Despite the importance of soil microorganisms for ecosystem services, long‐term surveys of their communities are largely missing. Using metabarcoding, we assessed temporal dynamics of soil bacterial and fungal communities in three land‐use types, i.e., arable land, permanent grassland, and forest, over five years. Soil microbial communities remained relatively stable and differences over time were smaller than those among sites. Temporal variability was highest in arable soils. Indications for consistent shifts in community structure over five years were only detected at one site for bacteria and at two sites for fungi, which provided further support for long‐term stability of soil microbial communities. A sliding window analysis was applied to assess the effect of OTU abundance on community structures. Partial communities with decreasing OTU abundances revealed a gradually decreasing structural similarity with entire communities. This contrasted with the steep decline of OTU abundances, as subsets of rare OTUs (<0.01%) revealed correlations of up to 0.97 and 0.81 with the entire bacterial and fungal communities. Finally, 23.4% of bacterial and 19.8% of fungal OTUs were identified as scarce, i.e., neither belonging to site‐cores nor correlating to environmental factors, while 67.3% of bacterial and 64.9% of fungal OTUs were identified as rare but not scarce. Our results demonstrate high stability of soil microbial communities in their abundant and rare fractions over five years. This provides a step towards defining site‐specific normal operating ranges of soil microbial communities, which is a prerequisite for detecting community shifts that may occur due to changing environmental conditions or anthropogenic activities.

Soil microbial diversity has major influences on ecosystem functions and services. However, due to its complexity and uneven distribution of abundant and rare taxa, quantification of soil microbial diversity remains challenging and thereby impeding its integration into long-term monitoring programs. Using metabarcoding, we analyzed soil bacterial and fungal communities at 30 long-term soil monitoring sites from the three land-use types arable land, permanent grassland, and forest with a yearly sampling between snowmelt and first fertilization over five years. Unlike soil microbial biomass and alpha-diversity, microbial community compositions and structures were site- and land-use-specific with CAP reclassification success rates of 100%. The temporally stable site core communities included 38.5% of bacterial and 33.1% of fungal OTUs covering 95.9% and 93.2% of relative abundances. We characterized bacterial and fungal core communities and their land-use associations at the family-level. In general, fungal families revealed stronger land-use associations as compared to bacteria. This is likely due to a stronger vegetation effect on fungal core taxa, while bacterial core taxa were stronger related to soil properties. The assessment of core communities can be used to form cultivation-independent reference lists of microbial taxa, which may facilitate the development of microbial indicators for soil quality and the use of soil microbiota for long-term soil biomonitoring.

Species of the fungal genus Metarhizium are globally distributed pathogens of arthropods, and a number of biological control products based on these fungi have been commercialized to control a variety of pest arthropods. In this study, we investigate the abundance and population structure of Metarhizium spp. in three land-use types—arable land, grassland, and forest—to provide detailed information on habitat selection and the factors that drive the occurrence and abundance of Metarhizium spp. in soil. At 10 sites of each land-use type, which are all part of the Swiss national soil-monitoring network (NABO), Metarhizium spp. were present at 8, 10, and 4 sites, respectively. On average, Metarhizium spp. were most abundant in grassland, followed by forest and then arable land; 349 Metarhizium isolates were collected from the 30 sites, and sequence analyses of the nuclear translation elongation factor 1α gene, as well as microsatellite-based genotyping, revealed the presence of 13 Metarhizium brunneum, 6 Metarhizium robertsii, and 3 Metarhizium guizhouense multilocus genotypes (MLGs). With 259 isolates, M. brunneum was the most abundant species, and significant differences were detected in population structures between forested and unforested sites. Among 15 environmental factors assessed, C:N ratio, basal respiration, total carbon, organic carbon, and bulk density significantly explained the variation among the M. brunneum populations. The information gained in this study will support the selection of best-adapted isolates as biological control agents and will provide additional criteria for the adaptation or development of new pest control strategies.

Entomopathogenic fungi are used for biological control of insect pests. Metarhizium brunneum Petch (Hypocreales) has potential to control Diabrotica virgifera virgifera LeConte (Chrysomelidae), which is a major pest of maize in North America and has recently invaded Europe. The inundative application of an entomopathogenic fungal strain in biological control results in high densities of fungal propagules in the soil which can potentially affect soil microbial communities and their multiple functions in soil. The objective of the present study was to assess potential effects of M. brunneum on soil fungal and prokaryotic communities in a pot experiment over a time course of 4 months using high-throughput sequencing (HTS) of ribosomal markers. The application of M. brunneum formulated as fungus colonised barley kernels (FCBK) led to a significant increase of the applied strain in soil, as assessed by cultivation-dependent (plating on selective medium followed by genotyping of Metarhizium isolates) and cultivation-independent (HTS of ribosomal markers) approaches. Data revealed that soil fungal and prokaryotic community structures did not change after the application of M. brunneum. Temporal changes of the fungal and prokaryotic communities were observed and the prokaryotic communities showed minor changes to barley kernels (BK), the matrix of the formulation. Results of this study are in accordance with other investigations lacking any evidence for adverse effects on microbial communities caused by applied entomopathogenic fungi.

Erwinia amylovora causes fire blight, a serious disease of Rosaceae plants, including apple and pear. A predominant path of bacterial infection is entry through nectartodes after multiplication on the stigma. Depending on the inhibitory abilities of the native blossom microbiota, it may control the outbreak of fire blight and, therefore, may bar potential plant protection with reduced input of synthetic chemicals. Blossoms of five apple varieties in a low-input orchard, which had no fire blight history despite disease outbreaks in close proximity, were analyzed to assess bacterial and fungal communities. Metabarcoding indicated low microbial diversity and the presence of a few dominant operational taxonomic units (OTUs), including known fire blight antagonists such as Metschnikowia pulcherrima and Aureobasidium pullulans. The most dominant bacterial taxon (bOTU_01) was classified as Erwinia spp. To resolve sequences of species within bOTU_01, we used analyses of sequence variants and DNA signatures (i.e., nucleotide polymorphisms that are indicative for different species or species groups). These analyses revealed that >94.5% of the sequences of bOTU_01 derived from E. tasmaniensis, a potential E. amylovora antagonist. The latter was represented by up to 0.006% of the sequences. Cultivation-based analyses confirmed the prevalence of E. tasmaniensis. The high abundance of native potential E. amylovora antagonists likely indicates that this special set of native apple blossom microbiota counteracted the establishment of E. amylovora in this low-input orchard. This may allow for a new approach to assess possible components of synthetic apple blossom communities to mitigate fire blight infections.

Soil microbial diversity has major influences on ecosystem functions and services. However, due to its complexity and uneven distribution of abundant and rare taxa, quantification of soil microbial diversity remains challenging and thereby impeding its integration into long-term monitoring programs. Using metabarcoding, we analyzed soil bacterial and fungal communities over five years at thirty long-term soil monitoring sites from the three land-use types, arable land, permanent grassland, and forest. Unlike soil microbial biomass and alpha-diversity, microbial community compositions and structures were site- and land-use-specific with CAP reclassification success rates of 100%. The temporally stable site core communities included 38.5% of bacterial and 33.1% of fungal OTUs covering 95.9% and 93.2% of relative abundances. We characterized bacterial and fungal core communities and their land-use associations at the family-level. In general, fungal families revealed stronger land-use type associations as compared to bacteria. This is likely due to a stronger vegetation effect on fungal core taxa, while bacterial core taxa were stronger related to soil properties. The assessment of core communities can be used to form cultivation-independent reference lists of microbial taxa, which may facilitate the development of microbial indicators for soil quality and the use of soil microbiota for long-term soil biomonitoring.