Marketa Sagova-Mareckova

Tree species influence below-ground soil chemistry and microbial communities, both of which are key drivers of soil formation. The study compared soils under native European beech and first-generation non-native Norway spruce growing at the same site. Soil under beech was classified as Dystric Cambisol, whereas soil under spruce had developed into Entic Podzol. The objective was to link soil chemical processes with microbial community composition and the resulting quantity and quality of soil organic carbon (SOC) across soil horizons. Soil pH and concentrations of available cations and anions were measured together with dissolved organic carbon (DOC), represented by low-molecular-weight organic acids (LMMOA; ion-exchange chromatography). SOC quantity and functional group composition were characterized using Fourier-transform infrared spectroscopy. Microbial abundance and community composition were assessed by 16S/18S rRNA gene amplicon sequencing and droplet digital PCR. Total carbon contents did not differ between soils, but DOC showed horizon-specific differences, with quinate strongly enriched under spruce. More pronounced differences were observed in carbon quality and its vertical distribution. Elevated concentrations and specific forms of Si, Al, P, and S under spruce indicated progressing podzolization, a process absent under beech. Distinct soil conditions and carbon sources supported contrasting microbial communities. Higher pH and labile carbon availability under beech promoted Pseudomonadota and Bacteroidota , distinguished particularly in the L horizon. In contrast, spruce soils, especially the H horizon were enriched in fungi and metabolically versatile Actinomycetota. Increased abundance of erm resistance genes under spruce also suggested a more competitive microbial environment. Tree species effects on soil properties were detectable throughout the soil profile but weakened with depth. Overall, differences in soil chemistry, microbial communities, and enzymatic activities reflect contrasting decomposition and carbon sequestration pathways, with implications for ecosystem resilience and microbial diversity.

Soil biodiversity reflects human impact on forest soils. It can be assumed that biodiversity will decrease with the increasing degree of soil disturbance compared to close-to-nature forests. This paper aims to compare the soil environment and soil microbial biodiversity in habitats with different degrees of disturbance within the Krkonoše National Park (KRNAP). A close-to-nature beech forest, a same-aged spruce monoculture and footpaths/roads were selected. Soil samples were taken from each area at 10 locations, based on the soil horizons present (mixture of organic horizons FH, organo-mineral A and mineral B). Basic soil characteristics were determined (organic C (Cox), active pH and base saturation). The composition of microbial communities and the reciprocal Simpson index were also determined for individual locations. Paths showed higher active pH and saturation of the sorption complex compared to forest habitats. No differences were found in the amount of Cox between habitats, apart from the FH horizon, where more Cox was determined in the near-natural stand. Prokaryotic and microeukaryotic communities are different in individual horizons and between habitats. Paths show a higher diversity of microbial populations in A horizons and B horizons showed higher numbers, even in prokaryotic microorganisms, compared to forest stands. Paths are an intrusion into the forest environment and are a significant element in the biodiversity of the forest environment of the KRNAP, most likely due to the differences in the soil environment, lower acidity and higher availability of nutrients compared to acidic and nutrient-poor forest areas.

Soil environments are inhabited by microorganisms adapted to its diversified microhabitats. The metabolic activity of individual strains/populations reflects resources available at a particular spot, quality of which may not comply with broad soil characteristics. To explore the potential of individual strains to adapt to particular micro-niches of carbon sources, a set of 331 Actinomycetia strains were collected at ten sites differing in vegetation, soil pH, organic matter content and quality. The strains were isolated on the same complex medium with neutral pH and their metabolites analyzed by UHPLC and LC-MS/MS in spent cultivation medium (metabolic profiles). For all strains, their metabolic profiles correlated with soil pH and organic matter content of the original sites. In comparison, strains phylogeny based on either 16S rRNA or the beta-subunit of DNA-dependent RNA polymerase (rpoB) genes was partially correlated with soil organic matter content but not soil pH at the sites. Antimicrobial activities of strains against Kocuria rhizophila, Escherichia coli, and Saccharomyces cerevisiae were both site- and phylogeny-dependent. The precise adaptation of metabolic profiles to overall sites characteristics was further supported by the production of locally specific bioactive metabolites and suggested that carbon resources represent a significant selection pressure connected to specific antibiotic activities.

Disease-suppressive soils encompass specific plant−pathogen−microbial interactions and represent a rare example of an agroecosystem where soil conditions and microbiome together prevent the pathogen from causing disease. Such soils have the potential to serve as a model for characterizing soil pathogen-related aspects of soil health, but the mechanisms driving the establishment of suppressive soils vary and are often poorly characterized. Yet, they can serve as a resource for identifying markers for beneficial activities of soil microorganisms concerning pathogen prevention. Many recent studies have focused on the nature of disease-suppressive soils, but it has remained difficult to predict where and when they will occur. This review outlines current knowledge on the distribution of these soils, soil manipulations leading to pathogen suppression, and markers including bacterial and fungal diversity, enzymes, and secondary metabolites. The importance to consider soil legacy in research on the principles that define suppressive soils is also highlighted. The goal is to extend the context in which we understand, study, and use disease-suppressive soils by evaluating the relationships in which they occur and function. Finally, we suggest that disease-suppressive soils are critical not only for the development of indicators of soil health, but also for the exploration of general ecological principles about the surrounding landscape, effects of deeper layers of the soil profile, little studied soil organisms, and their interactions for future use in modern agriculture.

In Mediterranean ecosystems, the projected rainfall reduction of up to 30% may alter plant–soil interactions, particularly litter decomposition and Home Field Advantage (HFA). We set up a litter transplant experiment in the three main forests encountered in the northern part of the Medi-terranean Basin (dominated by either Quercus ilex, Quercus pubescens, or Pinus halepensis) equipped with a rain exclusion device, allowing an increase in drought either throughout the year or concentrated in spring and summer. Senescent leaves and needles were collected under two precipitation treatments (natural and amplified drought plots) at their “home” forest and were left to decompose in the forest of origin and in other forests under both drought conditions. MS-based metabolomic analysis of litter extracts combined with multivariate data analysis enabled us to detect modifications in the composition of litter specialized metabolites, following amplified drought treatment. Amplified drought altered litter quality and metabolomes, directly slowed down litter decomposition, and induced a loss of home field (dis)advantage. No indirect effect mediated by a change in litter quality on decomposition was observed. These results may suggest major alterations of plant–soil interactions in Mediterranean forests under amplified drought conditions.

Actinobacteria are important cave inhabitants, but knowledge of how anthropization and anthropization‐related visual marks affect this community on cave walls is lacking. We compared Actinobacteria communities among four French limestone caves (Mouflon, Reille, Rouffignac, and Lascaux) ranging from pristine to anthropized, and within Lascaux Cave between marked (wall visual marks) and unmarked areas in different rooms (Sas‐1, Passage, Apse, and Diaclase). In addition to the 16S rRNA gene marker, 441 bp fragments of the hsp65 gene were used and an hsp65‐related taxonomic database was constructed for the identification of Actinobacteria to the species level by Illumina‐MiSeq analysis. The hsp65 marker revealed higher resolution for species and higher richness (99% operational taxonomic units cutoff) versus the 16S rRNA gene; however, more taxa were identified at higher taxonomic ranks. Actinobacteria communities varied between Mouflon and Reille caves (both pristine), and Rouffignac and Lascaux (both anthropized). Rouffignac displayed high diversity of Nocardia, suggesting human inputs, and Lascaux exhibited high Mycobacterium relative abundance, whereas Gaiellales were typical in pristine caves and the Diaclase (least affected area of Lascaux Cave). Within Lascaux, Pseudonocardiaceae dominated on unmarked walls and Streptomycetaceae (especially Streptomyces mirabilis) on marked walls, indicating a possible role in mark formation. A new taxonomic database was developed. Although not all Actinobacteria species were represented, the use of the hsp65 marker enabled species‐level variations of the Actinobacteria community to be documented based on the extent of anthropogenic pressure. This approach proved effective when comparing different limestone caves or specific conditions within one cave.