PhD Defence Yayu Wang

Microorganisms are widely distributed in both terrestrial and aquatic ecosystems and play key roles in biogeochemical cycles and extend various ecosystem services. The recent advances in metagenomics are providing an unprecedented ability to decipher the enormous diversity of microorganisms in sustaining soil health and water quality. Therefore, the scope of this thesis is to introduce the reader to the application of metagenomics in cropping soil, mangrove sediment and marine microbiome studies.
Soils are a significant reservoir of microbial diversity that underpins a broad range of key biogeochemical processes and moderate ecosystem functions. Plants host distinct microbial communities inside and around their roots, known as the root-associated microbiome, contributing to the fitness of the plant. The last two decades have witnessed an upsurge in studies describing the composition of soil-borne microbiome using metagenomics, and this has enabled a better understanding of the ecological linkages between root microbiome, and plant performance. However, few studies have dissected the associations of root microbiome with the medical plant-specific metabolism and how the specific genetic variation drive host-genotype dependent microbiome assembly in plants. One aim of this thesis was to demonstrate the microbial effects on bioactive compound production in the citrus peel by substantiating the links between the content of monoterpenes, genes expression, soil properties, and root-associated microbiome. In the core region, seven monoterpenes exhibited significantly higher concentrations in citrus peel compared to non-core regions. Metagenome data revealed that the microbial composition of rhizosphere soil and endophyte microbiome varied between core and other regions, and could be impacted by soil nutrients and high salinity. The rhizosphere soil and endophyte microorganisms co-contributed to the accumulation of monoterpenes by triggering the plant immune response or providing intermediate products. This study clearly illustrated the effects of soil properties and soil microorganisms on monoterpenes production in the citrus peel of core regions. The second aim of this thesis was to reveal the mechanism by which plant and microbiome interaction and its correlation with crop phenotypes. By conducting microbiome genome wide association study (GWAS) on root microbiome based on 827 foxtail millet cultivars, we uncover comprehensive plant genotype-microbiome networks that contribute to phenotype plasticity. Unlocking the mechanisms underlying the plant–microbe metabolic interaction would pave the way towards sustainable agriculture.
Sediment microorganisms are important components of mangrove ecosystems and help create and maintain mangrove ecosystems. Due to rapid industrialization and urbanization of coastal regions, mangrove wetlands are threatened by increasing pollution stress from anthropogenic activities. However, we know little about the potential impact of human activities on microbial communities and biochemical cycling in mangrove ecosystems. Therefore, another aim of this thesis was to reveal the taxonomic and functional shifts of mangrove microbiome under anthropogenic stress using metagenome sequencing. By comparing the taxonomic and functional compositions of two diverse mangroves in southern China, we found that the Nitrospira and ammonia-oxidizing archaea were dominated in anthropogenic mangrove from Shenzhen while sulfate-reducing bacteria and methanogens were more abundant in pristine mangroves from Guangxi. Secondary metabolites mining based on metagenome data identified a large number of microbial biosynthesis gene clusters (BGCs), and the different biosynthetic potentials in different microbial taxa. Our study ultimately helped in better understanding the ecological function and potential value of mangroves microbiome.
Finally, we performed metagenome sequencing on surface water samples along the 17 stations spanning nearly the entire Indian ocean, we systematically described the microbial and functional composition of Indian ocean microbial communities using an established gene set. These results shed light on the diversity of Prochlorococcus population in Indian and global oceans. The prochlorocaccal gene capacity for nitrogen assimilation and amino acid utilization provides evidence of the adaption mechanism of Prochlorococcus in oligotrophic oceans.

Microorganisms are widely distributed in both terrestrial and aquatic ecosystems and play key roles in biogeochemical cycles and extend various ecosystem services. The recent advances in metagenomics are providing an unprecedented ability to decipher the enormous diversity of microorganisms in sustaining soil health and water quality. Therefore, the scope of this thesis is to introduce the reader to the application of metagenomics in cropping soil, mangrove sediment and marine microbiome studies.
Soils are a significant reservoir of microbial diversity that underpins a broad range of key biogeochemical processes and moderate ecosystem functions. Plants host distinct microbial communities inside and around their roots, known as the root-associated microbiome, contributing to the fitness of the plant. The last two decades have witnessed an upsurge in studies describing the composition of soil-borne microbiome using metagenomics, and this has enabled a better understanding of the ecological linkages between root microbiome, and plant performance. However, few studies have dissected the associations of root microbiome with the medical plant-specific metabolism and how the specific genetic variation drive host-genotype dependent microbiome assembly in plants. One aim of this thesis was to demonstrate the microbial effects on bioactive compound production in the citrus peel by substantiating the links between the content of monoterpenes, genes expression, soil properties, and root-associated microbiome. In the core region, seven monoterpenes exhibited significantly higher concentrations in citrus peel compared to non-core regions. Metagenome data revealed that the microbial composition of rhizosphere soil and endophyte microbiome varied between core and other regions, and could be impacted by soil nutrients and high salinity. The rhizosphere soil and endophyte microorganisms co-contributed to the accumulation of monoterpenes by triggering the plant immune response or providing intermediate products. This study clearly illustrated the effects of soil properties and soil microorganisms on monoterpenes production in the citrus peel of core regions. The second aim of this thesis was to reveal the mechanism by which plant and microbiome interaction and its correlation with crop phenotypes. By conducting microbiome genome wide association study (GWAS) on root microbiome based on 827 foxtail millet cultivars, we uncover comprehensive plant genotype-microbiome networks that contribute to phenotype plasticity. Unlocking the mechanisms underlying the plant–microbe metabolic interaction would pave the way towards sustainable agriculture.
Sediment microorganisms are important components of mangrove ecosystems and help create and maintain mangrove ecosystems. Due to rapid industrialization and urbanization of coastal regions, mangrove wetlands are threatened by increasing pollution stress from anthropogenic activities. However, we know little about the potential impact of human activities on microbial communities and biochemical cycling in mangrove ecosystems. Therefore, another aim of this thesis was to reveal the taxonomic and functional shifts of mangrove microbiome under anthropogenic stress using metagenome sequencing. By comparing the taxonomic and functional compositions of two diverse mangroves in southern China, we found that the Nitrospira and ammonia-oxidizing archaea were dominated in anthropogenic mangrove from Shenzhen while sulfate-reducing bacteria and methanogens were more abundant in pristine mangroves from Guangxi. Secondary metabolites mining based on metagenome data identified a large number of microbial biosynthesis gene clusters (BGCs), and the different biosynthetic potentials in different microbial taxa. Our study ultimately helped in better understanding the ecological function and potential value of mangroves microbiome.
Finally, we performed metagenome sequencing on surface water samples along the 17 stations spanning nearly the entire Indian ocean, we systematically described the microbial and functional composition of Indian ocean microbial communities using an established gene set. These results shed light on the diversity of Prochlorococcus population in Indian and global oceans. The prochlorocaccal gene capacity for nitrogen assimilation and amino acid utilization provides evidence of the adaption mechanism of Prochlorococcus in oligotrophic oceans.