{"type": "FeatureCollection", "features": [{"id": "10.1016/j.pedobi.2017.05.003", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:50Z", "type": "Journal Article", "created": "2017-05-13", "title": "Priorities for research in soil ecology", "description": "The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia - Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia.The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.", "keywords": ["0301 basic medicine", "aboveground-belowground interactions", "Biologia", "Aboveground-belowground interactions", "910", "soil processes", "soil microbial ecology", "Microbial ecology", "Novel environments", "Soil food web", "11. Sustainability", "Climate change", "0503 Soil Sciences", "Global change", "biodiversity", "ecosystem management", "2. Zero hunger", "biodiversity\u2013ecosystem functioning", "0303 health sciences", "Plant-microbe interaction", "Agronomy & Agriculture", "Soil processes", "climate change", "ekosysteemipalvelut", "Biogeography", "international", "570", "Soil management", "Ecosystem service", "Biodiversity\u2013ecosystem functioning", "0607 Plant Biology", "plant-microbe interactions", "soil biodiversity", "Chemical ecology", "Aboveground-belowground interactions; Biodiversity\u2013ecosystem functioning; Biogeography; Chemical ecology; Climate change; Ecosystem services; Global change; Microbial ecology; Novel environments; Plant-microbe interactions; Soil biodiversity; Soil food web; Soil management; Soil processes", "climatic changes", "eli\u00f6maantiede", "12. Responsible consumption", "Aboveground-belowground interaction", "03 medical and health sciences", "soil food web", "Novel environment", "XXXXXX - Unknown", "Ecosystem services", "Biology", "global change", "maaper\u00e4nsuojelu", "chemical ecology", "500", "15. Life on land", "Soil biodiversity", "biodiversiteetti", "ekosysteemit (ekologia)", "mikrobiekologia", "13. Climate action", "ilmastonmuutos", "novel environments", "ta1181", "soil management", "Plant-microbe interactions", "0703 Crop And Pasture Production"]}, "links": [{"href": "https://usiena-air.unisi.it/bitstream/11365/1134372/2/Eisenhauer_et_al_research_priorities_20170503.pdf"}, {"href": "https://doi.org/10.1016/j.pedobi.2017.05.003"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Pedobiologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.pedobi.2017.05.003", "name": "item", "description": "10.1016/j.pedobi.2017.05.003", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.pedobi.2017.05.003"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-07-01T00:00:00Z"}}, {"id": "10.1111/gcb.13827", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:00Z", "type": "Journal Article", "created": "2017-07-20", "title": "What plant functional traits can reduce nitrous oxide emissions from intensively managed grasslands?", "description": "Abstract

Plant species exert a dominant control over the nitrogen (N) cycle of natural and managed grasslands. Although in intensively managed systems that receive large external N inputs the emission of the potent greenhouse gas nitrous oxide (N2O) is a crucial component of this cycle, a mechanistic relationship between plant species and N2O emissions has not yet been established. Here we use a plant functional trait approach to study the relation between plant species strategies and N2O emissions from soils. Compared to species with conservative strategies, species with acquisitive strategies have higher N uptake when there is ample N in the soil, but also trigger N mineralization when soil N is limiting. Therefore, we hypothesized that (1) compared to conservative species, species with acquisitive traits reduce N2O emissions after a high N addition; and (2) species with conservative traits have lower N2O emissions than acquisitive plants if there is no high N addition. This was tested in a greenhouse experiment using monocultures of six grass species with differing above\uffe2\uff80\uff90 and below\uffe2\uff80\uff90ground traits, growing across a gradient of soil N availability. We found that acquisitive species reduced N2O emissions at all levels of N availability, produced higher biomass and showed larger N uptake. As such, acquisitive species had 87% lower N2O emissions per unit of N uptake than conservative species (p\uffc2\uffa0<\uffc2\uffa0.05). Structural equation\uffc2\uffa0modelling revealed that specific leaf area and root length density were key traits regulating the effects of plants on N2O emission and biomass productivity. These results provide the first framework to understand the mechanisms through which plants modulate N2O emissions, pointing the way to develop productive grasslands that contribute optimally to climate change mitigation.

Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant nutrition and fitness is not well characterized due to a lack of in\uffc2\uffa0situ evidence of bacterial activity.

To address this knowledge gap, we developed an analytical approach that combines the identification and localization of individual bacteria on root surfaces via gold\uffe2\uff80\uff90based in\uffc2\uffa0situ hybridization with correlative NanoSIMS imaging of incorporated stable isotopes, indicative of metabolic activity.

We incubated Kosakonia strain DS\uffe2\uff80\uff901\uffe2\uff80\uff90associated, gnotobiotically grown rice plants with 15N\uffe2\uff80\uff93N2 gas to detect in\uffc2\uffa0situ N2 fixation activity. Bacterial cells along the rhizoplane showed\uffc2\uffa0heterogeneous patterns of 15N enrichment, ranging from the natural isotope abundance levels up to 12.07 at% 15N (average and median of 3.36 and 2.85 at% 15N, respectively, n\uffe2\uff80\uff89=\uffe2\uff80\uff89697 cells).

The presented correlative optical and chemical imaging analysis is applicable to a broad range of studies investigating plant\uffe2\uff80\uff93microbe interactions. For example, it enables verification of the in\uffc2\uffa0situ metabolic activity of host\uffe2\uff80\uff90associated commercialized strains or plant growth\uffe2\uff80\uff90promoting bacteria, thereby disentangling their role in plant nutrition. Such data facilitate the design of plant\uffe2\uff80\uff93microbe combinations for improvement of crop management.

Abstract

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 taxa; Burkholderiaceae and Actinobacteria showed similar pattern. 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.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "Plant microhabitat", "0303 health sciences", "Plant microbiome", "Trichomes", "15. Life on land", "Microbiology", "Bacterial communities", "QR1-502", "Environmental sciences", "03 medical and health sciences", "Solanum lycopersicum", "Solanum habrochaites", "plant microbiome", " bacterial communities", " plant-microbe interactions", " Solanum habrochaites", " Solanum lycopersicum", " plant microhabitat", " phyllosphere", " trichomes", "GE1-350", "Phyllosphere", "Plant-microbe interactions", "Research Article"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40793-020-00364-9.pdf"}, {"href": "https://doi.org/10.1186/s40793-020-00364-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40793-020-00364-9", "name": "item", "description": "10.1186/s40793-020-00364-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40793-020-00364-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-01T00:00:00Z"}}, {"id": "10.21203/rs.3.rs-25108/v1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:20:24Z", "type": "Journal Article", "created": "2020-05-01", "title": "Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato", "description": "Abstract

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 taxa; Burkholderiaceae and Actinobacteria showed similar pattern. 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.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "Plant microhabitat", "0303 health sciences", "Plant microbiome", "Trichomes", "15. Life on land", "Microbiology", "Bacterial communities", "QR1-502", "Environmental sciences", "03 medical and health sciences", "Solanum lycopersicum", "Solanum habrochaites", "plant microbiome", " bacterial communities", " plant-microbe interactions", " Solanum habrochaites", " Solanum lycopersicum", " plant microhabitat", " phyllosphere", " trichomes", "GE1-350", "Phyllosphere", "Plant-microbe interactions", "Research Article"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40793-020-00364-9.pdf"}, {"href": "https://doi.org/10.21203/rs.3.rs-25108/v1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.21203/rs.3.rs-25108/v1", "name": "item", "description": "10.21203/rs.3.rs-25108/v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.21203/rs.3.rs-25108/v1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-01T00:00:00Z"}}, {"id": "10.3390/microorganisms10122479", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:21:25Z", "type": "Journal Article", "created": "2022-12-15", "title": "Flavonoids Are Intra- and Inter-Kingdom Modulator Signals", "description": "

Flavonoids are a broad class of secondary metabolites with multifaceted functionalities for plant homeostasis and are involved in facing both biotic and abiotic stresses to sustain plant growth and health. Furthermore, they were discovered as mediators of plant networking with the surrounding environment, showing a surprising ability to perform as signaling compounds for a multitrophic inter-kingdom level of communication that influences the plant host at the phytobiome scale. Flavonoids orchestrate plant-neighboring plant allelopathic interactions, recruit beneficial bacteria and mycorrhizal fungi, counteract pathogen outbreak, influence soil microbiome and affect plant physiology to improve its resilience to fluctuating environmental conditions. This review focuses on the diversified spectrum of flavonoid functions in plants under a variety of stresses in the modulation of plant morphogenesis in response to environmental clues, as well as their role as inter-kingdom signaling molecules with micro- and macroorganisms. Regarding the latter, the review addresses flavonoids as key phytochemicals in the human diet, considering their abundance in fruits and edible plants. Recent evidence highlights their role as nutraceuticals, probiotics and as promising new drugs for the treatment of several pathologies.

", "keywords": ["0301 basic medicine", "phytochemicals; root exudates; phytobiome; plant-microbe interactions; beneficial microbes; plant secondary metabolites; abiotic stress; biotic stress; rhizosphere; microbiome", "0303 health sciences", "03 medical and health sciences", "beneficial microbes", "QH301-705.5", "phytobiome", "plant-microbe interactions", "Review", "Biology (General)", "phytochemicals", "root exudates", "plant secondary metabolites"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/949072/2/Ghitti%20et%20al%202022%20flavonoids%20are%20intra%20and%20inter%20kingdom%20modulator%20signals.pdf"}, {"href": "https://doi.org/10.3390/microorganisms10122479"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/microorganisms10122479", "name": "item", "description": "10.3390/microorganisms10122479", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms10122479"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-12-15T00:00:00Z"}}, {"id": "10.3389/fpls.2024.1325048", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:21:13Z", "type": "Journal Article", "created": "2024-02-02", "title": "Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400", "description": "Introduction

Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress.

Methods

By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400.

Results

Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden \uffe2\uff80\uff9ccry-for-help\uffe2\uff80\uff9d response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant\uffe2\uff80\uff93microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern.

Discussions

This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.The importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized.

Methods

Here the \uffe2\uff80\uff9ccry-for-help\uffe2\uff80\uff9d hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms.

Results

Arabidopsis exposure to 70 \uffc2\uffb5M PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography\uffe2\uff80\uff93mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the \uffe2\uff80\uff9ccry-for-help\uffe2\uff80\uff9d event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-\uffce\uffb2-alanine, hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6\uffe2\uff80\uff99h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation.

Discussion

These findings expand the knowledge on PCB-triggered \uffe2\uff80\uff9ccry-for-help\uffe2\uff80\uff9d and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments.

The use of microbial consortia (MC) with complementing features is considered to be a promising method of sustainable crop intensification, potentially trumping the limited performance of single-strain applications. We assessed the effect of two novel MC on early wheat growth and litterbag microbial activity in heated and unheated soil. Pot experiments were carried out in duplicate in a greenhouse over 63 days using a completely randomized design with six replications. A range of parameters of plant growth and nutrient uptake were regularly assessed and statistically analyzed by ANOVA. The litterbag-NIRS method was used to trace the microbial activity. Averaged over both trials, soil heating resulted in a significant increase in shoot biomass (+53%) and subsequent nitrogen uptake (+307 mg N pot\u22121) but strongly reduced root development (\u221246%) compared with unheated soil. The application of MC had no effect on wheat growth in the heated soil. By contrast, in the unheated soil, shoot (+12%) and root (+15%) biomass and shoot nitrogen uptake (+11%) were significantly increased after double inoculation with MC compared with autoclaved MC. The litterbag-NIRS method confirmed clear effects of soil heating on microbial activity. Differences between MC application and the control were noted, indicating a buffering effect of MC.

", "keywords": ["2. Zero hunger", "Greenhouse", "S", "Litterbag-NIRS method", "microbial consortia inoculants", "plant-microbe interactions", "Agriculture", "04 agricultural and veterinary sciences", "Microbial consortia inoculants", "Plant-growth-promoting microorganisms", "plant-growth-promoting microorganisms; microbial consortia inoculants; microbial fertilizer; plant-microbe interactions; pot experiments; greenhouse; litterbag-NIRS method", "microbial fertilizer", "Pot experiments", "plant-growth-promoting microorganisms", "greenhouse", "0401 agriculture", " forestry", " and fisheries", "pot experiments", "Plant-microbe interactions", "Microbial fertilizer"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/12/4/899/pdf"}, {"href": "https://iris.enea.it/bitstream/20.500.12079/70987/1/Effects%20of%20Multi-Species%20Microbial%20Inoculants%20on%20Early%20Wheat%20Growth%20and%20Litterbag%20Microbial%20Activity.pdf"}, {"href": "https://www.mdpi.com/2073-4395/12/4/899/pdf"}, {"href": "https://doi.org/10.3390/agronomy12040899"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/agronomy12040899", "name": "item", "description": "10.3390/agronomy12040899", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/agronomy12040899"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-04-08T00:00:00Z"}}, {"id": "10.5061/dryad.t4b8gtj8d", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:22:01Z", "type": "Dataset", "created": "2024-02-07", "title": "Data for: Male, female and mixed-sex poplar plantations support divergent soil microbial communities", "description": "unspecifiedMixed-species forests are often more productive than monocultures because of a lower niche overlap and higher taxonomic and functional diversity of soil microbial communities. Males and females of dioecious plants have sex-specific adaptations to diverse habitats. The potential of using sexual differences in establishing more diverse poplar plantations has not been explored in degraded areas. We conducted a series of greenhouse and field experiments to investigate how belowground competition, soil microbial communities and seasonal variation nitrogen content differ among female, male and mixed-sex Populus cathayana plantations. In the greenhouse experiment, female neighbors suppressed the growth of males under optimal nitrogen conditions. However, male neighbors enhanced \u03b415N of females under inter-sexual competition. In the field, the root length density, root area density and biomass of fine roots were lower in female plantations than in male or mixed-sex plantations. Bacterial networks of female, male and mixed-sex plantations were characterized by different composition of hub nodes, including connectors, module and network hubs. The sex composition of plantations altered bacterial and fungal community structures according to Bray-Curtis distances, with 44% and 65% of variance explained by the root biomass, respectively. The total soil nitrogen content of mixed-sex plantation was higher than that in female plantation in spring and summer. The mixed-sex plantation also had a higher \u03b2-1,4-N-acetyl-glucosaminidase activity in summer and a higher nitrification rate in autumn than the other two plantations. The seasonal soil N content, nitrification rate and root distribution traits demonstrated spatiotemporal niche separation in the mixed-sex plantation. We argue that a strong female-female competition and limited nitrogen content could strongly impede plant growth and reduce the resistance of monosex plantations to climate change and the mixed-sex plantations constitutes a promising way to restore degraded land.", "keywords": ["belowground competition", "plant-microbe interactions", "neighbor sexual identity", "FOS: Earth and related environmental sciences", "microbiota assembly", "dioecious species"], "contacts": [{"organization": "Guo, Qingxue", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.t4b8gtj8d"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.t4b8gtj8d", "name": "item", "description": "10.5061/dryad.t4b8gtj8d", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.t4b8gtj8d"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-23T00:00:00Z"}}, {"id": "20.500.12079/70987", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:25:57Z", "type": "Journal Article", "created": "2022-04-08", "title": "Effects of Multi-Species Microbial Inoculants on Early Wheat Growth and Litterbag Microbial Activity", "description": "

The use of microbial consortia (MC) with complementing features is considered to be a promising method of sustainable crop intensification, potentially trumping the limited performance of single-strain applications. We assessed the effect of two novel MC on early wheat growth and litterbag microbial activity in heated and unheated soil. Pot experiments were carried out in duplicate in a greenhouse over 63 days using a completely randomized design with six replications. A range of parameters of plant growth and nutrient uptake were regularly assessed and statistically analyzed by ANOVA. The litterbag-NIRS method was used to trace the microbial activity. Averaged over both trials, soil heating resulted in a significant increase in shoot biomass (+53%) and subsequent nitrogen uptake (+307 mg N pot\u22121) but strongly reduced root development (\u221246%) compared with unheated soil. The application of MC had no effect on wheat growth in the heated soil. By contrast, in the unheated soil, shoot (+12%) and root (+15%) biomass and shoot nitrogen uptake (+11%) were significantly increased after double inoculation with MC compared with autoclaved MC. The litterbag-NIRS method confirmed clear effects of soil heating on microbial activity. Differences between MC application and the control were noted, indicating a buffering effect of MC.

", "keywords": ["2. Zero hunger", "Greenhouse", "S", "Litterbag-NIRS method", "microbial consortia inoculants", "plant-microbe interactions", "Agriculture", "04 agricultural and veterinary sciences", "Microbial consortia inoculants", "Plant-growth-promoting microorganisms", "plant-growth-promoting microorganisms; microbial consortia inoculants; microbial fertilizer; plant-microbe interactions; pot experiments; greenhouse; litterbag-NIRS method", "microbial fertilizer", "Pot experiments", "plant-growth-promoting microorganisms", "greenhouse", "0401 agriculture", " forestry", " and fisheries", "pot experiments", "Plant-microbe interactions", "Microbial fertilizer"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/12/4/899/pdf"}, {"href": "https://iris.enea.it/bitstream/20.500.12079/70987/1/Effects%20of%20Multi-Species%20Microbial%20Inoculants%20on%20Early%20Wheat%20Growth%20and%20Litterbag%20Microbial%20Activity.pdf"}, {"href": "https://www.mdpi.com/2073-4395/12/4/899/pdf"}, {"href": "https://doi.org/20.500.12079/70987"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20.500.12079/70987", "name": "item", "description": "20.500.12079/70987", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.12079/70987"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-04-08T00:00:00Z"}}, {"id": "10.5281/zenodo.4462142", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:23:50Z", "type": "Dataset", "title": "ECOBREED WP3 entomopathogenic fungi-wireworm data related to Razinger et al. (2020)", "description": "Raw data related to Figures 1 to 5 and Table 1 plus suplementary raw data of the publication Razinger et al. (2020) Frontiers in Plant Science 11:535005; doi: 10.3389/fpls.2020.535005.", "keywords": ["2. Zero hunger", "Plant-microbe-insect interaction", "Wireworm", "Biological control", "Plant-microbe interaction", "Rhizosphere", "Sustainable agriculture", "Entomopathogenic fungus", "Biocontrol", "15. Life on land", "Biopesticide", "Plant-microbe-pest interaction", "Agriotes lineatus"], "contacts": [{"organization": "Razinger, Jaka, Praprotnik, Eva, Schroers, Hans-Josef,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.4462142"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.4462142", "name": "item", "description": "10.5281/zenodo.4462142", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.4462142"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-25T00:00:00Z"}}, {"id": "10.5281/zenodo.4462143", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:23:50Z", "type": "Dataset", "title": "ECOBREED WP3 entomopathogenic fungi-wireworm data related to Razinger et al. (2020)", "description": "Raw data related to Figures 1 to 5 and Table 1 plus suplementary raw data of the publication Razinger et al. (2020) Frontiers in Plant Science 11:535005; doi: 10.3389/fpls.2020.535005.", "keywords": ["2. Zero hunger", "Plant-microbe-insect interaction", "Wireworm", "Biological control", "Plant-microbe interaction", "Rhizosphere", "Sustainable agriculture", "Entomopathogenic fungus", "Biocontrol", "15. Life on land", "Biopesticide", "Plant-microbe-pest interaction", "Agriotes lineatus"], "contacts": [{"organization": "Razinger, Jaka, Praprotnik, Eva, Schroers, Hans-Josef,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.4462143"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.4462143", "name": "item", "description": "10.5281/zenodo.4462143", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.4462143"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-25T00:00:00Z"}}, {"id": "11353/10.2037573", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:25:26Z", "type": "Journal Article", "created": "2023-06-29", "title": "Gold\u2010FISH enables targeted NanoSIMS analysis of plant\u2010associated bacteria", "description": "Summary

Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant nutrition and fitness is not well characterized due to a lack of in\uffc2\uffa0situ evidence of bacterial activity.

To address this knowledge gap, we developed an analytical approach that combines the identification and localization of individual bacteria on root surfaces via gold\uffe2\uff80\uff90based in\uffc2\uffa0situ hybridization with correlative NanoSIMS imaging of incorporated stable isotopes, indicative of metabolic activity.

We incubated Kosakonia strain DS\uffe2\uff80\uff901\uffe2\uff80\uff90associated, gnotobiotically grown rice plants with 15N\uffe2\uff80\uff93N2 gas to detect in\uffc2\uffa0situ N2 fixation activity. Bacterial cells along the rhizoplane showed\uffc2\uffa0heterogeneous patterns of 15N enrichment, ranging from the natural isotope abundance levels up to 12.07 at% 15N (average and median of 3.36 and 2.85 at% 15N, respectively, n\uffe2\uff80\uff89=\uffe2\uff80\uff89697 cells).

The presented correlative optical and chemical imaging analysis is applicable to a broad range of studies investigating plant\uffe2\uff80\uff93microbe interactions. For example, it enables verification of the in\uffc2\uffa0situ metabolic activity of host\uffe2\uff80\uff90associated commercialized strains or plant growth\uffe2\uff80\uff90promoting bacteria, thereby disentangling their role in plant nutrition. Such data facilitate the design of plant\uffe2\uff80\uff93microbe combinations for improvement of crop management.

Plant species exert a dominant control over the nitrogen (N) cycle of natural and managed grasslands. Although in intensively managed systems that receive large external N inputs the emission of the potent greenhouse gas nitrous oxide (N2O) is a crucial component of this cycle, a mechanistic relationship between plant species and N2O emissions has not yet been established. Here we use a plant functional trait approach to study the relation between plant species strategies and N2O emissions from soils. Compared to species with conservative strategies, species with acquisitive strategies have higher N uptake when there is ample N in the soil, but also trigger N mineralization when soil N is limiting. Therefore, we hypothesized that (1) compared to conservative species, species with acquisitive traits reduce N2O emissions after a high N addition; and (2) species with conservative traits have lower N2O emissions than acquisitive plants if there is no high N addition. This was tested in a greenhouse experiment using monocultures of six grass species with differing above\uffe2\uff80\uff90 and below\uffe2\uff80\uff90ground traits, growing across a gradient of soil N availability. We found that acquisitive species reduced N2O emissions at all levels of N availability, produced higher biomass and showed larger N uptake. As such, acquisitive species had 87% lower N2O emissions per unit of N uptake than conservative species (p\uffc2\uffa0<\uffc2\uffa0.05). Structural equation\uffc2\uffa0modelling revealed that specific leaf area and root length density were key traits regulating the effects of plants on N2O emission and biomass productivity. These results provide the first framework to understand the mechanisms through which plants modulate N2O emissions, pointing the way to develop productive grasslands that contribute optimally to climate change mitigation.Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress.

Methods

By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400.

Results

Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden \uffe2\uff80\uff9ccry-for-help\uffe2\uff80\uff9d response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant\uffe2\uff80\uff93microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern.

Discussions

This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.The importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized.

Methods

Here the \uffe2\uff80\uff9ccry-for-help\uffe2\uff80\uff9d hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms.

Results

Arabidopsis exposure to 70 \uffc2\uffb5M PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography\uffe2\uff80\uff93mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the \uffe2\uff80\uff9ccry-for-help\uffe2\uff80\uff9d event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-\uffce\uffb2-alanine, hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6\uffe2\uff80\uff99h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation.

Discussion

These findings expand the knowledge on PCB-triggered \uffe2\uff80\uff9ccry-for-help\uffe2\uff80\uff9d and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments.

Flavonoids are a broad class of secondary metabolites with multifaceted functionalities for plant homeostasis and are involved in facing both biotic and abiotic stresses to sustain plant growth and health. Furthermore, they were discovered as mediators of plant networking with the surrounding environment, showing a surprising ability to perform as signaling compounds for a multitrophic inter-kingdom level of communication that influences the plant host at the phytobiome scale. Flavonoids orchestrate plant-neighboring plant allelopathic interactions, recruit beneficial bacteria and mycorrhizal fungi, counteract pathogen outbreak, influence soil microbiome and affect plant physiology to improve its resilience to fluctuating environmental conditions. This review focuses on the diversified spectrum of flavonoid functions in plants under a variety of stresses in the modulation of plant morphogenesis in response to environmental clues, as well as their role as inter-kingdom signaling molecules with micro- and macroorganisms. Regarding the latter, the review addresses flavonoids as key phytochemicals in the human diet, considering their abundance in fruits and edible plants. Recent evidence highlights their role as nutraceuticals, probiotics and as promising new drugs for the treatment of several pathologies.

", "keywords": ["0301 basic medicine", "phytochemicals; root exudates; phytobiome; plant-microbe interactions; beneficial microbes; plant secondary metabolites; abiotic stress; biotic stress; rhizosphere; microbiome", "0303 health sciences", "03 medical and health sciences", "beneficial microbes", "QH301-705.5", "phytobiome", "plant-microbe interactions", "Review", "Biology (General)", "phytochemicals", "root exudates", "plant secondary metabolites"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/949072/2/Ghitti%20et%20al%202022%20flavonoids%20are%20intra%20and%20inter%20kingdom%20modulator%20signals.pdf"}, {"href": "https://doi.org/2434/949072"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2434/949072", "name": "item", "description": "2434/949072", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2434/949072"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-12-15T00:00:00Z"}}, {"id": "28727214", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:26:23Z", "type": "Journal Article", "created": "2017-07-20", "title": "What plant functional traits can reduce nitrous oxide emissions from intensively managed grasslands?", "description": "Abstract

Plant species exert a dominant control over the nitrogen (N) cycle of natural and managed grasslands. Although in intensively managed systems that receive large external N inputs the emission of the potent greenhouse gas nitrous oxide (N2O) is a crucial component of this cycle, a mechanistic relationship between plant species and N2O emissions has not yet been established. Here we use a plant functional trait approach to study the relation between plant species strategies and N2O emissions from soils. Compared to species with conservative strategies, species with acquisitive strategies have higher N uptake when there is ample N in the soil, but also trigger N mineralization when soil N is limiting. Therefore, we hypothesized that (1) compared to conservative species, species with acquisitive traits reduce N2O emissions after a high N addition; and (2) species with conservative traits have lower N2O emissions than acquisitive plants if there is no high N addition. This was tested in a greenhouse experiment using monocultures of six grass species with differing above\uffe2\uff80\uff90 and below\uffe2\uff80\uff90ground traits, growing across a gradient of soil N availability. We found that acquisitive species reduced N2O emissions at all levels of N availability, produced higher biomass and showed larger N uptake. As such, acquisitive species had 87% lower N2O emissions per unit of N uptake than conservative species (p\uffc2\uffa0<\uffc2\uffa0.05). Structural equation\uffc2\uffa0modelling revealed that specific leaf area and root length density were key traits regulating the effects of plants on N2O emission and biomass productivity. These results provide the first framework to understand the mechanisms through which plants modulate N2O emissions, pointing the way to develop productive grasslands that contribute optimally to climate change mitigation.Abstract

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 taxa; Burkholderiaceae and Actinobacteria showed similar pattern. 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.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "Plant microhabitat", "0303 health sciences", "Plant microbiome", "Trichomes", "15. Life on land", "Microbiology", "Bacterial communities", "QR1-502", "Environmental sciences", "03 medical and health sciences", "Solanum lycopersicum", "Solanum habrochaites", "plant microbiome", " bacterial communities", " plant-microbe interactions", " Solanum habrochaites", " Solanum lycopersicum", " plant microhabitat", " phyllosphere", " trichomes", "GE1-350", "Phyllosphere", "Plant-microbe interactions", "Research Article"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40793-020-00364-9.pdf"}, {"href": "https://doi.org/3087201685"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3087201685", "name": "item", "description": "3087201685", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3087201685"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-01T00:00:00Z"}}, {"id": "PMC8067393", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:29:03Z", "type": "Journal Article", "created": "2020-05-01", "title": "Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato", "description": "Abstract

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 taxa; Burkholderiaceae and Actinobacteria showed similar pattern. 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.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "Plant microhabitat", "0303 health sciences", "Plant microbiome", "15. Life on land", "Microbiology", "Bacterial communities", "QR1-502", "Environmental sciences", "03 medical and health sciences", "Solanum lycopersicum", "Solanum habrochaites", "GE1-350", "Plant-microbe interactions", "Research Article"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40793-020-00364-9.pdf"}, {"href": "https://doi.org/PMC8067393"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC8067393", "name": "item", "description": "PMC8067393", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC8067393"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-01T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Plant-microbe+interaction&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Plant-microbe+interaction&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Plant-microbe+interaction&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Plant-microbe+interaction&offset=21", "hreflang": "en-US"}], "numberMatched": 21, "numberReturned": 21, "distributedFeatures": [], "timeStamp": "2026-04-05T07:18:12.518803Z"}