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Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics

ABSTRACT: Single-virus genomics (SVGs) has been successfully applied to ocean surface samples allowing the discovery of widespread dominant viruses overlooked for years by metagenomics, such as the uncultured virus vSAG 37-F6 infecting the ubiquitous Pelagibacter spp. In SVGs, one uncultured virus at a time is sorted from the environmental sample, whole-genome amplified, and sequenced. Here, we have applied SVGs to deep-ocean samples (200–4000 m depth) from global Malaspina and MEDIMAX expeditions, demonstrating the feasibility of this method in deep-ocean samples. A total of 1328 virus-like particles were sorted from the North Atlantic Ocean, the deep Mediterranean Sea, and the Pacific Ocean oxygen minimum zone (OMZ). For this proof of concept, sixty single viruses were selected at random for sequencing. Genome annotation identified 27 of these genomes as bona fide viruses, and detected three auxiliary metabolic genes involved in nucleotide biosynthesis and sugar metabolism. Massive protein profile analysis confirmed that these viruses represented novel viral groups not present in databases. Although they were not previously assembled by viromics, global fragment recruitment analysis showed a conserved profile of relative abundance of these viruses in all analyzed samples spanning different oceans. Altogether, these results reveal the feasibility in using SVGs in this vast environment to unveil the genomes of relevant viruses.

SUBMITTER: Martinez-Hernandez F

PROVIDER: S-EPMC9322844 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:The Big Five traits (i.e., openness, conscientiousness, extraversion, agreeableness, and neuroticism: OCEAN) have been suggested to provide a meaningful taxonomy for studying the Dark Triad: Machiavellianism, narcissism, and psychopathy. Nevertheless, current research consists of mixed and inconsistent associations between the Dark Triad and OCEAN. Here we used the Dark Cube (Garcia & Rosenberg, 2016), a model of malevolent character theoretically based on Cloninger's biopsychosocial model of personality and in the assumption of a ternary structure of malevolent character. We use the dark cube profiles to investigate differences in OCEAN between individuals who differ in one dark character trait while holding the other two constant (i.e., conditional relationships). METHOD:Participants (N = 330) responded to the Short Dark Triad Inventory and the Big Five Inventory and were grouped according to the eight possible combinations using their dark trait scores (M, high Machiavellianism; m, low Machiavellianism; N, high narcissism; n, low narcissism; P, high psychopathy; p, low psychopathy): MNP "maleficent", MNp "manipulative narcissistic", MnP "anti-social", Mnp "Machiavellian", mNP "psychopathic narcissistic", mNp "narcissistic", mnP "psychopathic", and mnp "benevolent". RESULTS:High narcissism-high extraversion and high psychopathy-low agreeableness were consistently associated across comparisons. The rest of the comparisons showed a complex interaction. For example, high Machiavellianism-high neuroticism only when both narcissism and psychopathy were low (Mnp vs. mnp), high narcissism-high conscientiousness only when both Machiavellianism and psychopathy were also high (MNP vs. MnP), and high psychopathy-high neuroticism only when Machiavellianism was low and narcissism was high (mNP vs. mNp). CONCLUSIONS:We suggest that the Dark Cube is a useful tool in the investigation of a consistent Dark Triad Theory. This approach suggests that the only clear relationships were narcissism-extraversion and psychopathy-agreeableness and that the malevolent character traits were associated to specific OCEAN traits only under certain conditions. Hence, explaining the mixed and inconsistent linear associations in the Dark Triad literature.

Project description:AimThe aim of this work was to improve understanding about the mode, geography and tempo of diversification in deep-sea organisms, using a time-calibrated molecular phylogeny of the heterobranch gastropod genus Scaphander.LocationAtlantic and Indo-West Pacific (IWP) oceans.MethodsTwo mitochondrial gene markers (COI and 16S) and one nuclear ribosomal gene (28S) from six Atlantic species of Scaphander, and four IWP species were used to generate a multilocus phylogenetic hypothesis using uncorrelated relaxed-clock Bayesian methods implemented in beast and calibrated with the first occurrence of Scaphander in the fossil record (58.7-55.8 Ma).ResultsTwo main clades were supported: clade A, with sister relationships between species and subclades from the Atlantic and IWP; and clade B, with two western Atlantic sister species. Our estimates indicate that the two earliest divergences in clade A occurred between the middle Eocene and late Miocene and the most recent speciation occurred within the middle Miocene to Pleistocene. The divergence between the two western Atlantic species in clade B was estimated at late Oligocene-Pliocene.Main conclusionsThe prevailing mode of speciation in Scaphander was allopatric, but one possible case of sympatric speciation was detected between two western Atlantic species. Sister relationships between IWP and Atlantic lineages suggest the occurrence both of vicariance events caused by the closure of the Tethyan Seaway and of dispersal between the two ocean basins, probably around South Africa during episodic disruptions of the deep-sea regional current system caused by glacial-interglacial cycles. Cladogenetic estimates do not support comparatively older diversification of deep-sea faunas, but corroborate the hypothesis of a pulse of diversification centred in the Oligocene and Miocene epochs. Amphi-Atlantic species were found to occur at deeper depths (bathyal-abyssal) and we hypothesize that trans-Atlantic connectivity is maintained by dispersal between neighbouring reproductive populations inhabiting the abyssal sea floor and by dispersal across the shelf and slope of Arctic and sub-Arctic regions.

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Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics

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