Cultivating epizoic diatoms provides insights into the evolution and ecology of both epibionts and hosts

11 pages, 3 figures, 1 table, supplementary information https://doi.org/10.1038/s41598-022-19064-0.-- Data availability: DNA sequence data generated for this study are published on the NCBI GenBank online sequence depository under the accession numbers listed in Table S1. Additional micrographs and cleaned voucher material from the sequenced cultures are available from lead author MPAOur understanding of the importance of microbiomes on large aquatic animals—such as whales, sea turtles and manatees—has advanced considerably in recent years. The latest observations indicate that epibiotic diatom communities constitute diverse, polyphyletic, and compositionally stable assemblages that include both putatively obligate epizoic and generalist species. Here, we outline a successful approach to culture putatively obligate epizoic diatoms without their hosts. That some taxa can be cultured independently from their epizoic habitat raises several questions about the nature of the interaction between these animals and their epibionts. This insight allows us to propose further applications and research avenues in this growing area of study. Analyzing the DNA sequences of these cultured strains, we found that several unique diatom taxa have evolved independently to occupy epibiotic habitats. We created a library of reference sequence data for use in metabarcoding surveys of sea turtle and manatee microbiomes that will further facilitate the use of environmental DNA for studying host specificity in epizoic diatoms and the utility of diatoms as indicators of host ecology and health. We encourage the interdisciplinary community working with marine megafauna to consider including diatom sampling and diatom analysis into their routine practicesFinancial support for sequencing and SEM comes from the Jane and the Roland Blumberg Centennial Professorship in Molecular Evolution at UT Austin and the US Department of Defense (grant number W911NF-17-2-0091). Sampling in South Africa was done with partial financial support from The Systematics Association (UK) through the Systematics Research Fund Award granted to RM (2017 and 2020). Work in the Adriatic Sea was supported by Croatian Science Foundation, project UIP-05-2017-5635 (TurtleBIOME). KF has been fully supported by the “Young researchers' career development project – training of doctoral students” of the CSF funded by the EU from the European Social Fund. NJR was funded by the Spanish government (AEI) through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

Optics and Quantum Electronics

Contains reports on eleven research projects.National Science Foundation (Grant EET 87-00474)Joint Services Electronics Program (Contract DAALO03-86-K-O002)Charles Stark Draper Laboratory, Inc. (Grant DL-H-2854018)National Science Foundation (Grant DMR 84-18718)National Science Foundation (Grant EET 87-03404)National Science Foundation (ECS 85-52701)US Air Force - Office of Scientific Research (Contract AFOSR-85-0213)National Institutes of Health (Contract 5-RO1-GM35459)US Navy - Office of Naval Research (Contract N00014-86-K-0117

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Revision of Ardissoneaceae (Bacillariophyta, Mediophyceae) from Micronesian populations, with descriptions of two new genera, Ardissoneopsis and Grunowago, and new species in Ardissonea, Synedrosphenia and Climacosphenia

Ardissonea was resurrected from Synedra in 1986 and was included as a genus by Round, Crawford and Mann (“The Diatoms”) in its own Family and Order. They commented that there might be several genera involved since the type species of the genus possesses a double-walled structure and other taxa placed in Ardissonea have only a single-walled structure. Two other genera of “big sticks,” Toxarium and Climacosphenia, were placed in their own Families and Orders but share many characters with Ardissoneaceae, especially growth from a bifacial annulus. Eighteen taxa (11 new species) from Micronesia were compared with the literature and remnant material from Grunow’s Honduras Sargassum sample to address the concepts of Ardissonea and Ardissoneaceae. Phylogenetic and morphological analyses showed three clades within Ardissonea sensu lato: Ardissonea emend. for the double-walled taxa, Synedrosphenia emend. and Ardissoneopsis gen. nov. for single-walled taxa. New species include Ardissonea densistriata sp. nov.; Synedrosphenia bikarensis sp. nov., S. licmophoropsis sp. nov., S. parva sp. nov., and S. recta sp. nov.; Ardissoneopsis fulgicans sp. nov., A. appressata sp. nov., and A. gracilis sp. nov. Transfers include Synedrosphenia crystallina comb. nov. and S. fulgens comb. nov. Synedra undosa, seen for the first time in SEM in Grunow’s material, is transferred to Ardissoneopsis undosa comb. nov. Three more genera have similar structure: Toxarium, Climacosphenia and Grunowago gen. nov., erected for Synedra bacillaris and a lanceolate species, G. pacifica sp. nov. Morphological characters of Toxarium in our region support separation of Toxarium hennedyanum and T. undulatum and suggest additional species here and elsewhere. Climacosphenia moniligera was not found but we clarify its characters based on the literature and distinguish C. soulonalis sp. nov. from it. Climacosphenia elongata and a very long, slender C. elegantissima sp. nov., previously identified as C. elongata, were present along with C. scimiter. Morphological and molecular phylogenetics strongly suggested that all these genera belong in one family and we propose to include them in the Ardissoneacae and to reinstate the Order Ardissoneales Round

Reassessment of the classification of Bryopsidales (Chlorophyta) based on chloroplast phylogenomic analyses

The Bryopsidales is a morphologically diverse group of mainly marine green macroalgae characterized by a siphonous structure. The order is composed of three suborders - Ostreobineae, Bryopsidineae, and Halimedineae. While previous studies improved the higher-level classification of the order, the taxonomic placement of some genera in Bryopsidineae (Pseudobryopsis and Lambia) as well as the relationships between the families of Halimedineae remains uncertain. In this study, we re-assess the phylogeny of the order with datasets derived from chloroplast genomes, drastically increasing the taxon sampling by sequencing 32 new chloroplast genomes. The phylogenies presented here provided good support for the major lineages (suborders and most families) in Bryopsidales. In Bryopsidineae, Pseudobryopsis hainanensis was inferred as a distinct lineage from the three established families allowing us to establish the family Pseudobryopsidaceae. The Antarctic species Lambia antarctica was shown to be an early-branching lineage in the family Bryopsidaceae. In Halimedineae, we revealed several inconsistent phylogenetic positions of macroscopic taxa, and several entirely new lineages of microscopic species. A new classification scheme is proposed, which includes the merger of the families Pseudocodiaceae, Rhipiliaceae and Udoteaceae into a more broadly circumscribed Halimedaceae, and the establishment of tribes for the different lineages found therein. In addition, the deep-water genus Johnson-sea-linkia, currently placed in Rhipiliopsis, was reinstated based on our phylogeny

Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats

<div><p>The red algal subclass Nemaliophycidae includes both marine and freshwater taxa that contribute to more than half of the freshwater species in Rhodophyta. Given that these taxa inhabit diverse habitats, the Nemaliophycidae is a suitable model for studying environmental adaptation. For this purpose, we characterized plastid genomes of two freshwater species, <i>Kumanoa americana</i> (Batrachospermales) and <i>Thorea hispida</i> (Thoreales), and one marine species <i>Palmaria palmata</i> (Palmariales). Comparative genome analysis identified seven genes (<i>ycf</i>34, <i>ycf</i>35, <i>ycf</i>37, <i>ycf</i>46, <i>ycf</i>91, <i>grx</i>, and <i>pbs</i>A) that were different among marine and freshwater species. Among currently available red algal plastid genomes (127), four genes (<i>pbs</i>A, <i>ycf</i>34, <i>ycf</i>35, <i>ycf</i>37) were retained in most of the marine species. Among these, the <i>pbs</i>A gene, known for encoding heme oxygenase, had two additional copies (<i>HMOX1</i> and <i>HMOX2</i>) that were newly discovered and were reported from previously red algal nuclear genomes. Each type of heme oxygenase had a different evolutionary history and special modifications (<i>e</i>.<i>g</i>., plastid targeting signal peptide). Based on this observation, we suggest that the plastid-encoded <i>pbs</i>A contributes to the iron controlling system in iron-deprived conditions. Thus, we highlight that this functional requirement may have prevented gene loss during the long evolutionary history of red algal plastid genomes.</p></div

Comparison of general features for 102 florideophycean plastid genomes.

<p>Comparison of general features for 102 florideophycean plastid genomes.</p

The sequence alignment of heme oxygenase proteins.

<p>(A) The alignment of <i>pbs</i>A and its homologous proteins. The alignment shows the conserved heme oxygenases amino acid sequences in different lineages. Conserved heme binding pockets are marked as a blue asterisk. N-terminal transit peptides (green) are unique for <i>HMOX1</i> proteins, with an exceptional transit peptide of <i>pbs</i>A gene in <i>Cyanophora paradoxa</i>, which was likely transferred to the nuclear genome independently. Heme oxygenase domain (grey) and putative transmembrane domain (red) are shown. (B) <i>HMOX2</i> and <i>pbs</i>A contain putative transmembrane domain(s) (TM domain; red box). Multiple TM domains were found in <i>HMOX2</i>.</p

The genome maps of three Nemaliophycidae plastids and their genome structure comparison.

<p>(A) Three plastid genome maps of <i>Kumanoa americana</i>, <i>Thorea hispida</i>, and <i>Palmaria palmata</i>. (B) A simplified comparative genome structure between three species based on MAUVE and UniMoG analyses. A large inversion in <i>rps</i>6-<i>chl</i>L region was observed consistently from two different analyses.</p