, known as plant growth‐promoting bacteria, showed higher relative abundances in DIV1 and DIV2 than MC. The genus Novosphingobium showed a higher relative abundance in DIV2, while MND1 showed a higher relative abundance in DIV1. Regarding potential gene abundances related to C and N cycling at the end of the experiment, only manB (hemicellulose degradation) showed a higher abundance in DIV2 than MC, while nifH (N fixation), amoA, and hao (nitrification) showed higher values in DIV1 and DIV2. Enzyme activities showed lower values in diversified treatments than in MC. Most significant changes were observed in the diversification of the alley with a sequence of different crops every year (DIV1), rather than repeating the same crops (DIV2). These alley cropping strategies (DIV1 and DIV2) seem an effective strategy to enhance the abundance of beneficial bacteria with increased potential activity related to N fixation and nitrification.
Comparing soil microarthropod communities derived directly from soil DNA metabarcoding with those from morphological assessment in a drought-prone and irrigated pine forest
Jessica Cuartero, Ivano Brunner, Marcus Schaub, Dariusz J. Gwiazdowicz, Piotr Skubała, Jiayi Qin, Paul Henning Krogh, Beat Frey
Applied Soil Ecology, 2025
Springtails (Collembola) and mites (Acari) are soil microarthropods, one of the most diverse animal groups in soils. They play a crucial role in organic matter cycling and are active throughout the food web as decomposers, bacterivores, fungivores, and carnivores. Only little is known about how these groups might respond to shifts in water availability, for example in the context of global change. Here, we investigated how soil microarthropods responded to long-term irrigation in a drought-prone Scots pine ( Pinus sylvestris ) forest in southern Switzerland. After more than a decade of doubling the annual rainfall, irrigation improved not only tree vitality but also soil quality, and with shifts in bacteria and fungi reflecting changes from oligotrophic to copiotrophic conditions. We assessed soil microarthropods with two approaches: (1) directly by soil DNA metabarcoding and (2) by morphological assessment after extraction of the animals with Macfadyen funnels. Another main aim of that study was to compare the results with the two approaches. The dominant Collembola genus in both assessment approaches was Parisotoma . The dominant Sarcoptiformes genus was Oppiella whereas Geolaelaps was the dominant Mesostigmata genus in both assessment approaches . Only the metabarcoding approach detected Trombidiformes genera, and only one genus, Microtydeus , had a classification confidence >80 %. The abundance and alpha-diversity of Collembola and Acari did not change significantly as a result of the irrigation treatment, regardless of the assessment approaches applied. In contrast, microarthropod beta-diversity showed significantly shifts for Collembola and Acari, and for the Collembola order Entomobryomorpha and the Acari orders Sarcoptiformes, Mesostigmata, and Trombidiformes. A Procrustes analysis comparing the two assessment approaches indicated a significant effect of the irrigation treatment for the mite order Sarcoptiformes and a nearly significant effect for Collembola. Using indicator species analysis a Parisotoma species was the only Collembola taxon in the metabarcoding assessment that was strongly associated with the irrigation treatment. With the morphological assessment, Parisotoma notabilis and Lepidocyrtus sp. were significantly associated with irrigation. For Acari, only the morphological approach let to Licnodamaeus pulcherrimus as a negative indicator taxon for irrigation. By using the morphospecies lists as a reference for validation and comparing it with the species list obtained through metabarcoding, we found that only a small percentage of Collembola and Acari morphospecies overlapped. The metabarcoding approach detected taxa that were not observed with the morphological assessment, such as Neelipleona, Symphypleona, or Trombidiformes. Due to the complexity of the taxa and the lack of comprehensive taxonomic identification and reference databases, identification at the species level is hardly possible. Further efforts to enrich the microarthropod reference database are urgently needed. • Abundance and alpha-diversity of microarthropods did not change under irrigation • Communities of Collembola and Sarcoptiformes shifted strongly under irrigation • DNA metabarcoding and morphological assessment revealed a small overlap of taxa • DNA metabarcoding resulted in higher Richness and Shannon index • Trombidiformes were only detected using soil DNA metabarcoding
Earthworm and enchytraeid indicator taxa of different land-use types identified using soil DNA metabarcoding
Jessica Cuartero, Maria J.I. Briones, Basil M. Rast, Beat Stierli, Claudia Maurer-Troxler, Anna-Sofia Hug, Franco Widmer, Jiří Schlaghamerský, Beat Frey
Applied Soil Ecology, 2025
Earthworms and enchytraeids play an important role in biogeochemical cycles and are good indicators of soil fertility. However, assessing their assemblages is difficult, mainly because the methods to identify them require expert knowledge, which becomes a technical challenge when surveying large areas. Soil DNA metabarcoding is a promising method that enables the identification of individual species directly from a bulk composite sample in large field experiments. Here, we investigated in parallel both earthworm (family Lumbricidae) and enchytraeid (family Enchytraeidae) assemblages in three land-use types (arable land, grassland, forest) across 29 Swiss Soil Monitoring Network (NABO) sites, using high-throughput amplicon sequencing of marker genes. For both earthworms and enchytraeids, α-diversity was higher in grasslands than in arable land and forests, and it was significantly affected by soil physico-chemical, climate and biological properties, especially pH and climate properties. In addition, we found negative correlations between earthworms α-diversity and soil total carbon (TC) content and the soil carbon to nitrogen ratio. Using the DNA metabarcoding, we observed sequences of Aporrectodea nocturna in soils with low pH, while other Aporrectodea species occurred in soils with high pH. We identified Bimastos rubidus in soils with low pH but higher TC, total nitrogen, organic C, and low silt content, while the enchytraeids Cognettia sphagnetorum and Cernosvitoviella atrata occurred in forest soils with high water and organic matter contents. We identified some indicator taxa for the different land-use types, for grassland: Aporrectodea icterica , Lumbricus rubellus , Marionina communis , Fridericia bisetosa and Fridericia connata ; arable land: Allolobophora chlorotica , Enchytraeus dichaetus , Achaeta iberica , Prodtodrilus antipae and Fridericia tuberosa ; and for forest: Octolasion cyaneum , Octolasion lacteum and Cognettia chlorophila . Although these indicator taxa are unlikely to provide information about the effect of land-use change on soil biodiversity at large spatial scales, these species do drive assemblage differences between land-use types. Soil DNA metabarcoding could therefore assist land managers in monitoring soil biodiversity and quality. • Earthworm and enchytraeid communities are patterned across land-use types. • Earthworm and enchytraeid communities are shaped by different abiotic drivers. • Enchytraeid community was highly affected by soil properties, especially pH • Indicator taxa can be used for soil monitoring.
Response of Portulaca oleracea biomass and its rhizospheric microbiome to the application of solid and liquid slumgum from beekeeping industry transformed with Penicillium chrysogenum
Ángel Carrascosa-Robles, José Antonio Pascual, Jessica Cuartero, Inmaculada García-Romera, Gloria Andrea Silva-Castro, Ana de Santiago, Margarita Ros, Spyridon A. Petropoulos, María del Mar Alguacil
Plant and Soil, 2025
Background and aims Slumgum, a by-product of the beeswax-rendering process, is a nutrient-rich organic waste with potential as a sustainable fertiliser. Unlike chemical fertilisers, which can degrade soil health and contribute to environmental pollution, slumgum may improve soil structure, enhance microbial activity, and support long-term soil fertility. This study assessed, for the first time, the effects of both solid and liquid slumgum, either transformed with Penicillium chrysogenum and non-transformed, on purslane (Portulaca oleracea) biomass and soil rhizosphere microbial communities. Methods The experiment involved applying different slumgum treatments to purslane plants, followed by the analysis of shoot biomass and foliar phosphorous content. Soil enzymatic activities related to carbon, nitrogen, and phosphorus cycles were measured. Additionally, bacterial and fungal community composition, diversity, and functional guilds in the rhizosphere were described. Results Both transformed solid and liquid slumgum along with untransformed liquid slumgum treatments increased purslane shoot biomass (by 60–77%) and foliar phosphorous content (by 87–100%) compared to the control. Slumgum treatments modified the microbial community composition, increasing saprotrophic fungi and reducing plant pathogens. Transformed solid slumgum also enhanced enzymatic activities involved in nutrient cycling, whereas the untransformed solid slumgum treatment promoted bacterial genes associated with denitrification. Conclusion Our findings highlight the potential of slumgum, particularly in its transformed forms, as a sustainable alternative to chemical fertilisers. Its application may improve soil fertility and crop productivity while reducing environmental impact. Further studies should investigate its long-term effects under field conditions and evaluate its economic feasibility.
Soil Health and Agricultural Production of Diversified Crops in Southeastern Spain
Virginia Sánchez‐Navarro, Jessica Cuartero, Onurcan Özbolat, Carolina Boix‐Fayos, María Martínez‐Mena, María Almagro, Elvira Díaz‐Pereira, Margarita Ros, Jose A. Pascual, Juan A. Fernández, Raúl Zornoza
Soil Health Series Volume 5 Soil Health and Sustainability in Spain and Portugal, 2025
Combining soil management strategies such as crop diversification, reduced tillage, and organic amendments can improve not only soil health but also the sustainability of agroecosystems. The combination of diversified crops and soil conservation practices increased soil microbial content in all crops. In almond and melon crops under diversification systems, crop yield and overall crop yield were related to increases in soil organic carbon, microbial richness, and nutrient availability and to decreases in bulk density. Owing to intensive agriculture, soil conservation agricultural practices need to be developed, with the aim of enhancing soil health while maintaining high crop production. Soil conservation practices include no-tillage, the introduction of crop rotations, cover crops, mulching, application of manure or compost, and incorporation of crop residues. DNA was used as an indicator of the soil microbial content.
More than a decade of irrigation alters soil nematode communities in a drought-prone Scots pine forest
Jessica Cuartero, Beat Frey, Reinhard Eder, Ivano Brunner
Applied Soil Ecology, 2024
Warming and rainfall reduction alter soil microbial diversity and co-occurrence networks and enhance pathogenic fungi in dryland soils
J. Cuartero, J.I. Querejeta, I. Prieto, B. Frey, M.M. Alguacil
Science of the Total Environment, 2024
Effect of no-till followed by crop diversification on the soil microbiome in a boreal short cereal rotation
Hannu Fritze, Tero Tuomivirta, Luigi Orrù, Loredana Canfora, Jessica Cuartero, Margarita Ros, Jose Antonio Pascual, Raúl Zornosa, Marcos Egea-Cortines, Kristiina Lång, Janne Kaseva, Krista Peltoniemi
Biology and Fertility of Soils, 2024
Optimizing purslane cultivation through legume intercropping and crop rotation: a study on yield and rhizosphere bacterial communities
Ángel Carrascosa-Robles, José Antonio Pascual, Jessica Cuartero, Ana de Santiago, Spyridon A. Petropoulos, María del Mar Alguacil
Plant and Soil, 2024
Impacts of snow-farming on alpine soil and vegetation: A case study from the Swiss Alps
Alexandre Buttler, Roland Teuscher, Nicolas Deschamps, Konstantin Gavazov, Luca Bragazza, Pierre Mariotte, Rodolphe Schlaepfer, Vincent E.J. Jassey, Lucas Freund, Jessica Cuartero, Juan Carlos Quezada, Beat Frey
Science of the Total Environment, 2023
How binomial (traditional rainfed olive grove-Crocus sativus) crops impact the soil bacterial community and enhance microbial capacities
Jesús Aguilera-Huertas, Jessica Cuartero, Margarita Ros, Jose Antonio Pascual, Luis Parras-Alcántara, Manuel González-Rosado, Onurcan Özbolat, Raúl Zornoza, Marcos Egea-Cortines, María Hurtado-Navarro, Beatriz Lozano-García
Journal of Environmental Management, 2023
Effects of solarisation combined with compost on soil pathogens and the microbial community in a spinach cropping system
Alicia Hernández-Lara, Margarita Ros, Jessica Cuartero, Juana-Maria Vivo, Pedro Lozano-Pastor, José Antonio Pascual
Agriculture Ecosystems and Environment, 2023
Polyurethane Foam Residue Biodegradation through the Tenebrio molitor Digestive Tract: Microbial Communities and Enzymatic Activity
Jose M. Orts, Juan Parrado, Jose A. Pascual, Angel Orts, Jessica Cuartero, Manuel Tejada, Margarita Ros
Polymers, 2023
Long-term adoption of reduced tillage and green manure improves soil physicochemical properties and increases the abundance of beneficial bacteria in a Mediterranean rainfed almond orchard
Onurcan Özbolat, Virginia Sánchez-Navarro, Raúl Zornoza, Marcos Egea-Cortines, Jessica Cuartero, Margarita Ros, Jose A. Pascual, Carolina Boix-Fayos, María Almagro, Joris de Vente, Elvira Díaz-Pereira, María Martínez-Mena
Geoderma, 2023
Melon/cowpea intercropping pattern influenced the N and C soil cycling and the abundance of soil rare bacterial taxa
Jessica Cuartero, Jose Antonio Pascual, Juana-María Vivo, Onurcan Özbolat, Virginia Sánchez-Navarro, Julia Weiss, Raúl Zornoza, María Martínez-Mena, Eloisa García, Margarita Ros
Frontiers in Microbiology, 2022
A first-year melon/cowpea intercropping system improves soil nutrients and changes the soil microbial community
Jessica Cuartero, Jose Antonio Pascual, Juana-María Vivo, Onurcan Özbolat, Virginia Sánchez-Navarro, Marcos Egea-Cortines, Raúl Zornoza, Maria Martinez Mena, Eloisa Garcia, Margarita Ros
Agriculture Ecosystems and Environment, 2022
Long-Term Compost Amendment Changes Interactions and Specialization in the Soil Bacterial Community, Increasing the Presence of Beneficial N-Cycling Genes in the Soil
Jessica Cuartero, Onurcan Özbolat, Virginia Sánchez-Navarro, Julia Weiss, Raúl Zornoza, José Antonio Pascual, Juana-María Vivo, Margarita Ros
Agronomy, 2022
Bacterial and fungal community dynamics during different stages of agro-industrial waste composting and its relationship with compost suppressiveness
Alicia Hernández-Lara, Margarita Ros, Jessica Cuartero, María Ángeles Bustamante, Raul Moral, Francisco Javier Andreu-Rodríguez, Juan A. Fernández, Catalina Egea-Gilabert, José Antonio Pascual
Science of the Total Environment, 2022
Changes in bacterial and fungal soil communities in long-term organic cropping systems
Jessica Cuartero, Onurcan Özbolat, Virginia Sánchez-Navarro, Marcos Egea-Cortines, Raúl Zornoza, Loredana Canfora, Luigi Orrù, Jose Antonio Pascual, Juana-María Vivo, Margarita Ros
Agriculture Switzerland, 2021

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