TY - JOUR AB - BACKGROUND: Plant beneficial microorganisms as inoculants can improve crop performance, but factors affecting their impact on plant performance under field conditions remain unclear, thereby limiting their use in farming. Here, we investigated how farming practices (e.g., tillage and N-fertilization intensity) and growing seasons influenced the impact of a beneficial microorganism consortium (BMc: Trichoderma, Bacillus, and Pseudomonas strains) in maize and affected the rhizosphere competence of each BMc strain. In addition, we tested whether the consortium affects the resident rhizosphere microbiome and crop performance. In two growing seasons (2020 and 2021), we assessed how BMc inoculation affects maize growth, nutritional status, gene expression, and rhizosphere microbiome under different farming practices at the flowering stage. RESULTS: Inoculated strains successfully colonized the maize rhizosphere independently of farming practice. BMc inoculation improved plant growth and iron uptake in 2020, regardless of farming practice. These effects co-occurred with lower precipitation levels in 2020 compared to 2021. BMc inoculation reduced the expression of several stress-related genes in maize in 2020 under drought. An increased iron uptake by the BMc-inoculated plants was observed in 2020 and was associated with the upregulation of the gene ZmNAS3, which is linked to iron uptake. Therefore, BMc inoculation mitigated the drought impact on maize. The microbial rhizosphere communities were altered by BMc inoculation in both years, but patterns of responder taxa differed between seasons. Metagenome analysis revealed that more genes (e.g., genes encoding biosurfactants and siderophores) were enriched in the rhizosphere of BMc-inoculated plants in 2020 than in 2021. Moreover, we identified bacterial and fungal taxa positively associated with maize iron uptake. The relative abundance of these iron uptake-associated bacterial and fungal taxa significantly increased due to BMc inoculation in 2020, while they showed overall higher relative abundances in 2021, independently of BMc inoculation. We mapped the sequences of these iron-associated taxa to publicly available genomes and verified the occurrence of various plant beneficial traits in several mapped genomes. CONCLUSIONS: Overall, we show that the growing season determined the effect of BMc inoculation on maize plants by shaping microbiome composition and function in the maize rhizosphere more than farming practice. These findings highlight the importance of the complex interplay between microbial inoculants and the resident rhizosphere microorganisms under abiotic stress conditions. AU - Kampouris, I.D.* AU - Kuhl-Nagel, T.* AU - Behr, J.H.* AU - Sommermann, L.* AU - Babin, D.* AU - Francioli, D.* AU - Zrenner, R.* AU - Kublik, S. AU - Schloter, M. AU - Ludewig, U.* AU - Smalla, K.* AU - Neumann, G.* AU - Grosch, R.* AU - Geistlinger, J.* C1 - 74921 C2 - 57720 CY - Campus, 4 Crinan St, London N1 9xw, England TI - Selective recruitment of beneficial microbes in the rhizosphere of maize affected by microbial inoculants, farming practice, and seasonal variations. JO - Environ. Microbiome VL - 20 IS - 1 PB - Bmc PY - 2025 SN - 2524-6372 ER - TY - JOUR AB - BACKGROUND: Plant growth-promoting bacteria (PGPB) can beneficially modulate rhizosphere microbial communities, potentially improving plant health and reducing disease incidence. Limited research exists on the influence of PGPB inoculation on the rhizosphere microbial communities of apple plants, particularly in soils affected by apple replant disease (ARD). Here, we evaluated the capacity of GFP-labelled Priestia megaterium B1 (designated as P. megaterium B1L5) to colonize the roots of apple plantlets grown in two soils: ARD-affected soil and ARD-unaffected grass soil. We investigated its influence on plant growth in ARD-affected soil and its potential to mitigate ARD-related symptoms. We also assessed how its inoculation modulates the rhizosphere microbial communities, with emphasis on changes that may support plant health, particularly in ARD-affected soils. RESULTS: P. megaterium B1L5 successfully colonized apple roots in both soils 6 days post-inoculation (dpi), but was not detectable at 33 dpi. In ARD-affected soil, plants inoculated with vegetative cells or spores displayed a lower proportion of blackened root tips compared to uninoculated controls. Beta diversity and PERMANOVA analyses demonstrated a significant influence of inoculation on the bacterial communities in both soils at 6 and 33 dpi (p = 0.001). Furthermore, inoculation enriched the rhizosphere of apple plantlets with potential plant-beneficial bacteria, such as Luteimonas, Lysobacter, Pseudomonas, Sphingomonas, Sphingobacterium, Rhodanobacter, Pedobacter and Flavobacterium. In contrast, fungal communities remained largely unaffected by inoculation. Most bacterial and fungal shifts observed in the rhizosphere of inoculated plantlets at 33 dpi did not exhibit similar patterns in uninoculated controls over time, indicating that these shifts were largely driven by the inoculum rather than by plant development or natural microbial succession. CONCLUSIONS: Our results highlight the capacity of P. megaterium B1L5’s to transiently colonize apple plant roots across different soil environments. The observed tendency toward reduced root tip blackening in inoculated plants grown in ARD-affected plants reflects its potential for alleviating stress associated with ARD. Additionally, inoculation with P. megaterium B1L5 promoted beneficial shifts in the rhizosphere microbiome by enriching bacterial taxa commonly linked to plant health. These findings indicate that P. megaterium B1L5 presents a candidate for ARD mitigation, however its long-term efficacy and practical application should be further evaluated. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40793-025-00762-x. AU - Mahmoud, F.M. AU - Edelmann, H.* AU - Si, Y.* AU - Endrejat, L. AU - Pritsch, K. AU - Gutjahr, C.* AU - Ehrenreich, A.* AU - Winkelmann, T.* AU - Winkler, J.B. AU - Schnitzler, J.-P. AU - Schloter, M. C1 - 75350 C2 - 58257 CY - Campus, 4 Crinan St, London N1 9xw, England TI - Transient colonization by Priestia megaterium B1L5 alters the structure of the rhizosphere microbiome towards potential plant beneficial bacterial groups in apple plantlets. JO - Environ. Microbiome VL - 20 IS - 1 PB - Bmc PY - 2025 SN - 2524-6372 ER - TY - JOUR AB - BACKGROUND: Non-rhizobial endophytes (NREs) support plant health and nodule function by enhancing symbiotic interactions and nitrogen fixation. However, their recruitment dynamics under fertilizers of varying phosphorus solubility remain poorly understood. This study investigated how four P fertilization treatments-no phosphorus (P0), bone char (BC), surface-modified bone char plus (BCplus), and triple superphosphate (TSP)-with increasing solubility influence microbial recruitment and diversity in Pisum sativum, leading to differences in plant-available phosphorus across bulk soil, rhizosphere, roots, and nodules. RESULTS: Using 16S rRNA amplicon sequencing, we found that nodule-associated microbial communities were primarily recruited from unknown sources, likely seeds, followed by roots, especially under BCplus. Phosphorus solubility of treatments significantly influenced recruitment patterns, with solubility further shaping microbial diversity. BCplus recruited beneficial taxa like Beijerinckiaceae and Flavobacteriaceae, which are associated with nitrogen fixation and biocontrol. In contrast, the highly soluble TSP treatment expanded recruitment from the rhizosphere, reflecting less stringent environmental filtering and promoting taxa like Steroidobacteraceae and Blastocatellaceae, known for nutrient cycling and pathogen suppression. In the absence of P fertilization (P0), recruitment relied heavily on seeds and roots, with arbuscular mycorrhizal fungi colonization prioritized over nodulation. Notably, TSP supported significantly more nodules with greater microbial diversity, potentially enhanced by NREs. CONCLUSIONS: Phosphorus solubility of the applied fertilizers strongly influences NRE recruitment dynamics in P. sativum. Seeds and roots act as primary reservoirs, while highly soluble fertilizers promote broader recruitment from the rhizosphere and increase microbial diversity in nodules. These results underscore the importance of the fertilization form in modulating NRE recruitment. AU - Thaqi, S.K.* AU - Hensel, N.* AU - Vitow, N.* AU - Baum, C.* AU - Streb, L.-M. AU - Kublik, S. AU - Leinweber, P.* AU - Panten, K.* AU - Schloter, M. AU - Schulz, S. C1 - 75218 C2 - 57855 CY - Campus, 4 Crinan St, London N1 9xw, England TI - Non-rhizobial endophyte recruitment and diversity in Pisum sativum are strongly shaped by phosphorus fertilizer form. JO - Environ. Microbiome VL - 20 IS - 1 PB - Bmc PY - 2025 SN - 2524-6372 ER - TY - JOUR AB - BACKGROUND: Seed endophytic bacteria are beneficial to plants. They improve seedling growth by enhancing plant nutrient uptake, modulating stress-related phytohormone production, and targeting pests and pathogens with antibiotics. Seed endophyte composition can be influenced by pollination, plant cultivar, and soil physicochemical conditions. However, the effects of plant community richness on seed endophytes are unknown. To investigate the effects of increasing plant species richness on the diversity and composition of the seed microbiome, we made use of a well-established long-term biodiversity experiment in Germany (The Jena Experiment). We sampled seeds from different Plantago lanceolata blossoms in a plant diversity gradient ranging from monoculture to 16 species mixtures. The seeds were surface sterilized to remove seed surface-associated bacteria and subjected to a metabarcoding approach to assess bacterial community structure. RESULTS: Our data indicate a very stable core microbiome, which accounted for more than 90% of the reads and was present in all seeds independent of the plant richness level the seeds originated from. It consisted mainly of reads linked to Pseudomonas rhizosphaerae, Sphingomonas faeni and Pirellulla spp. 9% of the obtained reads were not part of the core microbiome and were only present in plots of specific diversity levels. The number of unique ASVs was positively correlated with plant richness. Interestingly, most reads described as non-core members belonged to the same genera described as the core microbiome, indicating the presence of different strains or species with possibly different functional properties important for seed performance. CONCLUSION: Our data indicate that Plantago lanceolata maintains a large seeds core microbiome across the plant richness gradient. However, the number of unique ASVs increases alongside the plant community richness, indicating that ecosystem biodiversity also mitigates diversity loss in seed endophytes. AU - Pinheiro Alves de Souza, Y. AU - Schloter, M. AU - Weisser, W.* AU - Huang, Y.* AU - Schulz, S. C1 - 69886 C2 - 55304 CY - Campus, 4 Crinan St, London N1 9xw, England TI - The seeds of Plantago lanceolata comprise a stable core microbiome along a plant richness gradient. JO - Environ. Microbiome VL - 19 IS - 1 PB - Bmc PY - 2024 SN - 2524-6372 ER - TY - JOUR AB - Background: The fruit fly Drosophila melanogaster lives in natural habitats and has also long been used as a model organism in biological research. In this study, we used a molecular barcoding approach to analyse the airways microbiome of larvae of D. melanogaster, which were obtained from eggs of flies of the laboratory strain w1118 and from immune deficient flies (NF-kB-K), and from wild-caught flies. To assess intergenerational transmission of microbes, all eggs were incubated under the same semi-sterile conditions. Results: The airway microbiome of larvae from both lab-strains was dominated by the two families Acetobacteraceae and Lactobacillaceae, while larvae from wild-caught flies were dominated by Lactobacillaceae, Anaplasmataceae and Leuconostocaceae. Barcodes linked to Anaplasmataceae could be further assigned to Wolbachia sp., which is a widespread intracellular pathogen in arthropods. For Leuconostoceae, the most abundant reads were assigned to Weissella sp. Both Wolbachia and Weissella affect the development of the insects. Finally, a relative high abundance of Serratia sp. was found in larvae from immune deficient relish−/− compared to w1118 and wild-caught fly airways. Conclusions: Our results show for the first time that larvae from D. melanogaster harbor an airway microbiome, which is of low complexity and strongly influenced by the environmental conditions and to a lesser extent by the immune status. Furthermore, our data indicate an intergenerational transmission of the microbiome as shaped by the environment. AU - Angstmann, H.* AU - Pfeiffer, S. AU - Kublik, S. AU - Ehrhardt, B.* AU - Uliczka, K.* AU - Rabe, K.F.* AU - Roeder, T.* AU - Wagner, C.* AU - Schloter, M. AU - Krauss-Etschmann, S.* C1 - 68454 C2 - 54655 CY - Campus, 4 Crinan St, London N1 9xw, England TI - The microbial composition of larval airways from Drosophila melanogaster differ between specimens from laboratory and natural habitats. JO - Environ. Microbiome VL - 18 IS - 1 PB - Bmc PY - 2023 SN - 2524-6372 ER - TY - JOUR AB - BACKGROUND: Tremendous amounts of data generated from microbiome research studies during the last decades require not only standards for sampling and preparation of omics data but also clear concepts of how the metadata is prepared to ensure re-use for integrative and interdisciplinary microbiome analysis. RESULTS: In this Commentary, we present our views on the key issues related to the current system for metadata submission in omics research, and propose the development of a global metadata system. Such a system should be easy to use, clearly structured in a hierarchical way, and should be compatible with all existing microbiome data repositories, following common standards for minimal required information and common ontology. Although minimum metadata requirements are essential for microbiome datasets, the immense technological progress requires a flexible system, which will have to be constantly improved and re-thought. While FAIR principles (Findable, Accessible, Interoperable, and Reusable) are already considered, international legal issues on genetic resource and sequence sharing provided by the Convention on Biological Diversity need more awareness and engagement of the scientific community. CONCLUSIONS: The suggested approach for metadata entries would strongly improve retrieving and re-using data as demonstrated in several representative use cases. These integrative analyses, in turn, would further advance the potential of microbiome research for novel scientific discoveries and the development of microbiome-derived products. AU - Cernava, T.* AU - Rybakova, D.* AU - Buscot, F.* AU - Clavel, T.* AU - McHardy, A.C.* AU - Meyer, F.* AU - Overmann, J.* AU - Stecher, B.* AU - Sessitsch, A.* AU - Schloter, M. AU - Berg, G.* C1 - 65522 C2 - 52715 TI - Metadata harmonization-Standards are the key for a better usage of omics data for integrative microbiome analysis. JO - Environ. Microbiome VL - 17 IS - 1 PY - 2022 SN - 2524-6372 ER - TY - JOUR AB - The overarching biological impact of microbiomes on their hosts, and more generally their environment, reflects the co-evolution of a mutualistic symbiosis, generating fitness for both. Knowledge of microbiomes, their systemic role, interactions, and impact grows exponentially. When a research field of importance for planetary health evolves so rapidly, it is essential to consider it from an ethical holistic perspective. However, to date, the topic of microbiome ethics has received relatively little attention considering its importance. Here, ethical analysis of microbiome research, innovation, use, and potential impact is structured around the four cornerstone principles of ethics: Do Good; Don't Harm; Respect; Act Justly. This simple, but not simplistic approach allows ethical issues to be communicative and operational. The essence of the paper is captured in a set of eleven microbiome ethics recommendations, e.g., proposing gut microbiome status as common global heritage, similar to the internationally agreed status of major food crops. AU - Lange, L.* AU - Berg, G.* AU - Cernava, T.* AU - Champomier-Vergès, M.C.* AU - Charles, T.* AU - Cocolin, L.* AU - Cotter, P.D.* AU - D'Hondt, K.* AU - Kostic, T.* AU - Maguin, E.* AU - Makhalanyane, T.* AU - Meisner, A.* AU - Ryan, M.* AU - Kiran, G.S.* AU - de Souza, R.S.C.* AU - Sanz, Y.* AU - Schloter, M. AU - Smidt, H.* AU - Wakelin, S.* AU - Sessitsch, A.* C1 - 66368 C2 - 53154 TI - Microbiome ethics, guiding principles for microbiome research, use and knowledge management. JO - Environ. Microbiome VL - 17 IS - 1 PY - 2022 SN - 2524-6372 ER - TY - JOUR AB - Background: Stable soil aggregates are essential for optimal crop growth and preventing soil erosion. However, tillage is often used in agriculture to loosen the soil, which disrupts the integrity of these aggregates. Soil aggregation can be enhanced by bacteria through their ability to produce exopolysaccharides and lipopolysaccharides. These compounds stabilize soil aggregates by "gluing" soil particles together. However, it has yet to be shown how tillage influences the bacterial potential to produce aggregate-stabilizing agents. Therefore, we sampled conventional and reduced tillage treatments at 0-10 cm, 10-20 cm and 20-50 cm from a long-term field trial in Frick, Switzerland. We compared the stable aggregate fraction of the soil and the bacterial potential to produce exopolysaccharides (EPS) and lipopolysaccharides (LPS) under different tillage regimes by employing a shotgun metagenomic approach. We established a method which combines hidden Markov model searches with blasts against sequences derived from the Kyoto Encyclopedia of Genes and Genomes database to analyze genes specific for the biosynthesis of these compounds.Results: Our data revealed that the stable aggregate fraction as well as the bacterial potential to produce EPS and LPS were comparable under both tillage regimes. The highest potential to produce these compounds was found in the upper soil layer, which was disturbed by tillage, but had higher content of organic carbon compared to the layer below the tillage horizon. Additionally, key players of EPS and LPS production differed at different sampling depths. Some families with high potential to produce EPS and LPS, such as Chitinophagaceae and Bradyrhizobiaceae, were more abundant in the upper soil layers, while others, e.g. Nitrospiraceae and Planctomycetaceae, preferred the lowest sampled soil depth. Each family had the potential to form a limited number of different aggregate-stabilizing agents.Conclusions: Our results indicate that conventional tillage and reduced tillage equally promote the bacterial potential to produce EPS and LPS in the tillage horizon. However, as major bacterial groups triggering EPS and LPS formation were not the same, it is likely that gene expression pattern differ in the different treatments due to various pathways of gene induction and transcription in different bacterial species. AU - Cania, B. AU - Vestergaard, G. AU - Krauss, M.* AU - Fliessbach, A.* AU - Schloter, M. AU - Schulz, S. C1 - 55881 C2 - 46619 CY - Campus, 4 Crinan St, London N1 9xw, England TI - A long-term field experiment demonstrates the influence of tillage on the bacterial potential to produce soil structure-stabilizing agents such as exopolysaccharides and lipopolysaccharides. JO - Environ. Microbiome VL - 14 IS - 1 PB - Bmc PY - 2019 SN - 2524-6372 ER - TY - JOUR AB - Background: Apple replant disease (ARD) is a syndrome that occurs in areas where apple plants or closely related species have been previously cultivated. Even though ARD is a well-known phenomenon, which has been observed in different regions worldwide and occurs independent of the soil type, its causes still remain unclear.Results: As expected, the biomass of plants grown in replant soil was significantly lower compared to those grown in control (virgin) soil. A shotgun metagenome analysis showed a clear differentiation between the rhizosphere and bulk soil compartments independent from the soil used. However, significant differences associated with apple replant disease were only observed in the rhizosphere compartment, for which we detected changes in the abundance of major bacterial genera. Interestingly, reads assigned to Actinobacteria were significantly reduced in relative abundance in rhizosphere samples of the soil affected by replant disease. Even though reads assigned to pathogenic fungi were detected, their relative abundance was low and did not differ significantly between the two different soils. Differences in microbiome structure also resulted in shifts in functional pattern. We observed an increase in genes related to stress sensing in the rhizosphere of soils affected by replant disease, whereas genes linked to nutrient sensing and uptake dominated in control soils. Moreover, we observed a lower abundance of genes coding for enzymes which trigger the degradation of aromatic compounds in rhizosphere of soils affected by replant disease, which is probably connected with higher concentration of phenolic compounds, generally associated with disease progression.Conclusions: Our study shows, for the first time, how apple replanting affects soil functioning by altering the soil microbiome. Particularly, the decrease in the abundance of genes which code for enzymes catalyzing the degradation of aromatic compounds, observed in the rhizosphere of plants grown in soil affected by apple replant disease, is of interest. Apple rootstocks are known to synthetize many phenolic compounds, including defense related phytoalexins, which have been considered for long to be connected with the emergence of replant disease. The knowledge gained in this study might help to develop targeted strategies to overcome or at least reduce the effects of ARD symptoms. AU - Radl, V. AU - Winkler, J.B. AU - Kublik, S. AU - Yang, L. AU - Winkelmann, T.* AU - Vestergaard, G. AU - Schröder, P. AU - Schloter, M. C1 - 57360 C2 - 47761 CY - Campus, 4 Crinan St, London N1 9xw, England TI - Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease. JO - Environ. Microbiome VL - 14 IS - 1 PB - Bmc PY - 2019 SN - 2524-6372 ER - TY - JOUR AB - Following publication of the original article [1], the authors advised that their article had published with an error in the title. The title read "Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apples seedlings grown in soils affected by replant disease". While the correct title is "Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease". That is, the title referred to 'seedlings' in place of 'plant lets', which was the incorrect term because clonal plantlets (from the apple rootstock M26) were used, not seedlings. The title has since been corrected in the original article. The authors apologize for any inconvenience caused. AU - Radl, V. AU - Winkler, J.B. AU - Kublik, S. AU - Yang, L. AU - Winkelmann, T.* AU - Vestergaard, G. AU - Schröder, P. AU - Schloter, M. C1 - 57835 C2 - 47953 CY - Campus, 4 Crinan St, London N1 9xw, England TI - Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease (vol 14, 8 2019). JO - Environ. Microbiome VL - 14 IS - 1 PB - Bmc PY - 2019 SN - 2524-6372 ER -