Universität zu Köln

Zhang, Pengfan ORCID: 0000-0002-4197-3605 (2023). Computational analyses of the plant-associated microbiota. PhD thesis, Universität zu Köln.

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Abstract

Plants harbor phylogenetically diverse microbes on the exterior and interior of all organs and they form intimate relationships with the colonized microbiota. Multi-omics dramatically facilitates and expands our knowledge in plant-microbiota interactions and associations. To establish causalities, manipulation of microbiota populating plants under strictly controlled conditions is a necessity, which forged the development of reductionist approaches for studying plant-microbiota interactions, including the process of deconstruction and reconstruction of the plant microbiota. Deconstruction of the plant microbiota requires the establishment of genome-indexed microbial culture collections representing the plant microbiota of interests. The reconstruction step is to design synthetic microbial communities (SynComs) by mixing the strains from the culture collections and inoculate onto the plants. In this dissertation, I introduced a software named Rbec that is developed to exclusively characterize the accurate microbial composition in SynComs subject to amplicon sequencing by both correcting PCR/sequencing errors and identifying maker gene paralogues within the same strain. Rbec also provides a novel feature for contamination identification in the SynCom experiments, which has been overlooked in previous studies but is a necessity to verify the robustness of the readouts from SynCom experimentations. Further, with the established pipelines for analyzing amplicon sequencing data from either natural or synthetic communities, I analyzed the microbial compositions from different studies including the study of the host preference of Arabidopsis thaliana and Lotus Japonicus commensals, the phycosphere microbiota, the effects of plant metabolites on soil microbiota and how bacterial antibiotics shape root microbiota. Genome-indexed microbial culture collections allow us to study the functional capacities of microbiota. We systematically analyzed the biosynthetic gene clusters and the spread of antimicrobial 2,4-diacetylphloroglucinol synthetic gene clusters in Pseudomonas in established culture collections. Moreover, I studied the recent horizontal gene transfer (HGT) in bacteria from different culture collections assembled from different host plants and sites. This provides an atlas of the active taxa involved in HGT and the frequently transferred functional orthologues in plant-associated niches. In addition, it reveals the selection forces exerted on different taxa in the relevant environments. In summary, our work tried to move the reductionist approaches forward in the aspect of computational analyses. We not only introduced a new computational method for accurately profiling microbial compositions in SynComs, but also digged deeper into the genome- indexed culture collections by making full use of genome sequences. With the valuable integrated genome information of the plant microbiota, it’ll provide the opportunity to study the functional diversities, evolutionary trajectories, genomic contents related to adaptations to hosts. However, with the increased volume of available genomes, novel methodology will be required to fast processing large datasets in a computational-efficient way.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Zhang, Pengfan pzhang@mpipz.mpg.de orcid.org/0000-0002-4197-3605 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-654619
Date:	21 April 2023
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Außeruniversitäre Forschungseinrichtungen > MPI for Plant Breeding Research
Subjects:	Life sciences
Uncontrolled Keywords:	Keywords Language Plant-microbiota interactions English Bioinformatics English Microbial genomics English
Date of oral exam:	14 February 2023
Referee:	Name Academic Title Zuccaro, Alga Professor Kemen, Eric Professor
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/65461