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The efficient management of soil represents a mission of vital importance for meeting the continuously increasing agricultural demand in a sustainable way. Decades of research identified in the biotechnological potential of soil microorganisms an always more practicable channel for achieving these goals. Due to the complexity of soil microbial communities and their tight connection to soil characteristics, it is still difficult to define universal strategies for an efficient and sustainable agroecosystem management. We here propose a new framework for the assessment of the impact of agricultural practices in the agroecosystem that revolves around the concept of microbial community recovery. This assessment is based on the selection of (i) a representative temporal interval, (ii) a representative agricultural system and (iii) monitoring tools able to assess the expression levels of microbial functionality in soil. This approach can be especially valuable for evaluating the effects of agrochemicals and other agronomical amendments (of different nature: biological, physical, chemical) on the soil microbiota. In the same way precision-medicine tries to tailor drugs on an always smaller subset of patients’ characteristics, a new generation of agrochemicals can be developed and tested considering soil characteristics in order to minimize their off-target effects. What remains central in this paradigm is the promotion of Soil Health maintenance practices. As for healthy humans, a healthy soil is more resilient and tolerates treatments and stresses better while recovering more quickly.

The expanding antibiotic resistance crisis calls for a more in depth understanding of the importance of antimicrobial resistance genes (ARGs) in pristine environments. We, therefore, studied the microbiome associated with Sphagnum moss forming the main vegetation in undomesticated, evolutionary old bog ecosystems. In our complementary analysis of culture collections, metagenomic data and a fosmid library from different geographic sites in Europe, we identified a low abundant but highly diverse pool of resistance determinants, which targets an unexpectedly broad range of 29 antibiotics including natural and synthetic compounds. This derives both, from the extraordinarily high abundance of efflux pumps (up to 96%), and the unexpectedly versatile set of ARGs underlying all major resistance mechanisms. Multi-resistance was frequently observed among bacterial isolates, e.g. in Serratia, Rouxiella, Pandoraea, Paraburkholderia and Pseudomonas. In a search for novel ARGs, we identified the new class A β-lactamase Mm3. The native Sphagnum resistome comprising a highly diversified and partially novel set of ARGs contributes to the bog ecosystem´s plasticity. Our results reinforce the ecological link between natural and clinically relevant resistomes and thereby shed light onto this link from the aspect of pristine plants. Moreover, they underline that diverse resistomes are an intrinsic characteristic of plant-associated microbial communities, they naturally harbour many resistances including genes with potential clinical relevance.

Little is known about the influence of host genotype and phytohormones on the composition of fungal endophytic communities. We investigated the influence of host genotype and phytohormones on the structure of the fungal endophytic communities of tomato roots by amplicon sequencing of the ITS1 region and combined this approach with isolation and functional characterization of the isolates. A significant effect of the host genotype on the dominant fungal species was found by comparing the cultivars Castlemart and UC82B and, surprisingly, root pathogens were among the most abundant taxa. In contrast, smaller changes in the relative abundance of the dominant species were found in mutants impaired in jasmonic acid biosynthesis (def1) and ethylene biosynthesis (8338) compared to the respective wild types. However, def1 showed significantly higher species richness compared to the wild type. Analysis of the phytohormone profiles of these genotypes indicates that changes in the phytohormone balance may contribute to this difference in species richness. Assessing the lifestyle of isolated fungi on tomato seedlings revealed the presence of both beneficial endophytes and latent pathogens in roots of asymptomatic plants, suggesting that the interactions between members of the microbiome maintain the equilibrium in the community preventing pathogens from causing disease., This article provides novel insights into the role of plant hormones and host genotype in the structure of the fungal communities inhabiting tomato roots, while also exploring the fungal lifestyle.

The expanding antibiotic resistance crisis calls for a more in depth understanding of the importance of antimicrobial resistance genes (ARGs) in pristine environments. We, therefore, studied the microbiota associated with Sphagnum forming the main vegetation in undomesticated, evolutionary old bog ecosystems. In our complementary analysis of a culture collection, metagenomic data and a fosmid library, we identified a low abundant but highly diverse pool of resistance determinants, which targets an unexpected broad range of antibiotics including natural and synthetic compounds. This derives both, from the extraordinarily high abundance of efflux pumps (80%), and the unexpectedly versatile set of ARGs underlying all major resistance mechanisms. The overall target spectrum of detected resistance determinants spans 21 antibiotic classes, whereby β-lactamases and vancomycin resistance appeared as the predominant resistances in all screenings. Multi-resistance was frequently observed among bacterial isolates, e.g. in Serratia, Pandorea, Paraburkhotderia and Rouxiella. In a search for novel ARGs we identified the new class A β-lactamase Mm3. The native Sphagnum resistome comprising a highly diversified and partially novel set of ARGs contributes to the bog ecosystem’s plasticity. Our results shed light onto the antibiotic resistance background of non-agricultural plants and highlight the ecological link between natural and clinically relevant resistomes.

Soilborne plant pathogens are an increasing problem in modern agriculture, and their ability to survive long periods in soil as persistent sclerotia makes control and treatment particularly challenging. To develop new control strategies, we explored bacteria associated with sclerotia ofSclerotinia sclerotiorumandRhizoctonia solani, two soilborne fungi causing high yield losses. We combined different methodological approaches to get insights into the indigenous microbiota of sclerotia, to compare it to bacterial communities of the surrounding environment, and to identify novel biocontrol agents and antifungal volatiles. Analysis of 16S rRNA gene fragment amplicons revealed significant compositional differences in the bacterial microbiomes ofRhizoctoniasclerotia, the unaffected tuber surface and surrounding soil. Moreover, distinctive bacterial lineages were associated with specific sample types.FlavobacteriaceaeandCaulobacteraceaewere primarily found in unaffected areas, whilePhyllobacteriaceaeandBradyrhizobiaceaewere associated with sclerotia ofR. solani. In parallel, we studied a strain collection isolated from sclerotia of the pathogens for emission of bioactive volatile compounds. Isolates ofBacillus,Pseudomonas, andButtiauxellaexhibited high antagonistic activity toward both soilborne pathogens and were shown to produce novel, not yet described volatiles. Differential imaging showed that volatiles emitted by the antagonists altered the melanized sclerotia surface ofS. sclerotiorum. Interestingly, combinations of bacterial antagonists increased inhibition of mycelial growth up to 60% when compared with single isolates. Our study showed that fungal survival structures are associated with a specific microbiome, which is also a reservoir for new biocontrol agents.

Endophytes with plant growth-promoting activity can improve the health and development of plants during all life stages. However, less is known about their stability and transmission across plant genotypes, habitats, and generations. By combining community and isolate analyses, we found that each plant habitat and genotype harbored distinct bacterial communities and plant growth-promoting bacteria (PGPB). Soil, root endosphere, and rhizosphere were the habitats with the highest bacterial diversity, while seeds hosted more selective communities. Seeds generated under field conditions showed traces of a bacterial community composition connected to the suppression of plant pathogens. In contrast, seeds of the successive generation grown in a pathogen-free and low-nutrient environment showed a predominance of bacteria that facilitate the uptake of nutrients. These modifications of the microbiome can be explained by an adaptation to prevalent environmental conditions. Cultivation approaches revealed microhabitat-specific PGPB that were assigned to various species of Bacillus, Stenotrophomonas, and Ralstonia. Tracking down these bacteria among the whole tomato plant allowed us to identify the seed as a primary vehicle of PGPB transmission. This previously undescribed vertical transmission of PGPB represents a strategy to maintain plant beneficial bacteria over generations and has an impact for the design of seed treatments.

Endophytes are microbes capable of colonizing the inner part of plants without causing disease. In some cases, they improve host plant resilience to biotic and abiotic stresses and promote plant growth. The plant-endophyte interaction involves complex mechanisms ranging from the recruitment of the microorganisms to the colonization of internal plant tissue, with the need to escape the plant immune system. These processes are regulated by different plant and endophyte signalling molecules. Phytohormones are among these signalling compounds, but little is known about the specific ways by which they influence recruitment and colonization. The current project aims to obtain a deeper knowledge of the role of signalling compounds in plant-endophyte interactions.To understand how phytohormones influence the composition of endophytic communities, a microbiome analysis (isolation and amplicon sequencing) of endophytic fungi was conducted on roots of tomato mutants impaired in synthesis of ethylene and jasmonic acid. The amplicon sequencing analysis showed a significant effect of the phytohormones, but only the relative abundance of a few taxa was affected (e.g. Fusarium and Pseudogymnoascus). In contrast, there was a stronger effect of plant genotype (comparison of the two wild-types) where the abundance of e.g. Thielaviopsis, Apiotrichum, Fusarium, Saitozyma and Pyrenochaeta differed significantly. The community analysis also revealed high abundance of potential pathogens (e.g. Thielaviopsis basicola and Pyrenochaeta lycopersici) and isolated strains of these species were pathogenic when tested in planta. To understand why healthy plants can harbour such a high amount of pathogenic fungi, experiments with synthetic communities holding both endophytic and pathogenic isolates are currently conducted in order to elucidate possible “natural biocontrol effects” by the endophytic fungi present in the microbiome.“This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 676480”.

Background The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (Solanum lycopersicum LA4024, S. habrochaites LA1777) by targeting bacterial 16S rRNA gene fragments. Results Leaves, leaves without trichomes, and trichomes alone harbored similar abundances of bacteria (108–109 16S rRNA gene copy numbers per gram of sample). In contrast, bacterial diversity was found significantly increased in trichome samples (Shannon index: 4.4 vs. 2.5). Moreover, the community composition was significantly different when assessed with beta diversity analysis and corresponding statistical tests. At the bacterial class level, Alphaproteobacteria (23.6%) were significantly increased, whereas Bacilli (8.6%) were decreased in trichomes. The bacterial family Sphingomonadacea (8.4%) was identified as the most prominent, trichome-specific feature; Burkholderiaceae and Actinobacteriaceae showed similar patterns. Moreover, Sphingomonas was identified as a central element in the core microbiome of trichome samples, while distinct low-abundant bacterial families including Hymenobacteraceae and Alicyclobacillaceae were exclusively found in trichome samples. Niche preferences were statistically significant for both genotypes and genotype-specific enrichments were further observed. Conclusion Our results provide first evidence of a highly specific trichome microbiome in tomato and show the importance of micro-niches for the structure of bacterial communities on leaves. These findings provide further clues for breeding, plant pathology and protection as well as so far unexplored natural pathogen defense strategies.