Journal Article

Genome characterization of two novel deep-sea sediment fungi, Penicillium pacificagyrus sp. nov. and Penicillium pacificasedimenti sp. nov., from South Pacific Gyre subseafloor sediments, highlights survivability

Hoshino, Tatsuhiko, Delgado, Victor, Kadooka, Chihiro, Kiel Reese, Brandi, Inagaki, Fumio, Sobol, Morgan S., Futagami, Taiki

2023

Overview

Background Marine deep subsurface sediments were once thought to be devoid of eukaryotic life, but advances in molecular technology have unlocked the presence and activity of well-known closely related terrestrial and marine fungi. Commonly detected fungi in deep marine sediment environments includes Penicillium , Aspergillus , Cladosporium , Fusarium , and Schizophyllum , which could have important implications in carbon and nitrogen cycling in this isolated environment. In order to determine the diversity and unknown metabolic capabilities of fungi in deep-sea sediments, their genomes need to be fully analyzed. In this study, two Penicillium species were isolated from South Pacific Gyre sediment enrichments during Integrated Ocean Drilling Program Expedition 329. The inner gyre has very limited productivity, organic carbon, and nutrients. Results Here, we present high-quality genomes of two proposed novel Penicillium species using Illumina HiSeq and PacBio sequencing technologies. Single-copy homologues within the genomes were compared to other closely related genomes using OrthoMCL and maximum-likelihood estimation, which showed that these genomes were novel species within the genus Penicillium . We propose to name isolate SPG-F1 as Penicillium pacificasedimenti sp. nov. and SPG-F15 as Penicillium pacificagyrus sp. nov. The resulting genome sizes were 32.6 Mbp and 36.4 Mbp, respectively, and both genomes were greater than 98% complete as determined by the presence of complete single-copy orthologs. The transposable elements for each genome were 4.87% for P . pacificasedimenti and 10.68% for P . pacificagyrus . A total of 12,271 genes were predicted in the P . pacificasedimenti genome and 12,568 genes in P . pacificagyrus . Both isolates contained genes known to be involved in the degradation of recalcitrant carbon, amino acids, and lignin-derived carbon. Conclusions Our results provide the first constructed genomes of novel Penicillium isolates from deep marine sediments, which will be useful for future studies of marine subsurface fungal diversity and function. Furthermore, these genomes shed light on the potential impact fungi in marine sediments and the subseafloor could have on global carbon and nitrogen biogeochemical cycles and how they may be persisting in the most energy-limited sedimentary biosphere.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Amino acids / Animal Genetics and Genomics / Annotations / Biogeochemical cycles / Biomedical and Life Sciences / Biosphere / Biosynthesis / Carbohydrates / Carbon / Carbon cycle / Deep sea / Deep sea environments / Drilling / Energy limitation / Environmental aspects / Enzymes / Fungal genome / Fungi / Fungi - genetics / Genes / Genetic aspects / Genomes / Genomics / Geologic Sediments - microbiology / Identification and classification / IODP / Life Sciences / Lignin / Lignocellulose / Marine microbiology / Marine sediments / Marine subsurface / Maximum likelihood estimation / Metabolism / Metabolites / Microarrays / Microbial Genetics and Genomics / Microbiological research / Natural history / New species / Nitrogen / Nitrogen cycle / Nutrients / Organic carbon / Penicillium / Phylogeny / Plant Genetics and Genomics / Proteins / Proteomics / RNA, Ribosomal, 16S - genetics / Seawater - microbiology / Sediment / Sediments / Sequence Analysis, DNA / South Pacific Gyre / Survivability