{"type": "FeatureCollection", "features": [{"id": "10.1111/1574-6941.12018", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:18:34Z", "type": "Journal Article", "created": "2012-09-26", "title": "Acidobacterial Community Responses To Agricultural Management Of Soybean In Amazon Forest Soils", "description": "This study focused on the impact of land-use changes and agricultural management of soybean in Amazon forest soils on the abundance and composition of the acidobacterial community. Quantitative real-time PCR (q-PCR) assays and pyrosequencing of 16S rRNA gene were applied to study the acidobacterial community in bulk soil samples from soybean croplands and adjacent native forests, and mesocosm soil samples from soybean rhizosphere. Based on qPCR measurements, Acidobacteria accounted for 23% in forest soils, 18% in cropland soils, and 14% in soybean rhizosphere of the total bacterial signals. From the 16S rRNA gene sequences of Bacteria domain, the phylum Acidobacteria represented 28% of the sequences from forest soils, 16% from cropland soils, and 17% from soybean rhizosphere. Acidobacteria subgroups 1-8, 10, 11, 13, 17, 18, 22, and 25 were detected with subgroup 1 as dominant among them. Subgroups 4, 6, and 7 were significantly higher in cropland soils than in forest soils, which subgroups responded to decrease in soil aluminum. Subgroups 6 and 7 responded to high content of soil Ca, Mg, Mn, and B. These results showed a differential response of the Acidobacteria subgroups to abiotic soil factors, and open the possibilities to explore acidobacterial subgroups as early-warning bioindicators of agricultural soil management effects in the Amazon area.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Glycine max", "Agriculture", "Sequence Analysis", " DNA", "15. Life on land", "Acidobacteria", "Trees", "Soil", "03 medical and health sciences", "international", "RNA", " Ribosomal", " 16S", "Rhizosphere", "Brazil", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/1574-6941.12018"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1574-6941.12018", "name": "item", "description": "10.1111/1574-6941.12018", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1574-6941.12018"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-10-19T00:00:00Z"}}, {"id": "10.1111/j.1365-2486.2004.00883.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:18:47Z", "type": "Journal Article", "created": "2004-12-02", "title": "Carbon Flow In An Upland Grassland: Effect Of Liming On The Flux Of Recently Photosynthesized Carbon To Rhizosphere Soil", "description": "Abstract

The effect of liming on the flow of recently photosynthesized carbon to rhizosphere soil was studied using 13CO2 pulse labelling, in an upland grassland ecosystem in Scotland. The use of 13C enabled detection, in the field, of the effect of a 4\uffe2\uff80\uff90year liming period of selected soil plots on C allocation from plant biomass to soil, in comparison with unlimed plots. Photosynthetic rates and carbon turnover were higher in plants grown in limed soils than in those from unlimed plots. Higher \uffce\uffb413C\uffe2\uff80\uffb0 values were detected in shoots from limed plants than in those from unlimed plants in samples clipped within 15 days of the end of pulse labelling. Analysis of the aboveground plant production corresponding to the 4\uffe2\uff80\uff90year period of liming indicated that the standing biomass was higher in plots that received lime. Lower \uffce\uffb413C\uffe2\uff80\uffb0 values in limed roots compared with unlimed roots were found, whereas no significant difference was detected between soil samples. Extrapolation of our results indicated that more C has been lost through the soil than has been gained via photosynthetic assimilation because of pasture liming in Scotland during the period 1990\uffe2\uff80\uff931998. However, the uncertainty associated with such extrapolation based on this single study is high and these estimates are provided only to set our findings in the broader context of national soil carbon emissions.

", "keywords": ["2. Zero hunger", "/dk/atira/pure/subjectarea/asjc/2300/2306", "name=Global and Planetary Change", "/dk/atira/pure/subjectarea/asjc/2300/2304", "550", "rhizosphere soil", "liming", "04 agricultural and veterinary sciences", "15. Life on land", "630", "upland grassland", "name=Environmental Chemistry", "carbon pools", "name=Ecology", "0401 agriculture", " forestry", " and fisheries", "name=General Environmental Science", "carbon turnover", "/dk/atira/pure/subjectarea/asjc/2300/2303", "13C", "/dk/atira/pure/subjectarea/asjc/2300/2300"]}, "links": [{"href": "https://doi.org/10.1111/j.1365-2486.2004.00883.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1365-2486.2004.00883.x", "name": "item", "description": "10.1111/j.1365-2486.2004.00883.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1365-2486.2004.00883.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2004-12-01T00:00:00Z"}}, {"id": "10.1111/j.1365-2486.2005.001058.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:18:47Z", "type": "Journal Article", "created": "2005-11-28", "title": "Effects Of Experimental Drought On Soil Respiration And Radiocarbon Efflux From A Temperate Forest Soil", "description": "Abstract

Soil moisture affects microbial decay of SOM and rhizosphere respiration (RR) in temperate forest soils, but isolating the response of soil respiration (SR) to summer drought and subsequent wetting is difficult because moisture changes are often confounded with temperature variation. We distinguished between temperature and moisture effects by simulation of prolonged soil droughts in a mixed deciduous forest at the Harvard Forest, Massachusetts. Roofs constructed over triplicate 5 \uffc3\uff97 5\uffe2\uff80\uff83m2plots excluded throughfall water during the summers of 2001 (168\uffe2\uff80\uff83mm) and 2002 (344\uffe2\uff80\uff83mm), while adjacent control plots received ambient throughfall and the same natural temperature regime. In 2003, throughfall was not excluded to assess the response of SR under natural weather conditions after two prolonged summer droughts. Throughfall exclusion significantly decreased mean SR rate by 53\uffe2\uff80\uff83mg\uffe2\uff80\uff83C\uffe2\uff80\uff83m\uffe2\uff88\uff922\uffe2\uff80\uff83h\uffe2\uff88\uff921over 84 days in 2001, and by 68\uffe2\uff80\uff83mg\uffe2\uff80\uff83C\uffe2\uff80\uff83m\uffe2\uff88\uff922\uffe2\uff80\uff83h\uffe2\uff88\uff921over 126 days in 2002, representing 10\uffe2\uff80\uff9330% of annual SR in this forest and 35\uffe2\uff80\uff9375% of annual net ecosystem exchange (NEE) of C. The differences in SR were best explained by differences in gravimetric water content in the Oi horizon (r2=0.69) and the Oe/Oa horizon (r2=0.60). Volumetric water content of the A horizon was not significantly affected by throughfall exclusion. The radiocarbon signature of soil CO2efflux and of CO2respired during incubations of O horizon, A horizon and living roots allowed partitioning of SR into contributions from young C substrate (including RR) and from decomposition of older SOM. RR (root respiration and microbial respiration of young substrates in the rhizosphere) made up 43\uffe2\uff80\uff9371% of the total C respired in the control plots and 41\uffe2\uff80\uff9380% in the exclusion plots, and tended to increase with drought. An exception to this trend was an interesting increase in CO2efflux of radiocarbon\uffe2\uff80\uff90rich substrates during a period of abundant growth of mushrooms.

Our results suggest that prolonged summer droughts decrease primarily heterotrophic respiration in the O horizon, which could cause increases in the storage of soil organic carbon in this forest. However, the C stored during two summers of simulated drought was only partly released as increased respiration during the following summer of natural throughfall. We do not know if this soil C sink during drought is transient or long lasting. In any case, differential decomposition of the O horizon caused by interannual variation of precipitation probably contributes significantly to observed interannual variation of NEE in temperate forests.

", "keywords": ["Ecology", "04 agricultural and veterinary sciences", "Biological Sciences", "15. Life on land", "soil respiration", "6. Clean water", "soil drought", "heterotrophic respiration", "rhizosphere respiration", "13. Climate action", "soil organic matter", "temperate forest", "radiocarbon", "0401 agriculture", " forestry", " and fisheries", "soil wetting", "soil moisture", "Q(10)", "Environmental Sciences"]}, "links": [{"href": "https://escholarship.org/content/qt3mk9v58k/qt3mk9v58k.pdf"}, {"href": "https://doi.org/10.1111/j.1365-2486.2005.001058.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1365-2486.2005.001058.x", "name": "item", "description": "10.1111/j.1365-2486.2005.001058.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1365-2486.2005.001058.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2005-11-28T00:00:00Z"}}, {"id": "10.1128/msphere.00130-21", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:19:11Z", "type": "Journal Article", "created": "2021-08-11", "title": "Local Network Properties of Soil and Rhizosphere Microbial Communities in Potato Plantations Treated with a Biological Product Are Important Predictors of Crop Yield", "description": "

Our results reinforce the notion that each cultivar on each location recruits a unique microbial community and that these communities are modulated by the vegetative growth stage of the plant. Moreover, inoculation of a Bacillus amyloliquefaciens strain QST713-based product on potatoes also changed the abundance of specific taxonomic groups and the structure of local networks in those locations where the product caused an increase in the yield.

", "keywords": ["Crops", " Agricultural", "0301 basic medicine", "2. Zero hunger", "Biological Products", "0303 health sciences", "Bacteria", "Microbiota", "Fungi", "High-Throughput Nucleotide Sequencing", "Agriculture", "Agricultural Inoculants", "15. Life on land", "Microbiology", "QR1-502", "United States", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Rhizosphere", "Soil Microbiology", "Research Article", "Solanum tuberosum"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/mSphere.00130-21"}, {"href": "https://doi.org/10.1128/msphere.00130-21"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msphere.00130-21", "name": "item", "description": "10.1128/msphere.00130-21", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msphere.00130-21"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-25T00:00:00Z"}}, {"id": "10.1111/nph.15516", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:19:04Z", "type": "Journal Article", "created": "2018-10-06", "title": "Imaging microstructure of the barley rhizosphere: particle packing and root hair influences", "description": "Summary

Soil adjacent to roots has distinct structural and physical properties from bulk soil, affecting water and solute acquisition by plants. Detailed knowledge on how root activity and traits such as root hairs affect the three\uffe2\uff80\uff90dimensional pore structure at a fine scale is scarce and often contradictory.

Roots of hairless barley (Hordeum vulgare L. cv Optic) mutant (NRH) and its wildtype (WT) parent were grown in tubes of sieved (<250\uffc2\uffa0\uffce\uffbcm) sandy loam soil under two different water regimes. The tubes were scanned by synchrotron\uffe2\uff80\uff90based X\uffe2\uff80\uff90ray computed tomography to visualise pore structure at the soil\uffe2\uff80\uff93root interface. Pore volume fraction and pore size distribution were analysed vs distance within 1\uffc2\uffa0mm of the root surface.

Less dense packing of particles at the root surface was hypothesised to cause the observed increased pore volume fraction immediately next to the epidermis. The pore size distribution was narrower due to a decreased fraction of larger pores. There were no statistically significant differences in pore structure between genotypes or moisture conditions.

A model is proposed that describes the variation in porosity near roots taking into account soil compaction and the surface effect at the root surface.

Rising atmospheric carbon dioxide (CO2) could alter the carbon (C) and nitrogen (N) content of ecosystems, yet the magnitude of these effects are not well known. We examined C and N budgets of a subtropical woodland after 11\uffc2\uffa0yr of exposure to elevated CO2.

We used open\uffe2\uff80\uff90top chambers to manipulate CO2 during regrowth after fire, and measured C, N and tracer 15N in ecosystem components throughout the experiment.

Elevated CO2 increased plant C and tended to increase plant N but did not significantly increase whole\uffe2\uff80\uff90system C or N. Elevated CO2 increased soil microbial activity and labile soil C, but more slowly cycling soil C pools tended to decline. Recovery of a long\uffe2\uff80\uff90term 15N tracer indicated that CO2 exposure increased N losses and altered N distribution, with no effect on N inputs.

Increased plant C accrual was accompanied by higher soil microbial activity and increased C losses from soil, yielding no statistically detectable effect of elevated CO2 on net ecosystem C uptake. These findings challenge the treatment of terrestrial ecosystems responses to elevated CO2 in current biogeochemical models, where the effect of elevated CO2 on ecosystem C balance is described as enhanced photosynthesis and plant growth with decomposition as a first\uffe2\uff80\uff90order response.

", "keywords": ["Soil organic matter", "Long term experiment", "Elevated atmospheric CO2", "Florida scrub oak", "Scrub oak", "Research", "Plant Sciences", "Aboveground biomass", "Plant Biology", "Microbial communities", "04 agricultural and veterinary sciences", "Carbon Cycling", "15. Life on land", "Forest productivity", "Soil carbon", "Rhizosphere processes", "Terrestrial ecosystems", "Dioxide enrichment", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Elevated CO2", "Climate feedbacks", "Global change", "Subtropical woodland", "Nitrogen cycling"]}, "links": [{"href": "https://digitalcommons.odu.edu/context/biology_fac_pubs/article/1264/viewcontent/Day2013CumulativeResponseofEcosystemCarbonandNitrogenOCR.pdf"}, {"href": "https://doi.org/10.1111/nph.12333"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/nph.12333", "name": "item", "description": "10.1111/nph.12333", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.12333"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-05-30T00:00:00Z"}}, {"id": "10.1111/nph.14705", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:19:03Z", "type": "Journal Article", "created": "2017-07-31", "title": "High\u2010resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation", "description": "Summary

In this paper, we provide direct evidence of the importance of root hairs on pore structure development at the root\uffe2\uff80\uff93soil interface during the early stage of crop establishment.

This was achieved by use of high\uffe2\uff80\uff90resolution (c. 5\uffc2\uffa0\uffce\uffbcm) synchrotron radiation computed tomography (SRCT) to visualise both the structure of root hairs and the soil pore structure in plant\uffe2\uff80\uff93soil microcosms. Two contrasting genotypes of barley (Hordeum vulgare), with and without root hairs, were grown for 8\uffc2\uffa0d in microcosms packed with sandy loam soil at 1.2\uffc2\uffa0g\uffc2\uffa0cm\uffe2\uff88\uff923 dry bulk density. Root hairs were visualised within air\uffe2\uff80\uff90filled pore spaces, but not in the fine\uffe2\uff80\uff90textured soil regions.

We found that the genotype with root hairs significantly altered the porosity and connectivity of the detectable pore space (>\uffc2\uffa05\uffc2\uffa0\uffce\uffbcm) in the rhizosphere, as compared with the no\uffe2\uff80\uff90hair mutants. Both genotypes showed decreasing pore space between 0.8 and 0.1\uffc2\uffa0mm from the root surface. Interestingly the root\uffe2\uff80\uff90hair\uffe2\uff80\uff90bearing genotype had a significantly greater soil pore volume\uffe2\uff80\uff90fraction at the root\uffe2\uff80\uff93soil interface.

Effects of pore structure on diffusion and permeability were estimated to be functionally insignificant under saturated conditions when simulated using image\uffe2\uff80\uff90based modelling.

Rhizosphere soil has distinct physical and chemical properties from bulk soil. However, besides root\uffe2\uff80\uff90induced physical changes, chemical changes have not been extensively measured in situ on the pore scale.

In this study, we couple structural information, previously obtained using synchrotron X\uffe2\uff80\uff90ray computed tomography (XCT), with synchrotron X\uffe2\uff80\uff90ray fluorescence microscopy (XRF) and X\uffe2\uff80\uff90ray absorption near\uffe2\uff80\uff90edge structure (XANES) to unravel chemical changes induced by plant roots.

Our results suggest that iron (Fe) and sulfur (S) increase notably in the direct vicinity of the root via solubilization and microbial activity. XANES further shows that Fe is slightly reduced, S is increasingly transformed into sulfate (SO42\uffe2\uff88\uff92) and phosphorus (P) is increasingly adsorbed to humic substances in this enrichment zone. In addition, the ferrihydrite fraction decreases drastically, suggesting the preferential dissolution and the formation of more stable Fe oxides. Additionally, the increased transformation of organic S to sulfate indicates that the microbial activity in this zone is increased. These changes in soil chemistry correspond to the soil compaction zone as previously measured via XCT.

The fact that these changes are colocated near the root and the compaction zone suggests that decreased permeability as a result of soil structural changes acts as a barrier creating a zone with increased rhizosphere chemical interactions via surface\uffe2\uff80\uff90mediated processes, microbial activity and acidification.

Phosphorus (P) is essential for plant growth. Arbuscular mycorrhizal fungi (AMF) aid its uptake by acquiring P from sources distant from roots in return for carbon. Little is known about how AMF colonise soil pore\uffe2\uff80\uff90space, and models of AMF\uffe2\uff80\uff90enhanced P\uffe2\uff80\uff90uptake are poorly validated.

We used synchrotron X\uffe2\uff80\uff90ray computed tomography to visualize mycorrhizas in soil and synchrotron X\uffe2\uff80\uff90ray fluorescence/X\uffe2\uff80\uff90ray absorption near edge structure (XRF/XANES) elemental mapping for P, sulphur (S) and aluminium (Al) in combination with modelling.

We found that AMF inoculation had a suppressive effect on colonisation by other soil fungi and identified differences in structure and growth rate between hyphae of AMF and nonmycorrhizal fungi. Our results showed that AMF co\uffe2\uff80\uff90locate with areas of high P and low Al, and preferentially associate with organic\uffe2\uff80\uff90type P species over Al\uffe2\uff80\uff90rich inorganic P.

We discovered that AMF avoid Al\uffe2\uff80\uff90rich areas as a source of P. Sulphur\uffe2\uff80\uff90rich regions were found to be correlated with higher hyphal density and an increased organic\uffe2\uff80\uff90associated P\uffe2\uff80\uff90pool, whilst oxidized S\uffe2\uff80\uff90species were found close to AMF hyphae. Increased S oxidation close to AMF suggested the observed changes were microbiome\uffe2\uff80\uff90related. Our experimentally\uffe2\uff80\uff90validated model led to an estimate of P\uffe2\uff80\uff90uptake by AMF hyphae that is an order of magnitude lower than rates previously estimated \uffe2\uff80\uff93 a result with significant implications for the modelling of plant\uffe2\uff80\uff93soil\uffe2\uff80\uff93AMF interactions.

Feedback between plants and soil microbial communities can be a powerful driver of vegetation dynamics. Plants elicit changes in the soil microbiome that either promote or suppress conspecifics at the same location, thereby regulating population density\uffe2\uff80\uff90dependence and species co\uffe2\uff80\uff90existence. Such effects are often attributed to the accumulation of host\uffe2\uff80\uff90specific antagonistic or beneficial microbiota in the rhizosphere. However, the identity and host\uffe2\uff80\uff90specificity of the microbial taxa involved are rarely empirically assessed. Here we review the evidence for host\uffe2\uff80\uff90specificity in plant\uffe2\uff80\uff90associated microbes and propose that specific plant\uffe2\uff80\uff93soil feedbacks can also be driven by generalists. We outline the potential mechanisms by which generalist microbial pathogens, mutualists and decomposers can generate differential effects on plant hosts and synthesize existing evidence to predict these effects as a function of plant investments into defence, microbial mutualists and dispersal. Importantly, the capacity of generalist microbiota to drive plant\uffe2\uff80\uff93soil feedbacks depends not only on the traits of individual plants but also on the phylogenetic and functional diversity of plant communities. Identifying factors that promote specialization or generalism in plant\uffe2\uff80\uff93microbial interactions and thereby modulate the impact of microbiota on plant performance will advance our understanding of the mechanisms underlying plant\uffe2\uff80\uff93soil feedback and the ways it contributes to plant co\uffe2\uff80\uff90existence.

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.

Phosphorus (P) is essential for plant growth. Arbuscular mycorrhizal fungi (AMF) aid its uptake by acquiring P from sources distant from roots in return for carbon. Little is known about how AMF colonise soil pore\uffe2\uff80\uff90space, and models of AMF\uffe2\uff80\uff90enhanced P\uffe2\uff80\uff90uptake are poorly validated.

We used synchrotron X\uffe2\uff80\uff90ray computed tomography to visualize mycorrhizas in soil and synchrotron X\uffe2\uff80\uff90ray fluorescence/X\uffe2\uff80\uff90ray absorption near edge structure (XRF/XANES) elemental mapping for P, sulphur (S) and aluminium (Al) in combination with modelling.

We found that AMF inoculation had a suppressive effect on colonisation by other soil fungi and identified differences in structure and growth rate between hyphae of AMF and nonmycorrhizal fungi. Our results showed that AMF co\uffe2\uff80\uff90locate with areas of high P and low Al, and preferentially associate with organic\uffe2\uff80\uff90type P species over Al\uffe2\uff80\uff90rich inorganic P.

We discovered that AMF avoid Al\uffe2\uff80\uff90rich areas as a source of P. Sulphur\uffe2\uff80\uff90rich regions were found to be correlated with higher hyphal density and an increased organic\uffe2\uff80\uff90associated P\uffe2\uff80\uff90pool, whilst oxidized S\uffe2\uff80\uff90species were found close to AMF hyphae. Increased S oxidation close to AMF suggested the observed changes were microbiome\uffe2\uff80\uff90related. Our experimentally\uffe2\uff80\uff90validated model led to an estimate of P\uffe2\uff80\uff90uptake by AMF hyphae that is an order of magnitude lower than rates previously estimated \uffe2\uff80\uff93 a result with significant implications for the modelling of plant\uffe2\uff80\uff93soil\uffe2\uff80\uff93AMF interactions.

", "keywords": ["580", "X-ray computed tomography", "570", "Research", "X-ray fluorescence", "Fungi", "Hyphae", "500", "Phosphorus", "mycorrhizas", "04 agricultural and veterinary sciences", "15. Life on land", "plant phosphorus uptake", "Plant Roots", "Soil", "rhizosphere modelling", "Mycorrhizae", "synchrotron", "0401 agriculture", " forestry", " and fisheries", "Soil Microbiology"]}, "links": [{"href": "https://eprints.soton.ac.uk/454110/1/Keyes_et_al_Myco_Paper_TR_04_01_2022_unmarked.pdf"}, {"href": "https://eprints.soton.ac.uk/454110/2/Figures_TR_22_12_2021.pdf"}, {"href": "https://eprints.soton.ac.uk/454110/3/SI_1_TR_22_12_2021_no_markup.pdf"}, {"href": "https://eprints.soton.ac.uk/454110/4/SI_2_TR_22_12_2021.pdf"}, {"href": "https://doi.org/10.17863/cam.81466"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.17863/cam.81466", "name": "item", "description": "10.17863/cam.81466", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.17863/cam.81466"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-15T00:00:00Z"}}, {"id": "10.3390/microorganisms10122479", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:20:59Z", "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": "10.20944/preprints202008.0471.v1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:19:58Z", "type": "Journal Article", "created": "2020-08-24", "title": "Microbiome Management by Biological and Chemical Treatments in Maize is Linked to Plant Health", "description": "

The targeted application of plant growth promoting rhizobacteria (PGPR) provides the key for a future sustainable agriculture with reduced pesticide application. PGPR interaction with the indigenous microbiota is poorly understood but essential to develop reliable applications. Therefore, Stenotrophomonas rhizophila SPA-P69 was applied as seed coating and in combination with a fungicide based on the active ingredients fludioxonil, metalaxyl-M, captan and ziram. Plant performance and rhizosphere composition of treated and non-treated maize plants of two field trials were analyzed. Plant health was significantly increased by treatment; however overall corn yield was not changed. By applying high-throughput amplicon sequencing of the 16S rRNA and the ITS genes, the bacterial and fungal changes in the rhizosphere due to different treatments were determined. Despite treatments had a significant impact on the rhizosphere microbiota (9- 12%), the field site was identified as main driver (27- 37%). Soil microbiota composition from each site was significantly different, which explains the site-specific effects. In this study we were able to show first indications how PGPR treatments increase plant health via microbiome shifts in a site-specific manner. This way first steps towards a detailed understanding of PGPRs and developments of consistently efficient applications in diverse environments are set.

", "keywords": ["Zea mays", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "plant growth promoting rhizobacteria", "QH301-705.5", "15. Life on land", "maize", "Zea mays", "Article", "12. Responsible consumption", "corn", "03 medical and health sciences", "agricultural_sciences_agronomy", "fungicide", "16S rRNA gene", "ITS", "Biology (General)", "rhizosphere"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/10/1506/pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/10/1506/pdf"}, {"href": "https://doi.org/10.20944/preprints202008.0471.v1"}, {"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": "10.20944/preprints202008.0471.v1", "name": "item", "description": "10.20944/preprints202008.0471.v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.20944/preprints202008.0471.v1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-21T00:00:00Z"}}, {"id": "10.3389/fpls.2020.535005", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-01T16:20:47Z", "type": "Journal Article", "created": "2020-09-17", "title": "Bioaugmentation of Entomopathogenic Fungi for Sustainable Agriotes Larvae (Wireworms) Management in Maize", "description": "Soil microorganisms influence biotic and abiotic stress tolerance of crops. Most interactions between plant symbiotic and non-symbiotic soil microorganisms and plants occur in the rhizosphere and are sustained through plant exudation/rhizodeposition. Bioaugmentation, i.e., the introduction or amplification of certain plant beneficial microbes (e.g., entomopathogenic fungi) into the rhizosphere, could contribute to controlling insect crop pests and replacing chemical, environmentally unfriendly insecticides. Wireworms, the soil-burrowing larval stages of click beetles (Coleoptera: Elateridae), are major pests of crops including maize, wheat and potatoes, worldwide. Alternative strategies for controlling wireworms are needed because several chemical pesticides used successfully in the past are being phased out because of their ecotoxicity. Therefore, virulence to Agriotes lineatus L. wireworms and plant beneficial traits of entomopathogenic fungi were investigated in a series of laboratory experiments. Tested taxa included environmentally retrieved Metarhizium brunneum Petch. (two strains), M. robertsii Bisch., Rehner & Humber (Hypocreales: Clavicipitaceae), and Beauveria brongniartii (Sacc.) Petch. and commercially formulated B. bassiana (Bals.-Criv.) Vuill. (Cordycipitaceae) and Bacillus thuringiensis Berliner 1915 var. kurstaki. In-house reared larvae were dipped in conidial suspension, and maize and wheat seeds were coated with fungal conidia. Metarhizium brunneum strains 1154 and 1868 significantly increased wireworm mortality. Fungi were significantly more often re-isolated from maize than wheat rhizoplanes in laboratory assays. The strains tested were rarely isolated as endophytes. Metarhizium brunneum strain 1154 stimulated wheat growth, while M. robertsii 1880 stimulated maize growth, whereas M. brunneum 1868 and others did not affect root or shoot length or plant biomass significantly in laboratory settings. Metarhizium brunneum strain 1868, re-isolated most often from maize rhizoplane, caused the highest wireworm mortality. It was further evaluated whether M. brunneum 1868 can protect maize varieties FeroXXY, LG 34.90 and Chapalu from wireworm damage and promote plant growth at field conditions. Plants of all three varieties stemming from seeds treated with conidia of M. brunneum 1868 showed significantly less wireworm damage 3 to 4 weeks after sowing (5- to 6-leaf stage) resulting in a significantly higher initial maize stand. However, only in the variety LG 34.90\u00a0a significant increase of the maize stand was observed at harvest time.", "keywords": ["2. Zero hunger", "0106 biological sciences", "0301 basic medicine", "plant\u2013microbe interaction", "biological control", "Plant culture", "Plant Science", "15. Life on land", "01 natural sciences", "biopesticide", "plant\u2013microbe\u2013insect interaction", "SB1-1110", "12. Responsible consumption", "sustainable agriculture", "03 medical and health sciences", "plant-microbe-pest interaction", "13. Climate action", "biocontrol", "rhizosphere"]}, "links": [{"href": "https://doi.org/10.3389/fpls.2020.535005"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fpls.2020.535005", "name": "item", "description": "10.3389/fpls.2020.535005", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fpls.2020.535005"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-17T00:00:00Z"}}, {"id": "10.2136/vzj2017.04.0083", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:20:24Z", "type": "Journal Article", "created": "2018-02-15", "title": "Rhizosphere\u2010Scale Quantification of Hydraulic and Mechanical Properties of Soil Impacted by Root and Seed Exudates", "description": "Core Ideas

We hypothesized that plant exudates gel soil particles and on drying enhance water repellency.

This has been carried out using rhizosphere\uffe2\uff80\uff90scale mechanical and hydraulic measurements.

Plant exudates enhanced soil hardness and modulus of elasticity as chia seed > maize root > barley root.

Plant exudates caused measureable decreases in soil wetting rates through water repellency.

Using rhizosphere\uffe2\uff80\uff90scale physical measurements, we tested the hypothesis that plant exudates gel together soil particles and, on drying, enhance soil water repellency. Barley (Hordeum vulgare L. cv. Optic) and maize (Zea mays L. cv. Freya) root exudates were compared with chia (Salvia hispanica L.) seed exudate, a commonly used root exudate analog. Sandy loam and clay loam soils were treated with root exudates at 0.46 and 4.6 mg exudate g\uffe2\uff88\uff921 dry soil and chia seed exudate at 0.046, 0.46, 0.92, 2.3 and 4.6 mg exudate g\uffe2\uff88\uff921 dry soil. Soil hardness and modulus of elasticity were measured at \uffe2\uff88\uff9210 kPa matric potential using a 3\uffe2\uff80\uff90mm\uffe2\uff80\uff90diameter spherical indenter. The water sorptivity and repellency index of air\uffe2\uff80\uff90dry soil were measured using a miniaturized infiltrometer device with a 1\uffe2\uff80\uff90mm tip radius. Soil hardness increased by 28% for barley root exudate, 62% for maize root exudate, and 86% for chia seed exudate at 4.6 mg g\uffe2\uff88\uff921 concentration in the sandy loam soil. For the clay loam soil, root exudates did not affect soil hardness, whereas chia seed exudate increased soil hardness by 48% at 4.6 mg g\uffe2\uff88\uff921 concentration. Soil water repellency increased by 48% for chia seed exudate and 23% for maize root exudate but not for barley root exudate at 4.6 mg g\uffe2\uff88\uff921 concentration in the sandy loam soil. For the clay loam soil, chia seed exudate increased water repellency by 45%, whereas root exudates did not affect water repellency at 4.6 mg g\uffe2\uff88\uff921 concentration. Water sorptivity and repellency were both correlated with hardness, presumably due to the combined influence of exudates on the hydrological and mechanical properties of the soils.Forest fires alter soil microbial communities that are essential to support ecosystem recovery following land burning. These alterations have different responses according to soil abiotic pre- and post-fire conditions and fire severity, among others, and tend to decrease along vegetation recovery over time. Thus, understanding the effects of fires on microbial soil communities is critical to evaluate ecosystem resilience and restoration strategies in fire-prone ecosystems. We studied the state of community-level physiological profiles (CLPPs) and the prokaryotic community structure of rhizosphere and bulk soils from two fire-affected sclerophyll forests (one surveyed 17 months and the other 33 months after fire occurrence) in the Mediterranean climate zone of central Chile. Increases in catabolic activity (by average well color development of CLPPs), especially in the rhizosphere as compared with the bulk soil, were observed in the most recently affected site only. Legacy of land burning was still clearly shaping soil prokaryote community structure, as shown by quantitative PCR (qPCR) and Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene, particularly in the most recent fire-affected site. The qPCR copy numbers and alpha diversity indexes (Shannon and Pielou\uffe2\uff80\uff99s evenness) of sequencing data decreased in burned soils at both locations. Beta diversity analyses showed dissimilarity of prokaryote communities at both study sites according to fire occurrence, and NO3\uffe2\uff80\uff93 was the common variable explaining community changes for both of them. Acidobacteria and Rokubacteria phyla significantly decreased in burned soils at both locations, while Firmicutes and Actinobacteria increased. These findings provide a better understanding of the resilience of soil prokaryote communities and their physiological conditions in Mediterranean forests of central Chile following different time periods after fire, conditions that likely influence the ecological processes taking place during recovery of fire-affected ecosystems.Entomopathogenic fungi have been well exploited as biocontrol agents that can kill insects through direct contact. However, recent research has shown that they can also play an important role as plant endophytes, stimulating plant growth, and indirectly suppressing pest populations. In this study, we examined the indirect, plant-mediated, effects of a strain of entomopathogenic fungus, Metarhizium brunneum on plant growth and population growth of two-spotted spider mites (Tetranychus urticae) in tomato, using different inoculation methods (seed treatment, soil drenching and a combination of both). Furthermore, we investigated changes in tomato leaf metabolites (sugars and phenolics), and rhizosphere microbial communities in response to M. brunneum inoculation and spider mite feeding. A significant reduction in spider mite population growth was observed in response to M. brunneum inoculation. The reduction was strongest when the inoculum was supplied both as seed treatment and soil drench. This combination treatment also yielded the highest shoot and root biomass in both spider mite-infested and non-infested plants, while spider mite infestation increased shoot but reduced root biomass. Fungal treatments did not consistently affect leaf chlorogenic acid and rutin concentrations, but M. brunneum inoculation via a combination of seed treatment and soil drenching reinforced chlorogenic acid (CGA) induction in response to spider mites and under these conditions the strongest spider mite resistance was observed. However, it is unclear whether the M. brunneum-induced increase in CGA contributed to the observed spider mite resistance, as no general association between CGA levels and spider mite resistance was observed. Spider mite infestation resulted in up to two-fold increase in leaf sucrose concentrations and a three to five-fold increase in glucose and fructose concentrations, but these concentrations were not affected by fungal inoculation. Metarhizium, especially when applied as soil drench, impacted the fungal community composition but not the bacterial community composition which was only affected by the presence of spider mites. Our results suggest that in addition to directly killing spider mites, M. brunneum can indirectly suppress spider mite populations on tomato, although the underlying mechanism has not yet been resolved, and can also affect the composition of the soil microbial community.Root architectural and anatomical phenotypes are highly diverse. Specific root phenotypes can be associated with better plant growth under low nutrient and water availability. Therefore, root ideotypes have been proposed as breeding targets for more stress-resilient and resource-efficient crops. For example, root phenotypes that correspond to the Topsoil Foraging ideotype are associated with better plant growth under suboptimal phosphorus availability, and root phenotypes that correspond to the Steep, Cheap and Deep ideotype are linked to better performance under suboptimal availability of nitrogen and water. We propose that natural variation in root phenotypes translates into a diversity of different niches for microbial associations in the rhizosphere, rhizoplane and root cortex, and that microbial traits could have synergistic effects with the beneficial effect of specific root phenotypes. Oxygen and water content, carbon rhizodeposition, nutrient availability, and root surface area are all factors that are modified by root anatomy and architecture and determine the structure and function of the associated microbial communities. Recent research results indicate that root characteristics that may modify microbial communities associated with maize include aerenchyma, rooting angle, root hairs, and lateral root branching density. Therefore, the selection of root phenotypes linked to better plant growth under specific edaphic conditions should be accompanied by investigating and selecting microbial partners better adapted to each set of conditions created by the corresponding root phenotype. Microbial traits such as nitrogen transformation, phosphorus solubilization, and water retention could have synergistic effects when correctly matched with promising plant root ideotypes for improved nutrient and water capture. We propose that elucidation of the interactive effects of root phenotypes and microbial functions on plant nutrient and water uptake offers new opportunities to increase crop yields and agroecosystem sustainability.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.Soil microbial communities are crucial for plant growth and are already depleted by anthropogenic activities. The application of microbial transplants provides a strategy to restore beneficial soil traits, but less is known about the microbiota of traditional inoculants used in biodynamic agriculture. In this study, we used amplicon sequencing and quantitative PCR to decipher microbial communities of composts, biodynamic manures, and plant preparations from Austria and France. In addition, we investigated the effect of extracts derived from biodynamic manure and compost on the rhizosphere microbiome of apple trees. Microbiota abundance, composition, and diversity of biodynamic manures, plant preparations, and composts were distinct. Microbial abundances ranged between 1010-1011(bacterial 16S rRNA genes) and 109-1011(fungal ITS genes). The bacterial diversity was significantly higher in biodynamic manures compared to compost without discernible differences in abundance. Fungal diversity was not significantly different while abundance was increased in biodynamic manures. The microbial communities of biodynamic manures and plant preparations were specific for each production site, but all contain potentially plant-beneficial bacterial genera. When applied in apple orchards, biodynamic preparations (extracts) had the non-significant effect of reducing bacterial and fungal abundance in apple rhizosphere (4 months post-application), while increasing fungal and lowering bacterial Shannon diversity. One to four months after inoculation, individual taxa indicated differential abundance. We observed the reduction of the pathogenic fungusAlternaria, and the enrichment of potentially beneficial bacterial genera such asPseudomonas.Our study paves way for the science-based adaptation of empirically developed biodynamic formulations under different farming practices to restore the vitality of agricultural soils.The targeted application of plant growth promoting rhizobacteria (PGPR) provides the key for a future sustainable agriculture with reduced pesticide application. PGPR interaction with the indigenous microbiota is poorly understood but essential to develop reliable applications. Therefore, Stenotrophomonas rhizophila SPA-P69 was applied as seed coating and in combination with a fungicide based on the active ingredients fludioxonil, metalaxyl-M, captan and ziram. Plant performance and rhizosphere composition of treated and non-treated maize plants of two field trials were analyzed. Plant health was significantly increased by treatment; however overall corn yield was not changed. By applying high-throughput amplicon sequencing of the 16S rRNA and the ITS genes, the bacterial and fungal changes in the rhizosphere due to different treatments were determined. Despite treatments had a significant impact on the rhizosphere microbiota (9- 12%), the field site was identified as main driver (27- 37%). Soil microbiota composition from each site was significantly different, which explains the site-specific effects. In this study we were able to show first indications how PGPR treatments increase plant health via microbiome shifts in a site-specific manner. This way first steps towards a detailed understanding of PGPRs and developments of consistently efficient applications in diverse environments are set.

", "keywords": ["Zea mays", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "plant growth promoting rhizobacteria", "QH301-705.5", "15. Life on land", "maize", "Zea mays", "Article", "12. Responsible consumption", "corn", "03 medical and health sciences", "agricultural_sciences_agronomy", "fungicide", "16S rRNA gene", "ITS", "Biology (General)", "rhizosphere"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/10/1506/pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/10/1506/pdf"}, {"href": "https://doi.org/10.3390/microorganisms8101506"}, {"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/microorganisms8101506", "name": "item", "description": "10.3390/microorganisms8101506", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms8101506"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-21T00:00:00Z"}}, {"id": "10.3390/plants10112498", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-01T16:21:01Z", "type": "Journal Article", "created": "2021-11-19", "title": "Testing Virulence of Different Species of Insect Associated Fungi against Yellow Mealworm (Coleoptera: Tenebrionidae) and Their Potential Growth Stimulation to Maize", "description": "

This paper investigates 71 isolates of two genera of entomopathogens, Metarhizium and Beauveria, and a biostimulative genus Trichoderma, for their ability to infect yellow mealworms (Tenebrio molitor) and to stimulate maize (Zea mays) growth. Fungal origin, host, and isolation methods were taken into account in virulence analysis as well. Isolates Metarhizium brunneum (1154) and Beauveria bassiana (2121) showed the highest mortality (100%) against T. molitor. High virulence seems to be associated with fungi isolated from wild adult mycosed insects, meadow habitats, and Lepidopteran hosts, but due to uneven sample distribution, we cannot draw firm conclusions. Trichoderma atroviride (2882) and Trichoderma gamsii (2883) increased shoot length, three Metarhizium robertsii isolates (2691, 2693, and 2688) increased root length and two M. robertsii isolates (2146 and 2794) increased plant dry weight. Considering both criteria, the isolate M. robertsii (2693) was the best as it caused the death of 73% T. molitor larvae and also significantly increased maize root length by 24.4%. The results warrant further studies with this isolate in a tri-trophic system.

", "keywords": ["virulence", "0106 biological sciences", "rhizosphere competence", "plant\u2013microbe\u2013pest interactions", "QK1-989", "entomopathogenic fungi; Tenebrio molitor; virulence; pathogenicity; growth stimulation; plant\u2013microbe\u2013pest interactions; rhizosphere competence", "Botany", "pathogenicity", "entomopathogenic fungi", "Tenebrio molitor", "growth stimulation", "01 natural sciences", "Article"]}, "links": [{"href": "http://www.mdpi.com/2223-7747/10/11/2498/pdf"}, {"href": "https://www.mdpi.com/2223-7747/10/11/2498/pdf"}, {"href": "https://doi.org/10.3390/plants10112498"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plants", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/plants10112498", "name": "item", "description": "10.3390/plants10112498", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/plants10112498"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-11-18T00:00:00Z"}}, {"id": "10.4067/s0718-95162013005000017", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:21:16Z", "type": "Journal Article", "created": "2013-06-06", "title": "Growth And Nutrient Uptake By Schoenoplectus Californicus (Ca Meyer) Sojak In A Constructed Wetland Fed With Swine Slurry", "description": "The effects of long term no-till and crop residue on soil microbial community catabolic function and relevant carbon cycle in the rhizosphere and bulk soils were assessed in the 10th year of a maize-winter wheat-soybean crop rotation. Conventional and zero tillage were coupled with residue removal and residue retention in a factorial design. Soil microbial community catabolic diversity was determined using Biolog-Eco plate. Average well colour development value (AWCD) of the microbial community in the rhizosphere soil was significantly higher than that in the bulk soil. Soil organic carbon (SOC) and microbial biomass carbon (MB-C) content of rhizosphere soil under both zero tillage and residue removal treatments were significantly higher than those in the bulk soil. Microbes in bulk soil presented a preferential utilization of diverse carbon sources when crop residue was retained. Zero tillage significantly increased the utilization of most carbon sources of microbial in the rhizosphere compared to conventional tillage. Principal component analysis (PCA) of the distribution of carbon substrate utilization for all treatments suggests that the microbial community catabolic diversity is different between the tillage management treatments and between soil sampling positions. Effects of zero tillage and crop residue retention were different with respect to the microbial catabolic diversity in the rhizosphere and the bulk soil.", "keywords": ["soil organic carbon", "2. Zero hunger", "microbial biomass carbon", "conservation tillage", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "bulk soil", "15. Life on land", "Microbial catabolic diversity", "rhizosphere"], "contacts": [{"organization": "Yang, Q, Wang, X, Shen, Y,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.4067/s0718-95162013005000017"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20soil%20science%20and%20plant%20nutrition", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.4067/s0718-95162013005000017", "name": "item", "description": "10.4067/s0718-95162013005000017", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.4067/s0718-95162013005000017"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-01-01T00:00:00Z"}}, {"id": "10.5061/dryad.040jp22", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:21:22Z", "type": "Dataset", "title": "Data from: Plant economic strategies of grassland species control soil carbon dynamics through rhizodeposition", "description": "unspecified1. The plant economics spectrum is increasingly recognized as a major determinant of plant species effects on terrestrial ecosystem functioning related to carbon cycling. However, the role of plant economic strategies in the effects of living root activity on soil organic carbon (SOC) dynamics through rhizodeposition remains unexplored, despite SOC being the largest terrestrial carbon pool. 2. Using a continuous 13C-labeling method allowing partitioning of plant and soil sources to carbon fluxes and pools, we studied here the linkages between plant economic strategies and SOC cycling processes in a \u2018common garden\u2019 greenhouse experiment. It includes a panel of 12 grassland species selected along a gradient of economic traits and belonging to three functionnal groups (C3 grasses, forbs and legumes). 3. All species induced an acceleration of native SOC mineralization but this rhizosphere priming effect (RPE) substantially differed across species and varied eleven-fold by the end of the experiment (from +26 to +295 % relative to unplanted soil). Interspecific variation in RPE was primarily linked to plant photosynthetic activity associated to species economic strategies of light and CO2 resource acquisition and processing. Fast-growing acquisitive species, such as legumes, featured large RPE, in relation with their high canopy photosynthesis coupled to high leaf photosynthetic capacity and large net primary productivity allocated aboveground. This large RPE was further associated with high root metabolic activity, rhizodeposition and soil microbial activity. In contrast, fine-root growth and economic traits related to soil resource foraging ability were poor predictors of RPE. 4. The formation of new root-derived SOC varied nine-fold across species and was similarly positively related to the net primary productivity allocated aboveground. Fast-growing acquisitive species with a high photosynthetic activity induced a disproportionately large RPE relative to SOC formation. 5. Synthesis. Overall, our study demonstrates that rhizodeposition is a major mechanism through which plant economic strategies of grassland species control soil carbon dynamics. Acquisitive versus conservative species were associated with high versus low rates of photosynthesis and rhizodeposition, in turn leading to fast versus slow SOC turnover. This emphasizes the importance of considering rhizosphere processes for understanding plant species effects on soil biogeochemistry.", "keywords": ["2. Zero hunger", "Chamerion angustifolium", "Nardus stricta", "plant-soil (below-ground) interactions", "Festuca rubra", "Melilotus albus", "15. Life on land", "Rumex acetosa", "rhizosphere processes", "plant economics spectrum", "leaf and root traits", "Vicia cracca", "Lotus corniculatus", "Plantago lanceolata", "Taraxacum officinale", "Poa trivialis", "Photosynthesis", "Anthoxanthum odoratum", "Rhizosphere priming effect"], "contacts": [{"organization": "Henneron, Ludovic, Cros, Camille, Picon-Cochard, Catherine, Rahimian, Vida, Fontaine, S\u00e9bastien,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.040jp22"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.040jp22", "name": "item", "description": "10.5061/dryad.040jp22", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.040jp22"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-01T00:00:00Z"}}, {"id": "10.5061/dryad.9zw3r229b", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:21:27Z", "type": "Dataset", "title": "Data from: Switchgrass rhizosphere metabolite chemistry driven by nitrogen availability", "description": "unspecifiedPlants and soil microorganisms interact closely in the rhizosphere where plants may exchange carbon (C) for functional benefits from the microbial community. For example, the bioenergy crop, switchgrass (Panicum virgatum) is thought to exchange root-exuded C for nitrogen (N) fixed by diazotrophs (free-living N-fixers). However, this interaction is not well characterized and it is not known how or if switchgrass responds to diazotrophs or their activity. To explore this question, we assessed rhizosphere metabolite chemistry of switchgrass grown in a hydroponic system under two N levels and under inoculated or uninoculated conditions. Plants were grown with the inoculum Azotobacter vinelandii DJ for three days before harvest. We found switchgrass root exudate chemistry to be driven by N availability. Total metabolite concentrations were generally greater under high N versus low N and unaffected by inoculation. Examination of rhizosphere chemical fingerprints indicates metabolite chemistry was also driven strongly by N availability with a greater relative abundance of carbohydrates under high N and greater relative abundance of organic acids under low N. We also found evidence of changes in rhizosphere chemical fingerprints by inoculation treatment. However, we found little evidence of N treatment and inoculation interaction effects which suggests this response is not directly mediated by N availability.", "keywords": ["2. Zero hunger", "Switchgrass", "Rhizosphere", "NMR-based metabolomics", "Diazotroph", "15. Life on land", "Free-living nitrogen fixation"], "contacts": [{"organization": "Smercina, Darian, Bowsher, Alan W, Evans, Sarah E, Friesen, Maren L, Eder, Elizabeth K, Hoyt, David W, Tiemann, Lisa K,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.9zw3r229b"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.9zw3r229b", "name": "item", "description": "10.5061/dryad.9zw3r229b", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.9zw3r229b"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-26T00:00:00Z"}}, {"id": "10.5061/dryad.hhmgqnkk9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:21:30Z", "type": "Dataset", "title": "Visualization and quantification of carbon 'rusty sink' by rice root iron plaque: mechanisms, functions, and global implications", "description": "Paddies contain 78% higher organic carbon (C) stocks than adjacent upland soils, and iron (Fe) plaque formation on rice roots is one of the mechanisms that traps C. The process sequence, extent and global relevance of this C stabilization mechanism under oxic/anoxic conditions remains unclear. We quantified and localized the contribution of Fe plaque to C stabilization in a microoxic area (rice rhizosphere) and evaluated the role of this C trap toward global C sequestration in paddy soils. Visualization and localization of pH by imaging with planar optodes, enzyme activities by zymography, and root exudation by 14C imaging, as well as upscale modeling enabled linkage of three groups of rhizosphere processes that are responsible for C stabilization from the micro- (root) to the macro- (ecosystem) level. The 14C activity in soil (reflecting stabilization of rhizodeposits) with Fe2+ addition was 1.4\u22121.5 times higher than that in the control and phosphate addition soils. Perfect co-localization of the hotspots of \u03b2-glucosidase activity (by zymography) with exudation showed that labile C and high enzyme activities were localized within Fe plaques. Fe2+ addition to soil and its microbial oxidation to Fe3+ by radial oxygen release from rice roots increased Fe plaque (Fe3+) formation by 1.7\u22122.5 times. The C trapped by Fe plaque was 1.1 times higher after Fe2+ addition. Therefore, Fe plaque formed from amorphous and complex Fe on root surface act as a \u201crusty sink\u201d for C. Upscaling by model revealed the global significance of C preservation within Fe3+ complexes in paddy soils. Considering the area of coverage of paddy soils globally, radial oxygen loss from roots and bacterial Fe oxidation may trap up to 130 Mg C in Fe plaques per rice season. This represents an important annual surplus of new and stable C to the existing C pool under long-term rice cropping.", "keywords": ["2. Zero hunger", "Carbon sequestration", "Fe-oxidizing and Fe-reducing bacteria", "FOS: Agricultural sciences", "15. Life on land", "rhizosphere processes", "Iron plaque", "enzyme activity", "Fluctuating redox conditions"], "contacts": [{"organization": "Wei, Liang", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.hhmgqnkk9"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.hhmgqnkk9", "name": "item", "description": "10.5061/dryad.hhmgqnkk9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.hhmgqnkk9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-08-03T00:00:00Z"}}, {"id": "10.5061/dryad.sbcc2frbh", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:21:34Z", "type": "Dataset", "title": "Root functional traits determine the magnitude of the rhizosphere priming effect among eight tree species", "description": "Rhizosphere priming effect\u00a0can accelerate or decelerate the decomposition of soil organic matter.\u00a0Using a natural abundance 13C tracer method allowing partitioning of native soil organic carbon (SOC) decomposition and plant rhizosphere respiration, we studied the effects of eight tree species on the strength of the rhizosphere priming. All tree species enhanced the rate of SOC decomposition, by 82% on average.\u00a0Mean diameter of first-order roots and root exudate-derived respiration were positively correlated with the RPE, together explaining a large part of the observed variation in the RPE (R2 = 0.72), whereas root branching density was negatively associated with the RPE. Path analyses further suggested that mean diameter of first-order roots was the main driver of the RPE owing to its positive direct effect on the RPE and its indirect effects via root exudate-derived respiration and root branching density. These results demonstrate that the magnitude of the RPE is regulated by complementary aspects of root morphology, architecture and physiology, implying that comprehensive approaches are needed to reveal the multiple mechanisms driving plant effects on the RPE.", "keywords": ["13C natural abundance", "Plant functional traits", "rhizosphere priming effect", "Fine roots", "15. Life on land", "FOS: Natural sciences"], "contacts": [{"organization": "Chao, Lin, Liu, Yanyan, Zhang, Weidong, Wang, Qingkui, Guan, Xin, Yang, Qingpeng, Chen, Longchi, Zhang, Jianbing, Hu, Baoqing, Liu, Zhanfeng, Wang, Silong, Freschet, Gr\u00e9goire T.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.sbcc2frbh"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.sbcc2frbh", "name": "item", "description": "10.5061/dryad.sbcc2frbh", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.sbcc2frbh"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-02-20T00:00:00Z"}}, {"id": "1887/3631563", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:25:03Z", "type": "Journal Article", "created": "2023-05-24", "title": "Effects of tomato inoculation with the entomopathogenic fungus Metarhizium brunneum on spider mite resistance and the rhizosphere microbial community", "description": "

Entomopathogenic fungi have been well exploited as biocontrol agents that can kill insects through direct contact. However, recent research has shown that they can also play an important role as plant endophytes, stimulating plant growth, and indirectly suppressing pest populations. In this study, we examined the indirect, plant-mediated, effects of a strain of entomopathogenic fungus, Metarhizium brunneum on plant growth and population growth of two-spotted spider mites (Tetranychus urticae) in tomato, using different inoculation methods (seed treatment, soil drenching and a combination of both). Furthermore, we investigated changes in tomato leaf metabolites (sugars and phenolics), and rhizosphere microbial communities in response to M. brunneum inoculation and spider mite feeding. A significant reduction in spider mite population growth was observed in response to M. brunneum inoculation. The reduction was strongest when the inoculum was supplied both as seed treatment and soil drench. This combination treatment also yielded the highest shoot and root biomass in both spider mite-infested and non-infested plants, while spider mite infestation increased shoot but reduced root biomass. Fungal treatments did not consistently affect leaf chlorogenic acid and rutin concentrations, but M. brunneum inoculation via a combination of seed treatment and soil drenching reinforced chlorogenic acid (CGA) induction in response to spider mites and under these conditions the strongest spider mite resistance was observed. However, it is unclear whether the M. brunneum-induced increase in CGA contributed to the observed spider mite resistance, as no general association between CGA levels and spider mite resistance was observed. Spider mite infestation resulted in up to two-fold increase in leaf sucrose concentrations and a three to five-fold increase in glucose and fructose concentrations, but these concentrations were not affected by fungal inoculation. Metarhizium, especially when applied as soil drench, impacted the fungal community composition but not the bacterial community composition which was only affected by the presence of spider mites. Our results suggest that in addition to directly killing spider mites, M. brunneum can indirectly suppress spider mite populations on tomato, although the underlying mechanism has not yet been resolved, and can also affect the composition of the soil microbial community.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.Citrate (Cit) and Deferoxamine B (DFOB) are two important organic ligands coexisting in soils with distinct different affinities for metal ions. It has been theorized that siderophores and weak organic ligands play a synergistic role during the transport of micronutrients in the rhizosphere, but the geochemical controls of this process remain unknown. Here we test the hypothesis that gradients in pH and ion strength regulate and enable the cooperation. To this end, first we use potentiometric titrations to identify the dominant Zn(II)\uffe2\uff80\uff93Cit and Zn(II)\uffe2\uff80\uff93DFOB complexes and to determine their ionic strength dependent stability constants between 0 and 1\uffc2\uffa0mol\uffc2\uffa0dm\uffe2\uff88\uff923. We parametrise the Extended Debye-H\uffc3\uffbcckel (EDH) equation and determine accurate intrinsic association constants (log\uffce\uffb20) for the formation of the complexes present. The speciation model developed confirms the presence of [Zn(Cit)]\uffe2\uff88\uff92, [Zn(HCit)], [Zn2(Cit)2(OH)2]4\uffe2\uff88\uff92, and [Zn(Cit)2]4\uffe2\uff88\uff92, with [Zn(Cit)]\uffe2\uff88\uff92 and [Zn2(Cit)2(OH)2]4\uffe2\uff88\uff92 the dominant species in the pH range relevant to rhizosphere. We propose the existence of a\uffc2\uffa0new [Zn(Cit)(OH)3]4\uffe2\uff88\uff92 complex above pH 10. We also verify the existence of two hexadentate Zn(II)\uffe2\uff80\uff93DFOB species, i.e., [Zn(DFOB)]\uffe2\uff88\uff92 and [Zn(HDFOB)], and of one tetradentate species [Zn(H2DFOB)]+. Second, we identify the pH and ionic strength dependent ligand exchange points (LEP) of Zn with citrate and DFOB and the stability windows for Zn(II)\uffe2\uff80\uff93Cit and Zn(II)\uffe2\uff80\uff93DFOB complexes in NaCl and rice soil solutions. We find that the LEPs fall within the pH and ionic strength gradients expected in rhizospheres and that the stability windows for Zn(II)\uffe2\uff80\uff93citrate and Zn(II)\uffe2\uff80\uff93DFOB, i.e., low and high affinity ligands, can be distinctly set off. This suggests that pH and ion strength gradients allow for Zn(II) complexes with citrate and DFOB to dominate in different parts of the rhizosphere and this explains why mixtures of low and high affinity ligands increase leaching of micronutrients in soils. Speciation models of soil solutions using newly determined association constants demonstrate that the presence of dissolved organic matter and inorganic ligands (i.e., bicarbonate, phosphate, sulphate, or chlorides) do neither affect the position of the LEP nor the width of the stability windows significantly. In conclusion, we demonstrate that cooperative and synergistic ligand interaction between low and high affinity ligands is a valid mechanism for\uffc2\uffa0controlling zinc transport in the rhizosphere and possibly in other environmental reservoirs such as in the phycosphere. Multiple production of weak and strong ligands is therefore a valid strategy of plants and other soil organisms to improve access to micronutrients.

This paper investigates 71 isolates of two genera of entomopathogens, Metarhizium and Beauveria, and a biostimulative genus Trichoderma, for their ability to infect yellow mealworms (Tenebrio molitor) and to stimulate maize (Zea mays) growth. Fungal origin, host, and isolation methods were taken into account in virulence analysis as well. Isolates Metarhizium brunneum (1154) and Beauveria bassiana (2121) showed the highest mortality (100%) against T. molitor. High virulence seems to be associated with fungi isolated from wild adult mycosed insects, meadow habitats, and Lepidopteran hosts, but due to uneven sample distribution, we cannot draw firm conclusions. Trichoderma atroviride (2882) and Trichoderma gamsii (2883) increased shoot length, three Metarhizium robertsii isolates (2691, 2693, and 2688) increased root length and two M. robertsii isolates (2146 and 2794) increased plant dry weight. Considering both criteria, the isolate M. robertsii (2693) was the best as it caused the death of 73% T. molitor larvae and also significantly increased maize root length by 24.4%. The results warrant further studies with this isolate in a tri-trophic system.

", "keywords": ["virulence", "0106 biological sciences", "rhizosphere competence", "plant\u2013microbe\u2013pest interactions", "QK1-989", "entomopathogenic fungi; Tenebrio molitor; virulence; pathogenicity; growth stimulation; plant\u2013microbe\u2013pest interactions; rhizosphere competence", "Botany", "pathogenicity", "entomopathogenic fungi", "Tenebrio molitor", "growth stimulation", "01 natural sciences", "Article"]}, "links": [{"href": "http://www.mdpi.com/2223-7747/10/11/2498/pdf"}, {"href": "https://www.mdpi.com/2223-7747/10/11/2498/pdf"}, {"href": "https://doi.org/3213366455"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plants", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3213366455", "name": "item", "description": "3213366455", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3213366455"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-11-18T00:00:00Z"}}, {"id": "11353/10.2156897", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:24:47Z", "type": "Journal Article", "created": "2025-02-05", "title": "Preferential use of organic acids over sugars by soil microbes in simulated root exudation", "description": "Sugars and organic acids, primary components in plant root exudates, are thought to enhance microbial decomposition of organic matter in the rhizosphere. However, their specific impacts on microbial activity and nutrient mobilisation remain poorly understood. Here, we simulated passive root exudation to investigate the distinct effects of sugars and organic acids on microbial metabolism in the rhizosphere. We released 13C-labelled sugars and/or organic acids via reverse microdialysis into intact meadow and forest soils over 6-h. We measured substrate-induced microbial respiration, soil organic matter mineralization, metabolite concentrations, and substrate incorporation into lipid-derived fatty acids. Our results reveal a pronounced microbial preference for organic acids over sugars, with organic acids being removed faster from the exudation spot and preferentially respired by microbes. Unlike sugars, organic acids increased concentrations of microbial metabolic byproducts and cations (K, Ca, Mg) near the exudation spot. Our results challenge the prevailing assumption that sugars are the most readily available and rapidly consumed substrates for soil microbes. Microbial preference for organic acids indicates a trade-off between rapid biomass growth and ATP yield. Our findings underscore the significant role of exudate composition in influencing microbial dynamics and nutrient availability, and emphasize the importance of biotic and abiotic feedback mechanisms in the rhizosphere in regulating root exudation.", "keywords": ["106022 Mikrobiologie", "Short-chain fatty acids", "Microbial metabolites", "Artificial root exudate", "Cation mobilization", "Growth yield trade-off", "106022 Microbiology", "Biogeochemical feedback", "Rhizosphere processes"]}, "links": [{"href": "https://doi.org/11353/10.2156897"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11353/10.2156897", "name": "item", "description": "11353/10.2156897", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11353/10.2156897"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-04-01T00:00:00Z"}}, {"id": "10779/rcsi.24421873.v1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:24:41Z", "type": "Report", "title": "Root litter decomposition is suppressed in species mixtures and in the presence of living roots", "keywords": ["biotic interactions", "Plant biology", "plant species", "mixed-species litter", "living roots", "rhizosphere priming effect", "Plant biochemistry", "home-field advantage", "root litter decomposition", "interactions between species", "litter mixture", "root exudates", "plant diversity"]}, "links": [{"href": "https://doi.org/10779/rcsi.24421873.v1"}, {"rel": "self", "type": "application/geo+json", "title": "10779/rcsi.24421873.v1", "name": "item", "description": "10779/rcsi.24421873.v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10779/rcsi.24421873.v1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-11-01T00:00:00Z"}}, {"id": "11245.1/69372ae1-13cd-4095-b06a-b9146c8552fd", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-01T16:24:45Z", "type": "Journal Article", "created": "2022-03-26", "title": "Deciphering the role of specialist and generalist plant\u2013microbial interactions as drivers of plant\u2013soil feedback", "description": "Summary

Feedback between plants and soil microbial communities can be a powerful driver of vegetation dynamics. Plants elicit changes in the soil microbiome that either promote or suppress conspecifics at the same location, thereby regulating population density\uffe2\uff80\uff90dependence and species co\uffe2\uff80\uff90existence. Such effects are often attributed to the accumulation of host\uffe2\uff80\uff90specific antagonistic or beneficial microbiota in the rhizosphere. However, the identity and host\uffe2\uff80\uff90specificity of the microbial taxa involved are rarely empirically assessed. Here we review the evidence for host\uffe2\uff80\uff90specificity in plant\uffe2\uff80\uff90associated microbes and propose that specific plant\uffe2\uff80\uff93soil feedbacks can also be driven by generalists. We outline the potential mechanisms by which generalist microbial pathogens, mutualists and decomposers can generate differential effects on plant hosts and synthesize existing evidence to predict these effects as a function of plant investments into defence, microbial mutualists and dispersal. Importantly, the capacity of generalist microbiota to drive plant\uffe2\uff80\uff93soil feedbacks depends not only on the traits of individual plants but also on the phylogenetic and functional diversity of plant communities. Identifying factors that promote specialization or generalism in plant\uffe2\uff80\uff93microbial interactions and thereby modulate the impact of microbiota on plant performance will advance our understanding of the mechanisms underlying plant\uffe2\uff80\uff93soil feedback and the ways it contributes to plant co\uffe2\uff80\uff90existence.

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.

Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants\uffe2\uff80\uff99 large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3in size with as good as 5 \uffce\uffbcm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement ofBacillus subtilispopulations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point \uffe2\uff80\uff9cfirst contact\uffe2\uff80\uff9d, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.