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 - TY - JOUR A1 - Olimi, Expedito A1 - Bickel, Samuel A1 - Wicaksono, Wisnu Adi A1 - Kusstatscher, Peter A1 - Matzer, Robert A1 - Cernava, Tomislav A1 - Berg, Gabriele T1 - Deciphering the microbial composition of biodynamic preparations and their effects on the apple rhizosphere microbiome JF - Frontiers in soil science N2 - 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 fungus Alternaria, and the enrichment of potentially beneficial bacterial genera such as Pseudomonas. 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. KW - biodynamic farming KW - compost microbiome KW - biodynamic manures KW - biodynamic preparations KW - rhizosphere microbiome KW - 16S rRNA/ITS amplicon sequencing KW - organic soil amendments Y1 - 2022 U6 - https://doi.org/10.3389/fsoil.2022.1020869 SN - 2673-8619 VL - 2 PB - Frontiers Media CY - Lausanne ER -