Forty-nine metagenomic-assembled genomes from an aquatic virome expand Caudoviricetes by 45 potential new families and the newly uncovered Gossevirus of Bamfordvirae

Journal of General Virology, Journal Year: 2024, Volume and Issue: 105(3)

Published: March 6, 2024

Twenty complete genomes (29–63 kb) and 29 with an estimated completeness of over 90 % (30–90 were identified for novel dsDNA viruses in the Yangshan Harbor metavirome. These newly discovered contribute to expansion viral taxonomy by introducing 46 potential new families. Except one virus, all others belong class Caudoviricetes . The exception is a member recently characterized group known as Gossevirus. Fifteen predicted be temperate. hosts appear involved various aspects nitrogen cycle, including fixation, oxidation denitrification. Two have host Flavobacterium Tepidimonas fonticaldi , respectively, matching CRISPR spacers protospacers. Our findings provide overview characterizing identifying specific from Harbor. Gossevirus-like virus uncovered emphasizes need further comprehensive isolation investigation polinton-like viruses.

Language: Английский

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Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses

mSystems, Journal Year: 2024, Volume and Issue: 9(9)

Published: Aug. 19, 2024

Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic viral genomes. This study focuses on decomposing an estuarine obtain more accurate estimate of microbial diversity. To achieve this, we developed new bead-based DNA extraction method, novel bin refinement obtained 150 Gbp Nanopore sequencing. We that there are ~500 bacterial archaeal species in our sample 68 bins (>90% complete, <5% contamination, ≤5 contigs, contig length >100 kbp, all ribosomal tRNA genes). also contigs picoeukaryotes, environmental larger eukaryotes such as mammals, mitochondrial chloroplast detected ~40,000 populations. Our analysis indicates only few strains comprise most the abundances.

Language: Английский

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Mobilome impacts on physiology in the widely used non-toxic mutant Microcystis aeruginosa PCC 7806 ΔmcyB and toxic wildtype

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Oct. 3, 2024

Language: Английский

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DeepMicroClass sorts metagenomes into prokaryotes, eukaryotes and viruses, with marine applications

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: Oct. 27, 2021

Abstract Sequence classification reduces the complexity of metagenomes and facilitates a fundamental understanding structure function microbial communities. Binary metagenomic classifiers offer an insufficient solution because environmental are typically derived from multiple sequence sources, including prokaryotes, eukaryotes viruses both. Here we introduce deep-learning based (as opposed to alignment-based) classifier, DeepMicroClass, that classifies contigs into five classes, i.e., infecting prokaryotic or eukaryotic hosts, chromosomes, plasmids. At different lengths, DeepMicroClass achieved area under receiver operating characteristic curve (AUC) scores >0.98 for most with exception distinguishing plasmids chromosomes (AUC ≈ 0.97). By benchmarking on 20 designed datasets variable class composition, showed obtained average accuracy ∼0.99, ∼0.97, ∼0.99 eukaryotic, plasmid viral contig classification, respectively, which were significantly higher than other state-of-the-art individual predictors. Using 1-300 µm daily time-series dataset sampled coastal Southern California as case study, read proportions recruited by could be doubled DeepMicroClass’s compared counterparts alignment-based classifiers. With its inclusive modeling unprecedented performance, expect will useful addition toolbox ecologists, promote studies under-appreciated types.

Language: Английский

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Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 12, 2023

Abstract Deep sea cold seep sediments have been discovered to harbor novel, abundant, and diverse bacterial archaeal viruses. However, little is known about viral genetic features evolutionary patterns in these environments. Here, we examined the ecology of viruses across active extinct stages area Haima seeps South China Sea. Diverse antiviral defense systems 487 microbial genomes spanning 43 families inform dynamics host-virus interactions. Accordingly, a total 338 operational taxonomic units are identified linked 36 phyla. Cold predicted adaptive strategies persist this environment, including counter-defense systems, reverse transcriptases, auxiliary metabolic genes, alternative code assignments. Extremely low nucleotide diversity observed populations, being influenced by factors host, sediment depth stage. Most genes under strong purifying selection with trajectories that differ depending on whether or extinct. This work sheds light understanding environmental adaptation mechanisms sub-seafloor biosphere.

Language: Английский

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