ABSTRACT: metagenome assembly of PRJEB40332 data set (Predicted input of uncultured fungal symbionts to a lichen symbiosis from metagenome-assembled genomes).
Project description:Marine sponges are essential for coral reefs to thrive and harbour a diverse microbiome that is thought to contribute to host health. Although the overall function of sponge symbionts has been increasingly described, in-depth characterisation of each taxa remains challenging, with many sponge species hosting up to 3,000 distinct microbial species. Recently, the sponge Ianthella basta has emerged as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other minor taxa. Here, we retrieved metagenome assembled genomes (MAGs) for >90% of I. basta’s microbial community which allowed us to make a complete metabolic reconstruction of the sponge’s microbiome, identifying metabolic complementarity between microbes, as well as the importance of symbionts present in low abundance. We also mined the metagenomes for putative viral sequences, highlighting the contribution of viruses to the overall metabolism of the sponge, and complement this data with metaproteomic sequencing to identify active metabolic pathways in both prokaryotes and viruses. This data now allows us to use I. basta as a model organism for studying host-microbe interactions and provides a basis for future (genomic) manipulative experiments.
Project description:The global significance of marine non-cyanobacterial diazotrophs, notably heterotrophic bacterial diazotrophs (HBDs), has become increasingly clear. Understanding N2 fixation rates for these largely uncultured organisms poses a challenge due to uncertain growth requirements and complex nitrogenase regulation. We identified Candidatus Thalassolituus haligoni as an Oceanospirillales member, closely related to other significant γ-proteobacterial HBDs. Pangenome analysis reinforces this classification, indicating the isolate belongs to the same species as the uncultured metagenome-assembled genome Arc-Gamma-03. Analysis of the nifH gene in amplicon sequencing libraries reveals the extensive distribution of Cand. T. haligoni across the Pacific, Atlantic and Arctic Oceans. Through combined proteomic analysis and N2 fixation rate measurements, we confirmed the isolate’s capacity for nitrate independent N2 fixation, although a clear understanding of nitrogenase regulation remains unclear. Overall, our study highlights the significance of Cand. T. haligoni as the first globally distributed, cultured model species within the understudied group of Oceanospirillales, and γ-HBDs in general.
Project description:Here, we report the use of Illumina RNA-Seq for investigating the physiology of the digestive-tract microbiome within the medicinal leech, Hirudo verbana. About 12 million cDNA reads were mapped against the genomes of the two dominant members of this simple microbiome. Results suggested that the most abundant, yet uncultured Rikenella-like bacterium forages host mucin glycans and ferments the carbohydrates to acetate that is secreted into the environment. The second dominant symbiont, Aeromonas veronii, appears to utilize the acetate secreted by Rikenella as a carbon and energy source, possibly linking the physiologies of the dominant symbionts. This study demonstrates how RNA-seq can be used to reveal the physiology of a naturally occurring microbiome.
Project description:Most vascular flowering plants have the ability to form mutualistic associations with soil fungi from the Glomeromycota. The resulting symbiosis is called an arbuscular mycorrhiza and they are widespread in terrestrial ecosystems throughout the world. Although the physical interaction between the symbionts occurs in the root cortex, the symbiosis impacts the physiology of the whole plant. To gain a better understanding of the AM symbiosis, we have used the 16000 feature array to examine gene expression in the leaves of mycorrhizal plants to explore the transcriptional changes that are triggered systemically as a result of the AM symbiosis. Keywords: Medicago truncatula, Mycorrhizal, systemic regulation, microarray profiling
Project description:Large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. We investigated 1,529 microbial metagenome-assembled genomes recovered from our site to understand carbon processing in this environment. Metabolic reconstruction, supported by metatranscriptomic and metaproteomic data, revealed key populations involved in organic matter degradation, including bacteria encoding a pathway for xylose degradation only previously identified in fungi.