Dr. Jessica Cuartero Monino

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.

Aims
Mixed cropping systems such as intercropping and crop rotation have been proven to be sustainable agronomic tools that provide agro-ecological services and improve crop yield through soil physical, chemical and biological changes in the soil. In this study, we aimed to assess the impact of different mixed cropping systems on a crop well-adapted to high temperatures and low precipitation, like purslane (Portulaca oleracea L.) and to study the underlying microbial mechanisms involved.
Methods
A field experiment in a semiarid region of southern Spain was conducted to study the short-term effects of crop rotation (R) and intercropping (I) with peas or cowpeas, as well as a combination of both (IR) on purslane yield and soil quality parameters such as microbial enzymatic activity, bacterial diversity, microbial composition and functionality.
Results
All the tested treatments increased purslane yield without significant differences among each other, but only the R and IR treatments affected the rhizospheric soil properties, through the increase of the enzymatic activities and the modification of the bacterial composition and functionality, and promoted organic matter degrading bacteria such as Bacillaceae, Myxococcaceae, and Planococcaceae and nitrogen-fixing bacteria, mainly Rhizobiaceae and Beijerinckiaceae.
Conclusion
This study demonstrates how sustainable cropping practices may improve the yield of a low maintenance crop like purslane under low-maintenance conditions by improving soil fertility in semiarid areas and also provides insights into the biological mechanisms responsible for the recorded effects.

With their various feeding types, soil nematodes play a crucial role in the soil food web. Here, we investigated if and how soil nematodes responded to a long-term irrigation in a drought-prone Scots pine (Pinus sylvestris) forest in southern Switzerland, applied to study whether greater soil water availability would improve tree health and reduce tree mortality. After 14 years of irrigation, tree vitality and soil development had improved significantly. However, morphological observations of the soil nematodes revealed a decrease in their total number in the irrigated plots. Overall, the irrigated plots had a lower nematode richness compared with the dry control plots, but the Shannon index did not differ between the two treatments. In addition, the nematode community shifted significantly as a result of the irrigation. Soil physical parameters, such as sand and silt contents and bulk density, were significantly positively correlated with the nematode community in the irrigation treatment. According to a DNA marker sequence analysis, a total of 43 genera of nematodes were assigned. Predatory nematodes were significantly less abundant in the irrigated plots than in the dry control plots, as the average number decreased to 74 in the irrigated plots compared to 3579 in the dry control plots, while non-predators were not significantly affected. A differential abundance analysis revealed that the genera Tripyla and Anatonchus were the predators that declined the most. Overall, marker sequence analysis of forest soil nematodes appears to be a suitable tool for assessing changes in nematode communities and taxa. The disappearance of predatory nematodes under irrigation, however, can perhaps only be explained if other predatory animal groups, such as predatory mites or millipedes, are also analyzed at the same time.

In this 9-year manipulative field experiment, we examined the impacts of experimental warming (2 °C, W), rainfall reduction (30 % decrease in annual rainfall, RR), and their combination (W + RR) on soil microbial communities and native vegetation in a semi-arid shrubland in south-eastern Spain. Warming had strong negative effects on plant performance across five coexisting native shrub species, consistently reducing their aboveground biomass growth and long-term survival. The impacts of rainfall reduction on plant growth and survival were species-specific and more variable. Warming strongly altered the soil microbial community alpha-diversity and changed the co-occurrence network structure. The relative abundance of symbiotic arbuscular mycorrhizal fungi (AMF) increased under W and W + RR, which could help buffer the direct negative impacts of climate change on their host plants nutrition and enhance their resistance to heat and drought stress. Indicator microbial taxa analyses evidenced that the marked sequence abundance of many plant pathogenic fungi, such as Phaeoacremonium, Cyberlindnera, Acremonium, Occultifur, Neodevriesia and Stagonosporopsis, increased significantly in the W and W + RR treatments. Moreover, the relative abundance of fungal animal pathogens and mycoparasites in soil also increased significantly under climate warming. Our findings indicate that warmer and drier conditions sustained over several years can alter the soil microbial community structure, composition, and network topology. The projected warmer and drier climate favours pathogenic fungi, which could offset the benefits of increased AMF abundance under warming and further aggravate the severe detrimental impacts of increased abiotic stress on native vegetation performance and ecosystem services in drylands.

Diversification of agricultural practices, including changes in crop rotation, intercropping or cover cropping, influence the soil microbiome. Here the impact of tillage and crop diversification on the soil microbiome is reported, being one of the few boreal studies. The field experiment consisted of four treatments with four replications all having a short cereal rotation practice namely an oat (Avena sativa) – spring barley (Hordeum vulgare) – wheat (Triticum aestivum) rotation for the past 10 years until spring 2018. During that period two of the treatments were conventionally tilled with moldboard ploughing whereas the other two were no-tillage treatments. From the growing season 2018 until fall 2020 the main crop in all treatments was spring barley. The first conventional tillage treatment was diversified with English ryegrass (Lolium perenne) as an undersown cover crop for the next three growing seasons. The first no-tillage treatment continued with spring barley only. The second conventional tillage and no-tillage treatment had winter rapeseed in rotation in 2019. Bulk soils were sampled in May 2018 before diversification and then in October 2018, 2019, and 2020. The results showed a clear effect of tillage on the beta-diversity of the soil microbiome and an increase in fungal richness. Barley monoculture interrupted with winter rapeseed resulted in a minor change of the fungal and bacterial community composition. Other fungal and bacterial alpha diversity measures did not react to tillage or diversification nor did the gene copy abundances involved in the N cycle. In conclusion tillage had a profound effect on the soil microbiome hindering impact of the diversification.

Intercropping can favour the yield of the main crop. However, because of the potential competition among woody crops, this system is rarely used by farmers. To increase knowledge about the intercropping system, we have explored three different combinations of alley cropping in rainfed olive groves compared to conventional management (CP): (i) Crocus sativus (D-S); (ii) Vicia sativa/Avena sativa in annual rotation (D-O); and (iii) Lavandula x intermedia (D-L). Different soil chemical properties were analyzed to evaluate the effects of alley cropping, while 16S rRNA amplification and enzymatic activities were determined to study the changes that occurred in soil microbial communities and activity. In addition, the influence of intercropping on the potential functionality of the soil microbial community was measured.
Data revealed that the intercropping systems highly affected the microbial community and soil properties. The D-S cropping system increased soil total organic carbon and total nitrogen that were correlated with the bacterial community, indicating that both parameters were the main drivers shaping the structure of the bacterial community. The D-S soil cropping system had significantly higher relative abundances of the phyla Bacteroidetes, Proteobacteria, and Patescibacteria compared to the other systems and the genera Adhaeribacter, Arthrobacter, Rubellimicrobium, and Ramlibacter, related to C and N functions. D-S soil was also related to the highest relative abundances of Pseudoarthrobacter and Haliangium, associated with the plant growth-promoting effect, antifungal activity, and a potential P solubilizer. A potentially increase of C fixation and N fixation in soils was also observed in the D-S cropping system. These positive changes were related to the cessation of tillage and the development of a spontaneous cover crop, which increased soil protection. Thus, management practices that contribute to increasing soil cover should be encouraged to improve soil functionality.

Snow-farming is one of the adaptive strategies used to face the snow deficit in ski resorts. We studied the impact of a shifting snow-farming technique on a pasture slope in Adelboden, Switzerland. Specifically, we compared plots covered by a compressed snow pile for 1.5, 2.5 or 3.5 years, which then recovered from the snow cover for three, two or one vegetation seasons, respectively, with control plots situated around the snow pile.
In plots with >1.5 years of compressed snow pile, plant mortality was high, recovery of vegetation was very slow, and few plant species recolonized the bare surface. Soil biological activity decreased persistently under prolonged snow cover, as indicated by reduced soil respiration. The prolonged absence of fresh plant litter and root exudates led to carbon (C) limitation for soil microbial respiration, which resulted in a significant decrease in the ratio of total organic carbon to total nitrogen (TOC/TN) under the snow pile.
Microbial C, nitrogen (N) and phosphorus (P) immobilization decreased, while dissolved N concentration increased with compressed snow cover. Longer snow cover and a subsequent shorter recovery period led to higher microbial C/P and N/P but lower microbial C/N. Nitrate and ammonium were released massively once the biological activity resumed after snow clearance and soil aeration.
The soil microbial community composition persistently shifted towards oxygen-limited microbes with prolonged compressed snow cover. This shift reflected declines in the abundance of sensitive microorganisms, such as plant-associated symbionts, due to plant mortality or root die-off. In parallel, resistant taxa that benefit from environmental changes increased, including facultative anaerobic bacteria (Bacteroidota, Chloroflexota), obligate anaerobes (Euryarchaeota), and saprophytic plant degraders.
We recommend keeping snow piles in the same spot year after year to minimize the area of the impacted soil surface and plan from the beginning soil and ecosystem restoration measures.