TY - JOUR A1 - Wicaksono, Wisnu Adi A1 - Braun, Maria A1 - Bernhardt, Jörg A1 - Riedel, Katharina A1 - Cernava, Tomislav A1 - Berg, Gabriele T1 - Trade-off for survival BT - microbiome response to chemical exposure combines activation of intrinsic resistances and adapted metabolic activity JF - Environment international : a journal of science, technology, health, monitoring and policy N2 - The environmental micmbiota is increasingly exposed to chemical pollution. While the emergence of multi-resistant pathogens is recognized as a global challenge, our understanding of antimicrobial resistance (AMR) development from native microbiomes and the risks associated with chemical exposure is limited. By implementing a lichen as a bioindicator organism and model for a native microbiome, we systematically examined responses towards antimicrobials (colistin, tetracycline, glyphosate, and alkylpyrazine). Despite an unexpectedly high resilience, we identified potential evolutionary consequences of chemical exposure in terms of composition and functioning of native bacterial communities. Major shifts in bacterial composition were observed due to replacement of naturally abundant taxa; e.g. Chthoniobacterales by Pseudomonadales. A general response, which comprised activation of intrinsic resistance and parallel reduction of metabolic activity at RNA and protein levels was deciphered by a multi-omics approach. Targeted analyses of key taxa based on metagenome-assembled genomes reflected these responses but also revealed diversified strategies of their players. Chemical-specific responses were also observed, e.g., glyphosate enriched bacterial r-strategists and activated distinct ARGs. Our work demonstrates that the high resilience of the native micmbiota toward antimicrobial exposure is not only explained by the presence of antibiotic resistance genes but also adapted metabolic activity as a trade-off for survival. Moreover, our results highlight the importance of native microbiomes as important but so far neglected AMR reservoirs. We expect that this phenomenon is representative for a wide range of environmental microbiota exposed to chemicals that potentially contribute to the emergence of antibiotic-resistant bacteria from natural environments. Y1 - 2022 U6 - https://doi.org/10.1016/j.envint.2022.107474 SN - 1873-6750 VL - 168 PB - Elsevier Science CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Olimi, Expedito A1 - Kusstatscher, Peter A1 - Wicaksono, Wisnu Adi A1 - Abdelfattah, Ahmed A1 - Cernava, Tomislav A1 - Berg, Gabriele T1 - Insights into the microbiome assembly during different growth stages and storage of strawberry plants JF - Environmental microbiome N2 - Background: Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches.
Results: Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25%), Pseudomonadaceae (17%), and Burkholderiaceae (11%); and the fungal family Mycosphaerella (45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (10(7)-10(10) marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa.
Conclusion: Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety. KW - Fragaria x ananassa KW - Microbiome assembly KW - Fruit pathogens KW - Bacterial KW - communities KW - Fungal communities KW - Amplicon sequencing KW - CLSM Y1 - 2022 U6 - https://doi.org/10.1186/s40793-022-00415-3 SN - 2524-6372 VL - 17 IS - 1 PB - BMC CY - London ER - TY - JOUR A1 - Wassermann, Birgit A1 - Abdelfattah, Ahmed A1 - Wicaksono, Wisnu Adi A1 - Kusstatscher, Peter A1 - Müller, Henry A1 - Cernava, Tomislav A1 - Goertz, Simon A1 - Rietz, Steffen A1 - Abbadi, Amine A1 - Berg, Gabriele T1 - The Brassica napus seed microbiota is cultivar-specific and transmitted via paternal breeding lines JF - Microbial biotechnology N2 - Seed microbiota influence germination and plant health and have the potential to improve crop performance, but the factors that determine their structure and functions are still not fully understood. Here, we analysed the impact of plant-related and external factors on seed endophyte communities of 10 different oilseed rape (Brassica napus L.) cultivars from 26 field sites across Europe. All seed lots harboured a high abundance and diversity of endophytes, which were dominated by six genera: Ralstonia, Serratia, Enterobacter, Pseudomonas, Pantoea, and Sphingomonas. The cultivar was the main factor explaining the variations in bacterial diversity, abundance and composition. In addition, the latter was significantly influenced by diverse biotic and abiotic factors, for example host germination rates and disease resistance against Plasmodiophora brassicae. A set of bacterial biomarkers was identified to discriminate between characteristics of the seeds, for example Sphingomonas for improved germination and Brevundimonas for disease resistance. Application of a Bayesian community approach suggested vertical transmission of seed endophytes, where the paternal parent plays a major role and might even determine the germination performance of the offspring. This study contributes to the understanding of seed microbiome assembly and underlines the potential of the microbiome to be implemented in crop breeding and biocontrol programmes. Y1 - 2022 U6 - https://doi.org/10.1111/1751-7915.14077 SN - 1751-7915 VL - 15 IS - 9 SP - 2379 EP - 2390 PB - Wiley CY - Hoboken ER -