Epizoic and Apochlorotic Tursiocola species (Bacillariophyta) from the Skin of Florida Manatees (Trichechus manatus latirostris)

Taxonomic review of Tryblionella with special reference to the Apiculatae group-New characters of genus Tryblionella sensu stricto (Bacillariaceae)

Tryblionella (Bacillariaceae) was described by Smith in 1853, and for many years, the diagnosis of this genus was questionable. Recent molecular analysis based on the rbcL gene marker suggests that Tryblionella is a polyphyletic genus with T. apiculata, T. hungarica, and T. gaoana forming a distinct group from other Tryblionella representatives. Therefore, this study aimed to clarify the diagnosis of Tryblionella as a genus. The focus of this study was a selected group of species previously categorized within Grunow's section Apiculatae, which includes the type species T. acuminata. This classification serves as a foundation for conducting morphological and molecular comparisons with taxa of Tryblionella sensu lato, which are likely to represent distinct and highly diverse genera. Our review includes a detailed examination of frustule ultrastructure and ontogeny combined with a new molecular phylogenetic analysis derived from a three-gene concatenated dataset. The results of our research indicated that among Tryblionella, several monophyletic groups of taxa can be distinguished, including Tryblionella sensu stricto (s.s.), by three key characters: a porose valve cross-section; longitudinal valve undulation, where the peak of the undulation is located on the proximal side of the valve; and the presence of an axial sternum with thickened and relief virgae. Tryblionella s.s. taxa share a similar girdle structure: The girdle is graded, except that the first band bears a single row of poroids in the pars exterior and a crenulate margin on the side corresponding to the distal valve mantle.

A cryptic plastid and a novel mitochondrial plasmid in Leucomyxa plasmidifera gen. and sp. nov. (Ochrophyta) push the frontiers of organellar biology

Complete plastid loss seems to be very rare among secondarily non-photosynthetic eukaryotes. Leukarachnion sp. PRA-24, an amoeboid colourless protist related to the photosynthetic algal class Synchromophyceae (Ochrophyta), is a candidate for such a case based on a previous investigation by transmission electron microscopy. Here, we characterize this organism in further detail and describe it as Leucomyxa plasmidifera gen. et sp. nov., additionally demonstrating it is the first known representative of a broader clade of non-photosynthetic ochrophytes. We recovered its complete plastid genome, exhibiting a reduced gene set similar to plastomes of other non-photosynthetic ochrophytes, yet being even more extreme in sequence divergence. Identification of components of the plastid protein import machinery in the L. plasmidifera transcriptome assembly corroborated that the organism possesses a cryptic plastid organelle. According to our bioinformatic reconstruction, the plastid contains a unique combination of biosynthetic pathways producing haem, a folate precursor and tocotrienols. As another twist to its organellar biology, L. plasmidifera turned out to contain an unusual long insertion in its mitogenome related to a newly discovered mitochondrial plasmid exhibiting unprecedented features in terms of its size and coding capacity. Combined, our work uncovered further striking outcomes of the evolutionary course of semiautonomous organelles in protists.

Cooperative motility, force generation and mechanosensing in a foraging non-photosynthetic diatom

Diatoms are ancestrally photosynthetic microalgae. However, some underwent a major evolutionary transition, losing photosynthesis to become obligate heterotrophs. The molecular and physiological basis for this transition is unclear. Here, we isolate and characterize new strains of non-photosynthetic diatoms from the coastal waters of Singapore. These diatoms occupy diverse ecological niches and display glucose-mediated catabolite repression, a classical feature of bacterial and fungal heterotrophs. Live-cell imaging reveals deposition of secreted extracellular polymeric substance (EPS). Diatoms moving on pre-existing EPS trails (runners) move faster than those laying new trails (blazers). This leads to cell-to-cell coupling where runners can push blazers to make them move faster. Calibrated micropipettes measure substantial single-cell pushing forces, which are consistent with high-order myosin motor cooperativity. Collisions that impede forward motion induce reversal, revealing navigation-related force sensing. Together, these data identify aspects of metabolism and motility that are likely to promote and underpin diatom heterotrophy.

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

Our 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 practices.

Organismal and cellular interactions in vertebrate-alga symbioses

Photosymbioses, intimate interactions between photosynthetic algal symbionts and heterotrophic hosts, are well known in invertebrate and protist systems. Vertebrate animals are an exception where photosynthetic microorganisms are not often considered part of the normal vertebrate microbiome, with a few exceptions in amphibian eggs. Here, we review the breadth of vertebrate diversity and explore where algae have taken hold in vertebrate fur, on vertebrate surfaces, in vertebrate tissues, and within vertebrate cells. We find that algae have myriad partnerships with vertebrate animals, from fishes to mammals, and that those symbioses range from apparent mutualisms to commensalisms to parasitisms. The exception in vertebrates, compared with other groups of eukaryotes, is that intracellular mutualisms and commensalisms with algae or other microbes are notably rare. We currently have no clear cell-in-cell (endosymbiotic) examples of a trophic mutualism in any vertebrate, while there is a broad diversity of such interactions in invertebrate animals and protists. This functional divergence in vertebrate symbioses may be related to vertebrate physiology or a byproduct of our adaptive immune system. Overall, we see that diverse algae are part of the vertebrate microbiome, broadly, with numerous symbiotic interactions occurring across all vertebrate and many algal clades. These interactions are being studied for their ecological, organismal, and cellular implications. This synthesis of vertebrate-algal associations may prove useful for the development of novel therapeutics: pairing algae with medical devices, tissue cultures, and artificial ecto- and endosymbioses.

New and poorly known "araphid" diatom species (Bacillariophyta) from regions near Lake Titicaca, South America and a discussion on the continued use of morphological characters in "araphid" diatom taxonomy

Based on two Andean Altiplano samples and on light and scanning electron microscopy analyses, we present six new species of "araphid" diatoms in the genus Pseudostaurosira, P.aedes sp. nov., P.frankenae sp. nov., P.heteropolaris sp. nov., P.oblonga sp. nov., P.occulta sp. nov., and P.pulchra sp. nov. Additional data are provided for four other known taxa, Nanofrustulumcataractarum, N.rarissimum, P.sajamaensis and P.vulpina, the latter species corresponding to a stat. nov. based on a variety of P.laucensis. Each taxon is described morphologically and compared with closely related published taxa, using characters such as axial area, virgae, vimines, areolar shape, volae, internal striae depositions, spines, flaps and apical pore fields, which are not usually used for species distinction within the genus. It is our intention that the detailed morphological descriptions of each taxon and the elaborate comparative tables we provide serve as a basis for correction of neo and paleo-databases for the Altiplano to produce a better account of autecological data and ecological change in the region. Some arguments for our continued use of a morphologically based approach are given in the context of rapid environmental degradation in the Andes and the difficulties in applying molecular approaches in countries such as Bolivia.

The genome of a nonphotosynthetic diatom provides insights into the metabolic shift to heterotrophy and constraints on the loss of photosynthesis

Although most of the tens of thousands of diatom species are photoautotrophs, a small number of heterotrophic species no longer photosynthesize. We sequenced the genome of a nonphotosynthetic diatom, Nitzschia Nitz4, to determine how carbon metabolism was altered in the wake of this trophic shift. Nitzschia Nitz4 has retained its plastid and plastid genome, but changes associated with the transition to heterotrophy were cellular-wide and included losses of photosynthesis-related genes from the nuclear and plastid genomes, elimination of isoprenoid biosynthesis in the plastid, and remodeling of mitochondrial glycolysis to maximize adenosine triphosphte (ATP) yield. The genome contains a β-ketoadipate pathway that may allow Nitzschia Nitz4 to metabolize lignin-derived compounds. Diatom plastids lack an oxidative pentose phosphate pathway (oPPP), leaving photosynthesis as the primary source of NADPH to support essential biosynthetic pathways in the plastid and, by extension, limiting available sources of NADPH in nonphotosynthetic plastids. The genome revealed similarities between nonphotosynthetic diatoms and apicomplexan parasites for provisioning NADPH in their plastids and highlighted the ancestral absence of a plastid oPPP as a potentially important constraint on loss of photosynthesis, a hypothesis supported by the higher frequency of transitions to parasitism or heterotrophy in lineages that have a plastid oPPP.

Multigene phylogenetic data place monoraphid diatoms Schizostauron and Astartiella along with other fistula-bearing genera in the Stauroneidaceae1

Presented here are new insights into the marine monoraphid diatom genera Schizostauron and Astartiella, based on molecular and morphological data, including descriptions of new species. Although no unambiguous morphological synapomorphies between the two genera are currently recognized, they are closely related by DNA sequence data. Heterovalvate frustules of Schizostauron are characterized by a bifid stauros on the raphe-bearing valve and intricate areolate occlusions on the sternum valve. In Astartiella, the raphe-bearing valve is characterized by a process resembling a fistula by morphology, while the sternum valve presents a particular striation pattern. Observations by light and electron microscopy were made, along with a molecular phylogenetic analysis using a three-gene (SSU, rbcL, and psbC) concatenated dataset. Three new Schizostauron species are described (S. kajotkei, S. rawaii, S. papilliareae), and two new combinations proposed (S. citronella and S. trachyderma) for species that were previously included either in Achnanthes and Cocconeis, respectively. Likewise, six new species of Astartiella (A. almalikii, A. bornmanii, A. chunlianlii, A. marksii, A. persica, and A. wangii) are described. Molecular results exclude Schizostauron and Astartiella from three clades of exclusively monoraphid diatoms, the Achnanthaceae, Cocconeidaceae, and Achnanthidiaceae, instead placing them in the Stauroneidaceae. Morphological features of Schizostauron and Astartiella, such as the stauros, fistula, and coaxial internal proximal raphe endings, are found in other genera in this clade, whereas the only common feature with monoraphid diatoms as whole group is the heterovalvy of frustules.

Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life

DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.

DNA Sequence Analyses Reveal Two New Species of Caloglossa (Delesseriaceae, Rhodophyta) from the Skin of West Indian Manatees

Epizoic macroalgae collected from the skin of West Indian manatees included specimens of the red algal family Delesseriaceae. Morphological and rbcL sequence analyses indicated that these specimens represented two novel species of Caloglossa. One species, described here as Caloglossa kamiyana Freshwater, Cath.E. Miller & Frankovich sp. nov., had been previously studied and recognized as part of the C. ogasawaraensis species complex. The rbcL sequence divergence between C. kamiyana and other taxa within the complex ranged from 4.6–5.3%, and tetrasporangial mother cells are cut off from the lateral pericentral cells by oblique divisions instead of transverse divisions as in C. ogasawaraensis. The second species was resolved as a closely related sister species to C. fluviatilis, with a minimum interspecific sequence divergence of 2.0%. It was morphologically indistinguishable from C. fluviatilis except for one potential character—mostly one, instead of multiple rhizoids, developing from rhizoid-bearing pericentral and marginal wing cells. It is herein described as Caloglossa manaticola Freshwater, Cath.E. Miller & Frankovich sp. nov.

Ripe for reassessment: A synthesis of available molecular data for the speciose diatom family Bacillariaceae

The Bacillariaceae is a very species-rich family of raphid diatoms and includes the large and taxonomically difficult genus Nitzschia, whose species are often small-celled and finely structured and have few discrete morphological characters visible in the light microscope. The classification of Nitzschia is still mostly based on one developed in the second half of the 19th century by Grunow, who separated the genus into a series of sections largely on cell shape and symmetry, the position of the raphe, transverse extension of the fibulae, and folding of the valve. We assembled and analysed single-gene and concatenated alignments of nSSU, nLSU, rbcL, psbC and cox1 to test Grunow's and subsequent classifications and to examine selected morphological characters for their potential to help define monophyletic groups. The maximum likelihood trees were equivocal as to monophyly of the family itself but showed good support for each of eight main clades of Bacillariaceae, three of which corresponded more or less to existing genera (Hantzschia, Cylindrotheca and Bacillaria). The other five main clades and some subclades comprised groups of Nitzschia species or assemblies of Nitzschia species with other genera (Pseudo-nitzschia, Fragilariopsis, Neodenticula, Tryblionella, Psammodictyon). Relationships between most of the eight main clades were not resolved robustly but all analyses recovered Nitzschia as non-monophyletic. The Grunowian classification of Nitzschia into sections was not supported, though in some respects (e.g. treatment of sigmoid species) it is better than subsequent reclassifications. Several of the main clades and subclades are cryptic (lacking morphological synapomorphies) and homoplasy is common in both light microscopical and ultrastructural characters (to the extent that organisms initially assigned to the same species sometimes prove to belong to a different main clade). Nevertheless, some characters, including the structure of the raphe canal and girdle, seem to be sufficiently conservative evolutionarily to give a provisional estimate of relationships if molecular data are unavailable. No new formal classifications are proposed but various options are explored and research needs identified.

Diatom Diversity on the Skin of Frozen Historic Loggerhead Sea Turtle Specimens

In recent years, biofilm-forming diatoms have received increased attention as sea turtle epibionts. However, most of the research has focused on carapace-associated taxa and communities, while less is known about diatoms growing on sea turtle skin. The current study investigated diatom diversity on the skin of loggerhead sea turtle heads detached from the carcasses found along the Adriatic coast between 1995 and 2004 and stored frozen for a prolonged period of time. By using both light and scanning electron microscopy we have found diatom frustules in 7 out of 14 analysed sea turtle samples. Altogether, 113 diatom taxa were recorded, with a minimum of seven and a maximum of 35 taxa per sample. Eight taxa, Achnanthes elongata, Berkeleya cf. fennica, Chelonicola sp., Licmophora hyalina, Nagumoea sp., Navicula sp., Nitzschia cf. lanceolata, and Poulinea lepidochelicola exceeded 5% of relative abundance in any one sample. The presumably obligately epizoic diatom taxa, A. elongata, Chelonicola sp., and P. lepidochelicola, dominated in six loggerhead samples, contributing up to 97.1% of the total diatom abundance. These observations suggest that on the sea turtle skin highly specialised taxa gain even greater ecological advantage and dominance over the co-occurring benthic forms than in the carapace biofilms. The suitability of frozen sea turtle skin specimens for diatom analysis and limitations of this approach are discussed.

For Better, For Worse: Manatee-Associated Tursiocola (Bacillariophyta) Remain Faithful to Their Host

With the advent of more comprehensive research into the microbiome and interactions between animals and their microbiota, new solutions can be applied to address conservation challenges such as husbandry and medical care of captive animals. Although studies on epizoic algae are relatively rare, and the function and role of those mainly photosynthetic organisms in the animal microbiome is not well understood, recent surveys on epizoic diatoms show that some of them exhibit traits of obligate epibionts. This study explores diatom communities on captive-born manatees from the Africarium in Wroclaw, Poland. Light and scanning electron microscopy analyses revealed that skin of all animals sampled was dominated by apochlorotic Tursiocola cf. ziemanii, an epizoic species described recently from Florida manatees, that reached 99,9% of the total diatom abundance. Despite using media with a wide range of salinity (0-34), the isolated Tursiocola cells did not grow, whereas the normally pigmented Planothidium sp., that was only occasionally found on the animal substratum, survived in all culture media tested. Our observations provide direct evidence that manatee-associated Tursiocola endure the dramatic salinity changes that occur regularly during their host life cycle, and can thrive in an artificial captive setting, if the manatee substratum is available. The impact of practices and routines used by the Africarium on manatee-associated diatoms, as well as ultrastructure of areolae in Tursiocola, are briefly discussed.

Melanothamnus maniticola sp. nov. (Ceramiales, Rhodophyta): an epizoic species evolved for living on the West Indian Manatee

Over 35 macroalgae have been documented growing epizoically on sea turtles, and macroalgae are also known to grow on the West Indian Manatee, but the number and identity of these latter species have not been determined. Analysis of DNA sequences of 12 samples collected from different manatees captured in three areas of Florida indicated that they represented a single undescribed species within the Rhodomelaceae genus Melanothamnus. Morphological analysis revealed Melanothamnus characteristics but also a previously undescribed combination of character states. These include eight to nine, but as many as 11, pericentral cells; heavy cortication restricted to the base of thalli, and a sharp transition between the corticated and ecorticate sections of the thallus; cells surrounding the ostiole being similar in size to the outer pericarp cells immediately below, and robust rhizoids that have no terminal lobes and develop from central axial cell filaments instead of pericentral cells. The unique characteristics of the rhizoids may be evolutionary adaptations for anchoring the thalli to manatee epidermis. This species is described as M. maniticola sp. nov.

A single loss of photosynthesis in the diatom order Bacillariales (Bacillariophyta)

PREMISE OF THE STUDY

Loss of photosynthesis is a common and often repeated trajectory in nearly all major groups of photosynthetic eukaryotes. One small subset of "apochloritic" diatoms in the genus Nitzschia have lost their ability to photosynthesize and require extracellular carbon for growth. Similar to other secondarily nonphotosynthetic taxa, apochloritic diatoms maintain colorless plastids with highly reduced plastid genomes. Although the narrow taxonomic breadth of apochloritic Nitzschia suggests a single loss of photosynthesis in their common ancestor, previous phylogenetic analyses suggested that photosynthesis was lost multiple times.

METHODS

We analyzed genes from the nuclear, plastid, and mitochondrial genomes for a broad set of taxa to test whether photosynthesis was lost one or multiple times in Bacillariales. We also sequenced and characterized the plastid genome of a nonphotosynthetic Nitzschia species.

KEY RESULTS

Phylogenetic analyses showed that genes from all three genetic compartments either supported or failed to reject monophyly of apochloritic Nitzschia species, consistent with a single loss of photosynthesis in this group. The plastid genomes of two apochloritic Nitzschia are highly similar in all respects, indicating streamlining of the plastid genome before the split of these two species.

CONCLUSIONS

A better understanding of the phylogeny and ecology of apochloritic Nitzschia, together with emerging genomic resources, will help identify the factors that have driven and maintained the loss of photosynthesis in this group of diatoms. Finally, some habitats host diverse communities of co-occurring nonphotosynthetic diatoms, reflecting resource abundance or resource partitioning in ecologically favorable habitats.