@article{MinutilloRuanoRosaAbdelfattahetal.2022,
  author    = {Minutillo, Serena A. and Ruano-Rosa, David and Abdelfattah, Ahmed and Schena, Leonardo and Malacrino, Antonino},
  title     = {The fungal microbiome of wheat flour includes potential mycotoxin producers},
  series = {Foods},
  volume    = {11},
  journal   = {Foods},
  number    = {5},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2304-8158},
  doi       = {10.3390/foods11050676},
  pages     = {9},
  year      = {2022},
  abstract  = {Consumers are increasingly demanding higher quality and safety standards for the products they consume, and one of this is wheat flour, the basis of a wide variety of processed products. This major component in the diet of many communities can be contaminated by microorganisms before the grain harvest, or during the grain storage right before processing. These microorganisms include several fungal species, many of which produce mycotoxins, secondary metabolites that can cause severe acute and chronic disorders. Yet, we still know little about the overall composition of fungal communities associated with wheat flour. In this study, we contribute to fill this gap by characterizing the fungal microbiome of different types of wheat flour using culture-dependent and -independent techniques. Qualitatively, these approaches suggested similar results, highlighting the presence of several fungal taxa able to produce mycotoxins. In-vitro isolation of fungal species suggest a higher frequency of Penicillium, while metabarcoding suggest a higher abundance of Alternaria. This discrepancy might reside on the targeted portion of the community (alive vs. overall) or in the specific features of each technique. Thus, this study shows that commercial wheat flour hosts a wide fungal diversity with several taxa potentially representing concerns for consumers, aspects that need more attention throughout the food production chain.},
  language  = {en}
}
@article{WassermannAbdelfattahWicaksonoetal.2022,
  author    = {Wassermann, Birgit and Abdelfattah, Ahmed and Wicaksono, Wisnu Adi and Kusstatscher, Peter and M{\"u}ller, Henry and Cernava, Tomislav and Goertz, Simon and Rietz, Steffen and Abbadi, Amine and Berg, Gabriele},
  title     = {The Brassica napus seed microbiota is cultivar-specific and transmitted via paternal breeding lines},
  series = {Microbial biotechnology},
  volume    = {15},
  journal   = {Microbial biotechnology},
  number    = {9},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1751-7915},
  doi       = {10.1111/1751-7915.14077},
  pages     = {2379 -- 2390},
  year      = {2022},
  abstract  = {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.},
  language  = {en}
}
@article{OlimiKusstatscherWicaksonoetal.2022,
  author    = {Olimi, Expedito and Kusstatscher, Peter and Wicaksono, Wisnu Adi and Abdelfattah, Ahmed and Cernava, Tomislav and Berg, Gabriele},
  title     = {Insights into the microbiome assembly during different growth stages and storage of strawberry plants},
  series = {Environmental microbiome},
  volume    = {17},
  journal   = {Environmental microbiome},
  number    = {1},
  publisher = {BMC},
  address   = {London},
  issn      = {2524-6372},
  doi       = {10.1186/s40793-022-00415-3},
  pages     = {15},
  year      = {2022},
  abstract  = {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. <br /> 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. <br /> 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.},
  language  = {en}
}
@article{MalacrinoAbdelfattahBergetal.2022,
  author    = {Malacrin{\`o}, Antonino and Abdelfattah, Ahmed and Berg, Gabriele and Benitez, Maria-Soledad and Bennett, Alison E. and B{\"o}ttner, Laura and Xu, Shuqing and Schena, Leonardo},
  title     = {Exploring microbiomes for plant disease management},
  series = {Biological control : theory and application in pest management},
  volume    = {169},
  journal   = {Biological control : theory and application in pest management},
  publisher = {Academic Press},
  address   = {San Diego, Calif.},
  issn      = {1049-9644},
  doi       = {10.1016/j.biocontrol.2022.104890},
  pages     = {7},
  year      = {2022},
  abstract  = {Microbiome science is revolutionizing many concepts of plant biology, ecology, and evolution. Understanding plant microbiomes is key to developing solutions that protect crop health without impacting the environment. In this perspective article, we highlight the importance of both the structure and functions of plant-associated microbial communities in protecting their host from pathogens. These new findings have a high potential to aid biocontrol programs and to replace traditional chemical products, guiding the transition towards a sustainable production.},
  language  = {en}
}