Seasonal dynamics of algae-infecting viruses and their inferred interactions with protists

Viruses are a highly abundant, dynamic, and diverse component of planktonic communities that have key roles in marine ecosystems. We aimed to reveal the diversity and dynamics of marine large dsDNA viruses infecting algae in the Northern Skagerrak, South Norway through the year by metabarcoding, targeting the major capsid protein (MCP) and its correlation to protist diversity and dynamics. Metabarcoding results demonstrated a high diversity of algal viruses compared to previous metabarcoding surveys in Norwegian coastal waters. We obtained 313 putative algal virus operational taxonomic units (vOTUs), all classified by phylogenetic analyses to either the Phycodnaviridae or Mimiviridae families, most of them in clades without any cultured or environmental reference sequences. The viral community showed a clear temporal variation, with some vOTUs persisting for several months. The results indicate co-occurrences between abundant viruses and potential hosts during long periods. This study gives new insights into the virus-algal host dynamics and provides a baseline for future studies of algal virus diversity and temporal dynamics.publishedVersio

18S rDNA gene metabarcoding of microeukaryotes and epi-endophytes in the holobiome of seven species of large brown algae

Brown algae (Phaeophyceae) are habitat-forming species in coastal ecosystems and include kelp forests and seaweed beds that support a wide diversity of marine life. Host-associated microbial communities are an integral part of phaeophyte biology, and whereas the bacterial microbial partners have received considerable attention, the microbial eukaryotes associated with brown algae have hardly been studied. Here, we used broadly targeted “pan-eukaryotic” primers (metabarcoding) to investigate brown algal-associated eukaryotes (the eukaryome). Using this approach, we aimed to investigate the eukaryome of seven large brown algae that are important and common species in coastal ecosystems. We also aimed to assess whether these macroalgae harbor novel eukaryotic diversity and to ascribe putative functional roles to the host-associated eukaryome based on taxonomic affiliation and phylogenetic placement. We detected a significant diversity of microeukaryotic and algal lineages associated with the brown algal species investigated. The operational taxonomic units (OTUs) were taxonomically assigned to 10 of the eukaryotic major supergroups, including taxonomic groups known to be associated with seaweeds as epibionts, endobionts, parasites, and commensals. Additionally, we revealed previously unrecorded sequence types, including novel phaeophyte OTUs, particularly in the Fucus spp. samples, that may represent fucoid genomic variants, sequencing artifacts, or undescribed epi-/endophytes. Our results provide baseline data and technical insights that will be useful for more comprehensive seaweed eukaryome studies investigating the evidently lineage-rich and functionally diverse symbionts of brown algae.publishedVersio

Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change

The Arctic is experiencingthe fastest rates of globalwarming,leadingto shiftsin the distributionof its biotaandincreasingthe potentialfor hybridization. However, genomicevidenceof recenthybridization events in theArctic remainsunexpectedlyrare. Here, we use whole-genomesequencingof contemporary and 122-year-oldhistoricalspecimensto investigate the originof an Arctic hybridpopulation of Atlanticpuffins(Fr aterculaarctica)on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodiedsubspeciesF. a. naumanniand the temperate, smaller-sizedsubspeciesF. a. arcticabeganas recentlyas six generationsagodue to an unexpectedsouthward rangeexpansionofF. a. naumanni.Moreover, we find a significanttemporalloss of geneticdiversityacross Arctic and temperate puffinpopulations.Our observationsprovide compellinggenomicevidenceof the impacts of recentdistributionalshiftsand loss of diversityin Arctic communitiesduringthe 20th century.publishedVersio

Coping with the World: Tools of Pragmatism : Mind, Brain, and the Intentional Vocabulary

In this paper I explore the tension that arises when we describe ourselves as intentional beings, on one side, and biological or physical beings on the other. That is, I take a closer look at the age old problem of how the mind relates to the brain. In order to get a better grip on the tension between mental and physical descriptions I start of the discussion with a closer look at what it means to explain the same object, the brain, as two different kinds of thing. The pragmatic kind of naturalism endorsed in this paper draws on the idea that different vocabularies instantiate different interests and commitments. The vocabulary-vocabulary as Brandom has dubbed it allows you to talk about mental properties and physical properties without assuming the ontological primacy of the one over the other. Since the idea of vocabularies is significant to this paper I devote some time to explaining the central idea behind it and lay down some of it central virtues and spell out how it stands in relation to more traditional approaches to the mind-body problem. As the idea is elaborated it will be clear that it helps to fend off some major metaphysical and ontological problems inherent in the more orthodox approaches to the mind. I then proceed to evaluate a position that is intended to remove the tension by arguing that the intentional vocabulary is widely erroneous. This is the eliminative materialism of Paul and Patricia Churchland. They claim that Folk Psychology fail to meet up with the current findings of neuroscience and consequently should be eliminated. I assess their position by first stating what they mean by eliminativism and then examine five different objections against their position. The reason for examining these objections is to determine what the opposing sides in the debate believe are the important elements in the commonsensical and in the scientific description of our mental lives. In essence the Churchlands claim that the commonsensical framework of the mental will have to adapt according to the findings of neuroscience. The purpose of scientific explanation will be discussed further in the final part of the paper. For this purpose I turn to Paul Griffiths’ new and more flexible account of natural kinds. Griffiths thinks that the traditional view on natural kinds, with universal exceptionless laws, is too rigid to be of much help to science. He wants to leave the idea of natural kinds as the most fundamental category of nature and instead view them as non-arbitrary ways of classifying the subject matter under examination. He uses his findings to argue that the vernacular concept of emotion does not form a single natural kind and concludes that it has to be eliminated in favor of a better informed theory of emotion. I then compare and contrast the different reasons the Churchlands and Griffiths hold for arriving at the eliminativist conclusion. I take a look at the normative role the intentional vocabulary plays, since this is something they seem to disagree about

Vesicles From Vibrio cholerae Contain AT-Rich DNA and Shorter mRNAs That Do Not Correlate With Their Protein Products

Extracellular vesicles secreted by Gram-negative bacteria have proven to be important in bacterial defense, communication and host-pathogen relationships. They resemble smaller versions of the bacterial mother cell, with similar contents of proteins, LPS, DNA, and RNA. Vesicles can elicit a protective immune response in a range of hosts, and as vaccine candidates, it is of interest to properly characterize their cargo. Genetic sequencing data is already available for vesicles from several bacterial strains, but it is not yet clear how the genetic makeup of vesicles differ from that of their parent cells, and which properties may characterize enriched genetic material. The present study provides evidence for DNA inside vesicles from Vibrio cholerae O395, and key characteristics of their genetic and proteomic content are compared to that of whole cells. DNA analysis reveals enrichment of fragments containing ToxR binding sites, as well as a positive correlation between AT-content and enrichment. Some mRNAs were highly enriched in the vesicle fraction, such as membrane protein genes ompV, ompK, and ompU, DNA-binding protein genes hupA, hupB, ihfB, fis, and ssb, and a negative correlation was found between mRNA enrichment and transcript length, suggesting mRNA inclusion in vesicles may be a size-dependent process. Certain non-coding and functional RNAs were found to be enriched, such as VrrA, GcvB, tmRNA, RNase P, CsrB2, and CsrB3. Mass spectrometry revealed enrichment of outer membrane proteins, known virulence factors, phage components, flagella and extracellular proteins in the vesicle fraction, and a low, negative correlation was found between transcript-, and protein enrichment. This result opposes the hypothesis that a significant degree of protein translation occurs in vesicles after budding. The abundance of viral-, and flagellar proteins in the vesicle fraction underlines the importance of purification during vesicle isolation

Soil depth matters: shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils

Soil depth represents a strong physiochemical gradient that greatly affects soil-dwelling microorganisms. Fungal communities are typically structured by soil depth, but how other microorganisms are structured is less known. Here, we tested whether depth-dependent variation in soil chemistry affects the distribution and co-occurrence patterns of soil microbial communities. This was investigated by DNA metabarcoding in conjunction with network analyses of bacteria, fungi, as well as other micro-eukaryotes, sampled in four different soil depths in Norwegian birch forests. Strong compositional turnover in microbial assemblages with soil depth was detected for all organismal groups. Significantly greater microbial diversity and fungal biomass appeared in the nutrient-rich organic layer, with sharp decrease towards the less nutrient-rich mineral zones. The proportions of copiotrophic bacteria, Arthropoda and Apicomplexa were markedly higher in the organic layer, while patterns were opposite for oligotrophic bacteria, Cercozoa, Ascomycota and ectomycorrhizal fungi. Network analyses indicated more intensive inter-kingdom co-occurrence patterns in the upper mineral layer (0–5 cm) compared to the above organic and the lower mineral soil, signifying substantial influence of soil depth on biotic interactions. This study supports the view that different microbial groups are adapted to different forest soil strata, with varying level of interactions along the depth gradient.publishedVersio

Phylogenomic analysis restructures the Ulvophyceae

Here, we present new transcriptome sequencing data from seven species of Dasycladales (Ulvophyceae) and a phylogenomic analysis of the Chlorophyta with a particular focus on Ulvophyceae. We have focused on a broad selection of green algal groups and carefully selected genes suitable for reconstructing deep eukaryote evolutionary histories. Increasing the taxon sampling of Dasycladales restructures the Ulvophyceae by identifying Dasycladales as closely related to Scotinosphaerales and Oltmannsiellopsidales. Contrary to previous studies, we do not find support for a close relationship between Dasycladales and a group with Cladophorales and Trentepohliales. Instead, the latter group is sister to the remainder of the Ulvophyceae. Furthermore, our analyses show high and consistent statistical support for a sister relationship between Bryopsidales and Chlorophyceae in trees generated with both homogeneous and heterogeneous (heterotachy) evolutionary models. Our study provides a new framework for interpreting the evolutionary history of Ulvophyceae and the evolution of cellular morphologies

The sequenced genomes of non-flowering land plants reveal the innovative evolutionary history of peptide signaling

Abstract An understanding of land plant evolution is a prerequisite for in-depth knowledge of plant biology. Here we extract and explore information hidden in the increasing number of sequenced plant genomes, from bryophytes to angiosperms, to elucidate a specific biological question—how peptide signaling evolved. To conquer land and cope with changing environmental conditions, plants have gone through transformations that must have required innovations in cell-to-cell communication. We discuss peptides mediating endogenous and exogenous changes by interaction with receptors activating intracellular molecular signaling. Signaling peptides were discovered in angiosperms and operate in tissues and organs such as flowers, seeds, vasculature, and 3D meristems that are not universally conserved across land plants. Nevertheless, orthologs of angiosperm peptides and receptors have been identified in nonangiosperms. These discoveries provoke questions regarding coevolution of ligands and their receptors, and whether de novo interactions in peptide signaling pathways may have contributed to generate novel traits in land plants. The answers to such questions will have profound implications for the understanding of the evolution of cell-to-cell communication and the wealth of diversified terrestrial plants. Under this perspective, we have generated, analyzed, and reviewed phylogenetic, genomic, structural, and functional data to elucidate the evolution of peptide signaling

Niche adaptation promoted the evolutionary diversification of tiny ocean predators

Significance The oceans are populated by an astronomical number of predominantly uncultured microbes, which altogether guarantee ecosystem function. Unicellular eukaryotic predators represent basal links in marine food webs and have so far been predominantly characterized as a functional group, despite having different ecologies and evolutionary histories. In order to better understand the ecoevolution of the ocean’s smallest predators, we have investigated four species belonging to an uncultured cosmopolitan family: marine stramenopiles (MAST)-4. Using state-of-the-art single-cell genomics and metaomics approaches, we found that members of this predatory family have different distributions in the surface ocean and different genes to degrade food, which likely represent niche adaptations. Our work highlights the importance of understanding the species-level ecology and genomics of tiny ocean predators

Genetic variation and temperature affects hybrid barriers during interspecific hybridization

Genomic imprinting regulates parent‐specific transcript dosage during seed development and is mainly confined to the endosperm. Elucidation of the function of many imprinted genes has been hampered by the lack of corresponding mutant phenotypes, and the role of imprinting is mainly associated with genome dosage regulation or allocation of resources. Disruption of imprinted genes has also been suggested to mediate endosperm‐based post‐zygotic hybrid barriers depending on genetic variation and gene dosage. Here, we have analyzed the conservation of a clade from the MADS‐box type I class transcription factors in the closely related species Arabidopsis arenosa, A. lyrata, and A. thaliana, and show that AGL36‐like genes are imprinted and maternally expressed in seeds of Arabidopsis species and in hybrid seeds between outbreeding species. In hybridizations between outbreeding and inbreeding species the paternally silenced allele of the AGL36‐like gene is reactivated in the hybrid, demonstrating that also maternally expressed imprinted genes are perturbed during hybridization and that such effects on imprinted genes are specific to the species combination. Furthermore, we also demonstrate a quantitative effect of genetic diversity and temperature on the strength of the post‐zygotic hybridization barrier. Markedly, a small decrease in temperature during seed development increases the survival of hybrid F1 seeds, suggesting that abiotic and genetic parameters play important roles in post‐zygotic species barriers, pointing at evolutionary scenarios favoring such effects