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  1. Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines

    Zhong, Zhi-Ping ; Vik, Dean ; Rapp, Josephine Z. ; ... - Microbiome
    Climate change threatens Earth’s ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions. We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUsmore » (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred “active” vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races. Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth’s destabilized and rapidly disappearing cryosphere.« less

  2. The eco-evolutionary role of fire in shaping terrestrial ecosystems

    Santos, Fernanda ; Bailey, Joseph K. ; Schweitzer, Jennifer A. - Functional Ecology
    Fire is an inherently evolutionary process, even though much more emphasis has been given to ecological responses of plants and their associated communities to fire. Here, in this work, we synthesize contributions to a Special Feature entitled ‘Fire as a dynamic ecological and evolutionary force’ and place them in a broader context of fire research. Topics covered in this Special Feature include a perspective on the impacts of novel fire regimes on differential forest mortality, discussions on new approaches to investigate vegetation-fire feedbacks and resulting plant syndromes, synthesis of fire impacts on plant–fungal interactions, and a meta-analysis of arthropod communitymore » responses to fire. We conclude by suggesting pathways forward to better understand the ecological and evolutionary consequences of fire. These include developing ecological and evolutionary databases for fire ecology, integrating hierarchical genetic structure or phylogenetic structure, and developing new experimental frameworks that limit context-dependent outcomes.« less

  3. The evolution of anaerobic growth in Saccharomycotina yeasts

    Krause, David J. - Yeast
    Humans rely on the ability of budding yeasts to grow without oxygen in industrial scale fermentations that produce beverages, foods, and biofuels. Oxygen is deeply woven into the energy metabolism and biosynthetic capabilities of budding yeasts. While diverse ecological habitats may provide wide varieties of different carbon and nitrogen sources for yeasts to utilize, there is no direct substitute for molecular oxygen, only a range of availability. Understanding how a small subset of budding yeasts evolved the ability to grow without oxygen could expand the set of useful species in industrial scale fermentations as well as provide insight into themore » cryptic field of yeast ecology. Furthermore, we still do not yet appreciate the full breadth of species that can growth without oxygen, what genes underlie this adaptation, and how these genes have evolved.« less

  4. A single oscillating proto-hypothalamic neuron gates taxis behavior in the primitive chordate Ciona

    Chung, Janeva ; Newman-Smith, Erin ; Kourakis, Matthew J. ; ... - Current Biology
    Ciona larvae display a number of behaviors, including negative phototaxis. In negative phototaxis, the larvae first perform short spontaneous rhythmic casting swims. As larvae cast in a light field, their photoreceptors are directionally shaded by an associated pigment cell, providing a phototactic cue. This then evokes an extended negative taxis swim. We report here that the larval forebrain of Ciona has a previously uncharacterized single slow-oscillating inhibitory neuron (neuron cor-assBVIN78) that projects to the midbrain, where it targets key interneurons of the phototaxis circuit known as the photoreceptor relay neurons. The anatomical location, gene expression and oscillation of cor-assBVIN78 suggestmore » homology to oscillating neurons of the vertebrate hypothalamus. Ablation of cor-assBVIN78 results in larvae showing extended phototaxis-like swims, but which occur in the absence of phototactic cues. These results indicate that cor-assBVIN78 has a gating activity on phototaxis by projecting temporally-oscillating inhibition to the photoreceptor relay neurons. However, in intact larvae the frequency of cor-assBVIN78 oscillation does not match that of the rhythmic spontaneous swims, indicating that the troughs in oscillations do not themselves initiate swims, but rather that cor-assBVIN78 may modulate the phototaxis circuit by filtering out low level inputs while restricting them temporally to the troughs in inhibition.« less

  5. The MeerKAT Fornax Survey: II. The rapid removal of H I from dwarf galaxies in the Fornax cluster

    Kleiner, D. ; Serra, P. ; Maccagni, F. M. ; ... - Astronomy and Astrophysics
    We present MeerKAT Fornax Survey atomic hydrogen (H I) observations of the dwarf galaxies located in the central ~2.5 × 4 deg2 of the Fornax galaxy cluster (Rvir ~2°). The H I images presented in this work have a 3σ column density sensitivity between 2.7 and 50 × 1018 cm–2 over 25 km s–1 for spatial resolution between 4 and 1 kpc. We are able to detect an impressive MHI = 5 × 105 M⊙ 3σ point source with a line width of 50 km s–1 at a distance of 20 Mpc. We detected H I in 17 out ofmore » the 304 dwarfs in our field, with 14 out of the 36 late-type dwarfs (LTDs) and three out of the 268 early-type dwarfs (ETDs). The H I-detected LTDs have likely just joined the cluster and are on their first infall as they are located at large clustocentric radii, with comparable MHI and mean stellar surface brightness at fixed luminosity as blue, star-forming LTDs in the field. By contrast, the H I-detected ETDs have likely been in the cluster longer than the LTDs and acquired their H I through a recent merger or accretion from nearby H I. Eight of the H I-detected LTDs host irregular or asymmetric H I emission and disturbed or lopsided stellar emission. There are two clear cases of ram pressure shaping the H I, with the LTDs displaying compressed H I on the side closest to the cluster centre and a one-sided, starless tail pointing away from the cluster centre. The H I-detected dwarfs avoid the most massive potentials (i.e. cluster centre and massive galaxies), consistent with massive galaxies playing an active role in the removal of H I. We created a simple toy model to quantify the timescale of H I stripping in the cluster by reproducing the observed Mr'–MHI relation. We find that a MHI = 108 M⊙ dwarf is stripped in ~240 Myr. The model is consistent with our observations, where low-mass LTDs are directly stripped of their H I from a single encounter and more massive LTDs can harbour a disturbed H I morphology due to longer times or multiple encounters being required to fully strip their H I. This is the first time dwarf galaxies with MHI ≲ 1 × 106 M⊙ have been detected and resolved beyond the local group and in a galaxy cluster.« less

  6. A conserved gene regulatory network controls root epidermal cell patterning in superrosid species

    Zhu, Yan ; Schiefelbein, John - New Phytologist
    Summary In superrosid species, root epidermal cells differentiate into root hair cells and nonhair cells. In some superrosids, the root hair cells and nonhair cells are distributed randomly (Type I pattern), and in others, they are arranged in a position‐dependent manner (Type III pattern). The model plant Arabidopsis ( Arabidopsis thaliana ) adopts the Type III pattern, and the gene regulatory network (GRN) that controls this pattern has been defined. However, it is unclear whether the Type III pattern in other species is controlled by a similar GRN as in Arabidopsis, and it is not known how the different patternsmore » evolved. In this study, we analyzed superrosid species Rhodiola rosea , Boehmeria nivea , and Cucumis sativus for their root epidermal cell patterns. Combining phylogenetics, transcriptomics, and cross‐species complementation, we analyzed homologs of the Arabidopsis patterning genes from these species. We identified R. rosea and B. nivea as Type III species and C. sativus as Type I species. We discovered substantial similarities in structure, expression, and function of Arabidopsis patterning gene homologs in R. rosea and B. nivea , and major changes in C. sativus . We propose that in superrosids, diverse Type III species inherited the patterning GRN from a common ancestor, whereas Type I species arose by mutations in multiple lineages.« less

  7. Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history

    Batarseh, Tiffany N. ; Batarseh, Sarah N. ; Morales-Cruz, Abraham ; ... - Frontiers in Microbiology
    ‘Candidatus Liberibacter’ is a group of bacterial species that are obligate intracellular plant pathogens and cause Huanglongbing disease of citrus trees and Zebra Chip in potatoes. Here, we examined the extent of intra- and interspecific genetic diversity across the genus using comparative genomics. Our approach examined a wide set of Liberibacter genome sequences including five pathogenic species and one species not known to cause disease. By performing comparative genomics analyses, we sought to understand the evolutionary history of this genus and to identify genes or genome regions that may affect pathogenicity. With a set of 52 genomes, we performed comparativemore » genomics, measured genome rearrangement, and completed statistical tests of positive selection. We explored markers of genetic diversity across the genus, such as average nucleotide identity across the whole genome. These analyses revealed the highest intraspecific diversity amongst the ‘Ca. Liberibacter solanacearum’ species, which also has the largest plant host range. We identified sets of core and accessory genes across the genus and within each species and measured the ratio of nonsynonymous to synonymous mutations (dN/dS) across genes. We identified ten genes with evidence of a history of positive selection in the Liberibacter genus, including genes in the Tad complex, which have been previously implicated as being highly divergent in the ‘Ca. L. capsica’ species based on high values of dN.« less

  8. Astrovirology: how viruses enhance our understanding of life in the Universe

    Trubl, Gareth ; Stedman, Kenneth M. ; Bywaters, Kathryn F. ; ... - International Journal of Astrobiology
    Abstract Viruses are the most numerically abundant biological entities on Earth. As ubiquitous replicators of molecular information and agents of community change, viruses have potent effects on the life on Earth, and may play a critical role in human spaceflight, for life-detection missions to other planetary bodies and planetary protection. However, major knowledge gaps constrain our understanding of the Earth's virosphere: (1) the role viruses play in biogeochemical cycles, (2) the origin(s) of viruses and (3) the involvement of viruses in the evolution, distribution and persistence of life. As viruses are the only replicators that span all known types ofmore » nucleic acids, an expanded experimental and theoretical toolbox built for Earth's viruses will be pivotal for detecting and understanding life on Earth and beyond. Only by filling in these knowledge and technical gaps we will obtain an inclusive assessment of how to distinguish and detect life on other planetary surfaces. Meanwhile, space exploration requires life-support systems for the needs of humans, plants and their microbial inhabitants. Viral effects on microbes and plants are essential for Earth's biosphere and human health, but virus–host interactions in spaceflight are poorly understood. Viral relationships with their hosts respond to environmental changes in complex ways which are difficult to predict by extrapolating from Earth-based proxies. These relationships should be studied in space to fully understand how spaceflight will modulate viral impacts on human health and life-support systems, including microbiomes. In this review, we address key questions that must be examined to incorporate viruses into Earth system models, life-support systems and life detection. Tackling these questions will benefit our efforts to develop planetary protection protocols and further our understanding of viruses in astrobiology.« less

  9. Divergent Evolution of Early Terrestrial Fungi Reveals the Evolution of Mucormycosis Pathogenicity Factors

    Wang, Yan ; Chang, Ying ; Ortañez, Jericho ; ... - Genome Biology and Evolution
    Abstract Fungi have evolved over millions of years and their species diversity is predicted to be the second largest on the earth. Fungi have cross-kingdom interactions with many organisms that have mutually shaped their evolutionary trajectories. Zygomycete fungi hold a pivotal position in the fungal tree of life and provide important perspectives on the early evolution of fungi from aquatic to terrestrial environments. Phylogenomic analyses have found that zygomycete fungi diversified into two separate clades, the Mucoromycota which are frequently associated with plants and Zoopagomycota that are commonly animal-associated fungi. Genetic elements that contributed to the fitness and divergence ofmore » these lineages may have been shaped by the varied interactions these fungi have had with plants, animals, bacteria, and other microbes. To investigate this, we performed comparative genomic analyses of the two clades of zygomycetes in the context of Kingdom Fungi, benefiting from our generation of a new collection of zygomycete genomes, including nine produced for this study. We identified lineage-specific genomic content that may contribute to the disparate biology observed in these zygomycetes. Our findings include the discovery of undescribed diversity in CotH, a Mucormycosis pathogenicity factor, which was found in a broad set of zygomycetes. Reconciliation analysis identified multiple duplication events and an expansion of CotH copies throughout the Mucoromycotina, Mortierellomycotina, Neocallimastigomycota, and Basidiobolus lineages. A kingdom-level phylogenomic analysis also identified new evolutionary relationships within the subphyla of Mucoromycota and Zoopagomycota, including supporting the sister-clade relationship between Glomeromycotina and Mortierellomycotina and the placement of Basidiobolus as sister to other Zoopagomycota lineages.« less

  10. Hidden deep in the halo: selection of a reduced proper motion halo catalogue and mining retrograde streams in the velocity space

    Viswanathan, Akshara ; Starkenburg, Else ; Koppelman, Helmer H. ; ... - Monthly Notices of the Royal Astronomical Society
    ABSTRACT The Milky Way halo is one of the few galactic haloes that provides a unique insight into galaxy formation by resolved stellar populations. Here, we present a catalogue of ∼47 million halo stars selected independent of parallax and line-of-sight velocities, using a combination of Gaia DR3 proper motion and photometry by means of their reduced proper motion. We select high tangential velocity (halo) main sequence stars and fit distances to them using their simple colour-absolute-magnitude relation. This sample reaches out to ∼21 kpc with a median distance of 6.6 kpc thereby probing much further out than would be possible using reliablemore » Gaia parallaxes. The typical uncertainty in their distances is $$0.57_{-0.26}^{+0.56}$$ kpc. Using the colour range 0.45 < (G0 − GRP, 0) < 0.715, where the main sequence is narrower, gives an even better accuracy down to $$0.39_{-0.12}^{+0.18}$$ kpc in distance. The median velocity uncertainty for stars within this colour range is 15.5 km s−1. The distribution of these sources in the sky, together with their tangential component velocities, are very well-suited to study retrograde substructures. We explore the selection of two complex retrograde streams: GD-1 and Jhelum. For these streams, we resolve the gaps, wiggles and density breaks reported in the literature more clearly. We also illustrate the effect of the kinematic selection bias towards high proper motion stars and incompleteness at larger distances due to Gaia’s scanning law. These examples showcase how the full RPM catalogue made available here can help us paint a more detailed picture of the build-up of the Milky Way halo.« less
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